> > > Modified: > branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb > (1286 => 1287) > > > --- branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb 2009-11-16 18:16:56 UTC (rev 1286) > +++ branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb 2009-11-17 10:58:32 UTC (rev 1287) > @@ -235,14 +235,9 @@ > binding = test_binding(script[4], db).fetch_row[1] > a_test = TestScript.new(:name => name, > :exec_name => script[7], > - #:filename => 'package.zip', > - #:content_type => 'application/zip', > :prog_language => binding.to_s.downcase, > - :user_id => existing_service.submitter.id, > - :testable_id => existing_service.id, > - :testable_type => existing_service.class.name, > - :created_at => Time.now, > - :updated_at => Time.now) > + :user_id => existing_service.submitter.id > + ) > > a_test.content_blob = ContentBlob.new({:data => script[6]}) > a_test.filename = 'package.zip' > @@ -258,7 +253,7 @@ > begin > if existing_service.save! > @stats.counts[:success_script_imports] +=1 > - relationship = TestScriptHistory.new(:subject_type => a_test.class.name, > + relationship = Relationship.new(:subject_type => a_test.class.name, > :subject_id => a_test.id, > :predicate => 'BioCatalogue:sameAs', > :object_type => 'EmbraceTest', > @@ -274,7 +269,7 @@ > end > > def self.already_imported?(test_id) > - hist = TestScriptHistory.find(:first, :conditions => {:object_id => test_id} ) > + hist = Relationship.find(:first, :conditions => {:object_id => test_id, :object_type => 'EmbraceTest'} ) > unless hist.nil? > return true > end > > > Modified: > branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py > (1286 => 1287) > > > --- branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py 2009-11-16 18:16:56 UTC (rev 1286) > +++ branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py 2009-11-17 10:58:32 UTC (rev 1287) > @@ -26,7 +26,10 @@ > cursor = db.cursor() > # > # Get the tests that need to be run > -cursor.execute("SELECT testable_id, id, exec_name FROM test_scripts WHERE exec_name IS NOT NULL;") > +sql_stmt = "SELECT service_tests.service_id, service_tests.test_id, test_scripts.exec_name " > +sql_stmt += "FROM test_scripts,service_tests WHERE service_tests.test_id=test_scripts.id AND service_tests.test_type='TestScript';" > +#cursor.execute("SELECT testable_id, id, exec_name FROM test_scripts WHERE exec_name IS NOT NULL;") > +cursor.execute(sql_stmt) > queue = cursor.fetchall() > > if len(queue) == 0: > > > Modified: > branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py > (1286 => 1287) > > > --- branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py 2009-11-16 18:16:56 UTC (rev 1286) > +++ branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py 2009-11-17 10:58:32 UTC (rev 1287) > @@ -1,6 +1,15 @@ > #!/usr/bin/python > +################################################################ > +# > +# This scripts wraps a test scripts and executes it > +# as a sub process. If the script does not complete within > +# half an hour, it is kill and a corresponding message inserted > +# in the log > +# > +# The script then posts the result (exit code) of the script to > +# to a url specified in a config file under ../config/ > > -import smtplib > + > import datetime > import os, subprocess > import time > @@ -13,17 +22,17 @@ > > from ConfigReader import ConfigReader > > -timeout = 30 * 60 # lenght of timeout (in seconds) > +timeout = 30 * 60 # length of timeout (in seconds) > kill_delay = 2 # number of seconds that have to pass before proceeding after a process is killed > > configs = ConfigReader('../config/tests_script_runner.config').read() > harnessroot = configs['harnessroot'] > result_url = configs['result_url'] > > -UNKNOWN = 0 > -PASSED = 1 > -WARNING = 2 > -FAILED = 3 > +#UNKNOWN = 0 > +#PASSED = 1 > +#WARNING = 2 > +#FAILED = 3 > > def signal_handler(signum, frame): > os.kill(child.pid, signal.SIGKILL) > @@ -50,15 +59,16 @@ > startdate= time.strftime("%Y-%m-%d %H:%M:%S") > print startdate > > -#db = MySQLdb.connect(host="localhost", user="root", passwd="biocat", db="biocat_dev") > -db = MySQLdb.connect(host=configs['host'],user=configs['user'], passwd=configs['password'], db=configs['database']) > +db = MySQLdb.connect(host=configs['host'],user=configs['user'], > + passwd=configs['password'], db=configs['database']) > > cursor = db.cursor() > > -#testdir = os.path.join(harnessroot, os.path.join(sys.argv[1], sys.argv[2])) > +#test run dir > testdir = os.path.join(configs['executionroot'], os.path.join(sys.argv[1], sys.argv[2])) > cwd = os.path.join(testdir, "package") > logfilename = os.path.join(testdir, os.path.join("logs", ("%s.tmp.log" % datetime.datetime.now()))) > + > try: > logfile = open(logfilename, 'w') > prev_handler = signal.signal(signal.SIGALRM, signal_handler) > @@ -75,7 +85,7 @@ > > except: > sys.stdout = stdout_bak > - err_string = "Test harness failure" > + err_string = "Test Wrapper failure" > returncode= 1 > print sys.exc_info() > # make a note in the logfile if the process was forcefully killed > @@ -91,13 +101,22 @@ > > enddate= time.strftime("%Y-%m-%d %H:%M:%S") > > +comments = """Test began: %s ; Test ended: %s ; Result : %s """ % (startdate, enddate, returncode) > + > +def service_test_id(script_id): > + stmt = "SELECT id from service_tests WHERE test_type='TestScript' and test_id=%d ;"%script_id > + results = cursor.execute(stmt) > + reference = cursor.fetchone() > + return reference[0] > + > + > #-------------------------------------------------------------------------------------------------------------- > > def save_result(test_id, result, action, message, start, end, dbcursor): > - print (int(test_id), 'TestScript', int(result), action, escape_string(message), start, end) > + st_id = service_test_id(test_id) > try: > - statement = "INSERT INTO test_results (`test_id`, `test_type`, `result`, `action`, `message`, `created_at`, `updated_at`) " > - statement += "VALUES (%s, '%s', %d, '%s', '%s', '%s', '%s') ;" %(int(test_id), "TestScript", int(result), action, escape_string(message), start, end) > + statement = "INSERT INTO test_results (`service_test_id`, `test_id`, `test_type`, `result`, `action`, `message`, `created_at`, `updated_at`) " > + statement += "VALUES (%d, %s, '%s', %d, '%s', '%s', '%s', '%s') ;" %(int(st_id), int(test_id), "TestScript", int(result), action, escape_string(message), start, end) > dbcursor.execute(statement) > db.commit() > except Exception, e: > @@ -118,7 +137,7 @@ > #--------------------------------------------------------------------------------- > > > -comments = """Test began: %s ; Test ended: %s ; Result : %s """ % (startdate, enddate, returncode) > + > #--------------------------------------------------------------------------------- > def log_contents(log): > msg = '' > @@ -127,13 +146,16 @@ > msg += line > return msg > > + > + > # User curl to post the test results back to the application > -def post_result_with_curl(url, test_id, return_code, action, message): > +def post_result_with_curl(url, test_id, return_code, action, message=''): > > test_type ="TestScript" > user = configs['api_user'] > password = configs['api_pass'] > message = log_contents(logfilename) > + st_id = service_test_id(test_id) > > data = '' > data +=' ' > @@ -142,7 +164,8 @@ > data +='%d'%(return_code) > data +='%s'%(action) > data +='%s'%(message) > - data +='' #%(test_id,return_code, action, message) > + data +='%d'%(st_id) > + data +='' > curl = "curl -X POST -u %s:%s -d '%s' -H 'Content-Type:application/xml' %s" %(user, password,data, url) > print curl > > @@ -182,8 +205,8 @@ > > ## print comments before stdio of the process is added, since otherwise the process might block > ## because of a full stdout-buffer (for example with hk-test.pl...) > -#print comments > -# > +print comments > + > if response: > comments += "\n------ stderr and stdout follow ------\n%s" % response > sys.stdout.flush() > > > Modified: > branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py > (1286 => 1287) > > > --- branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py 2009-11-16 18:16:56 UTC (rev 1286) > +++ branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py 2009-11-17 10:58:32 UTC (rev 1287) > @@ -18,9 +18,11 @@ > self.configs = ConfigReader(fn).read() > > def get_script_references(self, db): > - stmt = "SELECT test_scripts.testable_id, test_scripts.id, test_scripts.filename, content_blobs.data " > - stmt += "FROM test_scripts,content_blobs WHERE test_scripts.content_blob_id = content_blobs.id;" > > + stmt = "SELECT service_tests.service_id, service_tests.test_id, test_scripts.filename, content_blobs.data " > + stmt += "FROM service_tests,test_scripts,content_blobs " > + stmt += "WHERE service_tests.test_id =test_scripts.id AND service_tests.test_type ='TestScript' AND test_scripts.content_blob_id = content_blobs.id;" > + > results = db.execute(stmt) > references = db.fetchall() > return references > @@ -61,7 +63,6 @@ > fh.write(data) > fh.close() > > - print "does this dir exist? = %s"%dir > if self.is_zip(fname): > os.chdir(dir) > os.system("unzip %s"%fname ) > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From MAILER-DAEMON at ebi.ac.uk Tue Nov 17 07:02:41 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 17 Nov 2009 12:02:41 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911171202.nAHC2fnU030616@spike.ebi.ac.uk> The original message was received at Tue, 17 Nov 2009 12:01:07 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Tue, 17 Nov 2009 12:01:07 +0000 Size: 9539 URL: From noreply at rubyforge.org Tue Nov 17 07:58:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Nov 2009 07:58:45 -0500 (EST) Subject: [BioCatalogue-developers] [1288] branches/rest-services-support: ui for rest resources Message-ID: <20091117125846.1C8911858316@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Nov 17 08:00:03 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 17 Nov 2009 13:00:03 +0000 Subject: [BioCatalogue-developers] [1287] branches/test-scripts: fixes to take care of the re-factoring of the db model for service tests In-Reply-To: <4B028C25.3050605@cs.man.ac.uk> References: <20091117105833.AC1271858312@rubyforge.org> <4B028C25.3050605@cs.man.ac.uk> Message-ID: <4B029E53.5030708@ebi.ac.uk> I certainly can, should and will. Eric Jiten Bhagat wrote: > Hi Eric, > > Just wondering if you could change this: > > + def test_scripts > + sts = ServiceTest.find(:all, :conditions => {:test_type => 'TestScript', :service_id => self.id}) > + sts.collect{|st| st.test}.compact > + end > > ... in the Service model, to something like: > > def service_tests_by_type(type) > ServiceTest.find(:all, :conditions => {:test_type => type.to_s, :service_id => self.id}) > end > > def service_test_instances_by_type(type) > service_tests_by_type(type).collect{|st| st.test}.compact > end > > ... that way making some generic methods that can easily be reused when building the views. > > Cheers, > Jits > > > > noreply at rubyforge.org wrote: > >> Revision >> 1287 >> Author >> ebontane >> Date >> 2009-11-17 05:58:32 -0500 (Tue, 17 Nov 2009) >> >> >> Log Message >> >> fixes to take care of the re-factoring of the db model for service tests >> >> >> Modified Paths >> >> * branches/test-scripts/app/controllers/test_results_controller.rb >> <#branchestestscriptsappcontrollerstest_results_controllerrb> >> * branches/test-scripts/app/controllers/test_scripts_controller.rb >> <#branchestestscriptsappcontrollerstest_scripts_controllerrb> >> * branches/test-scripts/app/models/service.rb >> <#branchestestscriptsappmodelsservicerb> >> * branches/test-scripts/app/models/service_test.rb >> <#branchestestscriptsappmodelsservice_testrb> >> * branches/test-scripts/app/models/test_result.rb >> <#branchestestscriptsappmodelstest_resultrb> >> * branches/test-scripts/app/models/test_script.rb >> <#branchestestscriptsappmodelstest_scriptrb> >> * branches/test-scripts/app/views/shared/_service_test.html.erb >> <#branchestestscriptsappviewsshared_service_testhtmlerb> >> * branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb >> <#branchestestscriptsscriptbiocatalogueembrace_test_scripts_importrb> >> * branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py >> <#branchestestscriptsvendorembrace_scriptssrcbiocat_harnesspy> >> * branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py >> <#branchestestscriptsvendorembrace_scriptssrcbiocat_wrapperpy> >> * branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py >> <#branchestestscriptsvendorembrace_scriptssrcmake_biocat_test_scripts_rundirspy> >> >> >> Diff >> >> >> Modified: >> branches/test-scripts/app/controllers/test_results_controller.rb >> (1286 => 1287) >> >> >> --- branches/test-scripts/app/controllers/test_results_controller.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/controllers/test_results_controller.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -1,3 +1,9 @@ >> +# BioCatalogue: app/controllers/test_results_controller.rb >> +# >> +# Copyright (c) 2008, University of Manchester, The European Bioinformatics >> +# Institute (EMBL-EBI) and the University of Southampton. >> +# See license.txt for details. >> + >> class TestResultsController < ApplicationController >> >> # POST /test_results >> @@ -3,4 +9,16 @@ >> def create >> # TODO: implement code for the submission of test_results via XML API >> + @test_result = TestResult.new(params[:test_result]) >> + >> + respond_to do |format| >> + if @test_result.save >> + flash[:notice] = 'TestResult was successfully created.' >> + #format.html { redirect_to(@test_result.service_test.service) } >> + format.xml { render :xml => @test_result.service_test.service, :status => :created, :location => @@test_result.service_test.service } >> + else >> + #format.html { render :action => "new" } >> + format.xml { render :xml => @test_result.errors, :status => :unprocessable_entity } >> + end >> + end >> end >> >> >> >> Modified: >> branches/test-scripts/app/controllers/test_scripts_controller.rb >> (1286 => 1287) >> >> >> --- branches/test-scripts/app/controllers/test_scripts_controller.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/controllers/test_scripts_controller.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -1,3 +1,9 @@ >> +# BioCatalogue: app/controllers/test_scripts_controller.rb >> +# >> +# Copyright (c) 2009, University of Manchester, The European Bioinformatics >> +# Institute (EMBL-EBI) and the University of Southampton. >> +# See license.txt for details. >> + >> class TestScriptsController < ApplicationController >> >> before_filter :login_required, :only => [ :create ] >> @@ -7,11 +13,10 @@ >> # FIXME & TODO: need to redo this code - need's to handle both creation of test script >> # from an HTML web form and (possibly) from the XML REST API. TBD >> >> - testable_type = params[:test_script][:testable_type] >> - testable_id = params[:test_script][:testable_id] >> + testable_id = params[:testable_id] >> >> - # Get the object associated with this test >> - testable = TestScript.find_testable(testable_type, testable_id) >> + # Get the Service associated with this test >> + testable = Service.find(testable_id) >> logger.info("got testable #{testable.class.to_s}") >> >> #create a test with user supplied content >> @@ -24,10 +29,10 @@ >> #create service test instance >> service_test = ServiceTest.new(:service_id => testable_id, >> :test_type => test_script.class.name) >> - test_script.service_test = service_test >> + service_test.test = test_script >> >> #add the test >> - testable.test_scripts << test_script >> + testable.service_tests << service_test >> >> redirect_to testable >> end >> >> >> Modified: branches/test-scripts/app/models/service.rb (1286 => >> 1287) >> >> >> --- branches/test-scripts/app/models/service.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/models/service.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -181,6 +181,11 @@ >> end >> end >> >> + def test_scripts >> + sts = ServiceTest.find(:all, :conditions => {:test_type => 'TestScript', :service_id => self.id}) >> + sts.collect{|st| st.test}.compact >> + end >> + >> protected >> >> def generate_unique_code >> >> >> Modified: branches/test-scripts/app/models/service_test.rb >> (1286 => 1287) >> >> >> --- branches/test-scripts/app/models/service_test.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/models/service_test.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -19,13 +19,25 @@ >> has_many :test_results, >> :dependent => :destroy >> >> - validates_presence_of :service_id, >> - :test_type, >> - :test_id >> - >> - validates_associated :test >> +# validates_presence_of :service_id, >> +# :test_type, >> +# :test_id >> +# >> +# validates_associated :test >> >> if USE_EVENT_LOG >> acts_as_activity_logged(:models => { :referenced => { :model => :service } }) >> end >> + >> + def latest_result >> + res = self.test_results.last >> + if res.nil? >> + return TestResult.new(:result => -1) >> + end >> + res >> + end >> + >> + def recent_status_history(entries =5) >> + self.test_results.last(entries) >> + end >> end >> >> >> Modified: branches/test-scripts/app/models/test_result.rb >> (1286 => 1287) >> >> >> --- branches/test-scripts/app/models/test_result.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/models/test_result.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -12,9 +12,10 @@ >> :action, >> :service_test_id >> >> - validates_inclusion_of :result, >> - :in => [ ], >> - :message => "Maybe the programming language for this test is not supported yet. Supported are : perl, python, java, ruby, utopia and rest" >> +# validates_inclusion_of :result, >> +# :in => [ -1..255 ], >> +# :message => "test result is should be an integer in range [-1..255] " >> + validates_numericality_of :result >> >> # Helper class method to find a "monitorable" object >> # given the monitorable object class name and id >> >> >> Modified: branches/test-scripts/app/models/test_script.rb >> (1286 => 1287) >> >> >> --- branches/test-scripts/app/models/test_script.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/models/test_script.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -63,6 +63,14 @@ >> end >> end >> >> + def latest_result >> + self.service_test.latest_result >> + end >> + >> + def recent_status_history >> + self.service_test.recent_status_history >> + end >> + >> # def filename=(new_filename) >> # write_attribute("filename", sanitize_filename(new_filename)) >> # end >> >> >> Modified: >> branches/test-scripts/app/views/shared/_service_test.html.erb >> (1286 => 1287) >> >> >> --- branches/test-scripts/app/views/shared/_service_test.html.erb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/app/views/shared/_service_test.html.erb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -4,9 +4,9 @@ >> >>

Upload a test for this <%= testable_item.class %>

>> >> >> Modified: >> branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb >> (1286 => 1287) >> >> >> --- branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/script/biocatalogue/embrace_test_scripts_import.rb 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -235,14 +235,9 @@ >> binding = test_binding(script[4], db).fetch_row[1] >> a_test = TestScript.new(:name => name, >> :exec_name => script[7], >> - #:filename => 'package.zip', >> - #:content_type => 'application/zip', >> :prog_language => binding.to_s.downcase, >> - :user_id => existing_service.submitter.id, >> - :testable_id => existing_service.id, >> - :testable_type => existing_service.class.name, >> - :created_at => Time.now, >> - :updated_at => Time.now) >> + :user_id => existing_service.submitter.id >> + ) >> >> a_test.content_blob = ContentBlob.new({:data => script[6]}) >> a_test.filename = 'package.zip' >> @@ -258,7 +253,7 @@ >> begin >> if existing_service.save! >> @stats.counts[:success_script_imports] +=1 >> - relationship = TestScriptHistory.new(:subject_type => a_test.class.name, >> + relationship = Relationship.new(:subject_type => a_test.class.name, >> :subject_id => a_test.id, >> :predicate => 'BioCatalogue:sameAs', >> :object_type => 'EmbraceTest', >> @@ -274,7 +269,7 @@ >> end >> >> def self.already_imported?(test_id) >> - hist = TestScriptHistory.find(:first, :conditions => {:object_id => test_id} ) >> + hist = Relationship.find(:first, :conditions => {:object_id => test_id, :object_type => 'EmbraceTest'} ) >> unless hist.nil? >> return true >> end >> >> >> Modified: >> branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py >> (1286 => 1287) >> >> >> --- branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/vendor/embrace_scripts/src/biocat_harness.py 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -26,7 +26,10 @@ >> cursor = db.cursor() >> # >> # Get the tests that need to be run >> -cursor.execute("SELECT testable_id, id, exec_name FROM test_scripts WHERE exec_name IS NOT NULL;") >> +sql_stmt = "SELECT service_tests.service_id, service_tests.test_id, test_scripts.exec_name " >> +sql_stmt += "FROM test_scripts,service_tests WHERE service_tests.test_id=test_scripts.id AND service_tests.test_type='TestScript';" >> +#cursor.execute("SELECT testable_id, id, exec_name FROM test_scripts WHERE exec_name IS NOT NULL;") >> +cursor.execute(sql_stmt) >> queue = cursor.fetchall() >> >> if len(queue) == 0: >> >> >> Modified: >> branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py >> (1286 => 1287) >> >> >> --- branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/vendor/embrace_scripts/src/biocat_wrapper.py 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -1,6 +1,15 @@ >> #!/usr/bin/python >> +################################################################ >> +# >> +# This scripts wraps a test scripts and executes it >> +# as a sub process. If the script does not complete within >> +# half an hour, it is kill and a corresponding message inserted >> +# in the log >> +# >> +# The script then posts the result (exit code) of the script to >> +# to a url specified in a config file under ../config/ >> >> -import smtplib >> + >> import datetime >> import os, subprocess >> import time >> @@ -13,17 +22,17 @@ >> >> from ConfigReader import ConfigReader >> >> -timeout = 30 * 60 # lenght of timeout (in seconds) >> +timeout = 30 * 60 # length of timeout (in seconds) >> kill_delay = 2 # number of seconds that have to pass before proceeding after a process is killed >> >> configs = ConfigReader('../config/tests_script_runner.config').read() >> harnessroot = configs['harnessroot'] >> result_url = configs['result_url'] >> >> -UNKNOWN = 0 >> -PASSED = 1 >> -WARNING = 2 >> -FAILED = 3 >> +#UNKNOWN = 0 >> +#PASSED = 1 >> +#WARNING = 2 >> +#FAILED = 3 >> >> def signal_handler(signum, frame): >> os.kill(child.pid, signal.SIGKILL) >> @@ -50,15 +59,16 @@ >> startdate= time.strftime("%Y-%m-%d %H:%M:%S") >> print startdate >> >> -#db = MySQLdb.connect(host="localhost", user="root", passwd="biocat", db="biocat_dev") >> -db = MySQLdb.connect(host=configs['host'],user=configs['user'], passwd=configs['password'], db=configs['database']) >> +db = MySQLdb.connect(host=configs['host'],user=configs['user'], >> + passwd=configs['password'], db=configs['database']) >> >> cursor = db.cursor() >> >> -#testdir = os.path.join(harnessroot, os.path.join(sys.argv[1], sys.argv[2])) >> +#test run dir >> testdir = os.path.join(configs['executionroot'], os.path.join(sys.argv[1], sys.argv[2])) >> cwd = os.path.join(testdir, "package") >> logfilename = os.path.join(testdir, os.path.join("logs", ("%s.tmp.log" % datetime.datetime.now()))) >> + >> try: >> logfile = open(logfilename, 'w') >> prev_handler = signal.signal(signal.SIGALRM, signal_handler) >> @@ -75,7 +85,7 @@ >> >> except: >> sys.stdout = stdout_bak >> - err_string = "Test harness failure" >> + err_string = "Test Wrapper failure" >> returncode= 1 >> print sys.exc_info() >> # make a note in the logfile if the process was forcefully killed >> @@ -91,13 +101,22 @@ >> >> enddate= time.strftime("%Y-%m-%d %H:%M:%S") >> >> +comments = """Test began: %s ; Test ended: %s ; Result : %s """ % (startdate, enddate, returncode) >> + >> +def service_test_id(script_id): >> + stmt = "SELECT id from service_tests WHERE test_type='TestScript' and test_id=%d ;"%script_id >> + results = cursor.execute(stmt) >> + reference = cursor.fetchone() >> + return reference[0] >> + >> + >> #-------------------------------------------------------------------------------------------------------------- >> >> def save_result(test_id, result, action, message, start, end, dbcursor): >> - print (int(test_id), 'TestScript', int(result), action, escape_string(message), start, end) >> + st_id = service_test_id(test_id) >> try: >> - statement = "INSERT INTO test_results (`test_id`, `test_type`, `result`, `action`, `message`, `created_at`, `updated_at`) " >> - statement += "VALUES (%s, '%s', %d, '%s', '%s', '%s', '%s') ;" %(int(test_id), "TestScript", int(result), action, escape_string(message), start, end) >> + statement = "INSERT INTO test_results (`service_test_id`, `test_id`, `test_type`, `result`, `action`, `message`, `created_at`, `updated_at`) " >> + statement += "VALUES (%d, %s, '%s', %d, '%s', '%s', '%s', '%s') ;" %(int(st_id), int(test_id), "TestScript", int(result), action, escape_string(message), start, end) >> dbcursor.execute(statement) >> db.commit() >> except Exception, e: >> @@ -118,7 +137,7 @@ >> #--------------------------------------------------------------------------------- >> >> >> -comments = """Test began: %s ; Test ended: %s ; Result : %s """ % (startdate, enddate, returncode) >> + >> #--------------------------------------------------------------------------------- >> def log_contents(log): >> msg = '' >> @@ -127,13 +146,16 @@ >> msg += line >> return msg >> >> + >> + >> # User curl to post the test results back to the application >> -def post_result_with_curl(url, test_id, return_code, action, message): >> +def post_result_with_curl(url, test_id, return_code, action, message=''): >> >> test_type ="TestScript" >> user = configs['api_user'] >> password = configs['api_pass'] >> message = log_contents(logfilename) >> + st_id = service_test_id(test_id) >> >> data = '' >> data +=' ' >> @@ -142,7 +164,8 @@ >> data +='%d'%(return_code) >> data +='%s'%(action) >> data +='%s'%(message) >> - data +='' #%(test_id,return_code, action, message) >> + data +='%d'%(st_id) >> + data +='' >> curl = "curl -X POST -u %s:%s -d '%s' -H 'Content-Type:application/xml' %s" %(user, password,data, url) >> print curl >> >> @@ -182,8 +205,8 @@ >> >> ## print comments before stdio of the process is added, since otherwise the process might block >> ## because of a full stdout-buffer (for example with hk-test.pl...) >> -#print comments >> -# >> +print comments >> + >> if response: >> comments += "\n------ stderr and stdout follow ------\n%s" % response >> sys.stdout.flush() >> >> >> Modified: >> branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py >> (1286 => 1287) >> >> >> --- branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py 2009-11-16 18:16:56 UTC (rev 1286) >> +++ branches/test-scripts/vendor/embrace_scripts/src/make_biocat_test_scripts_rundirs.py 2009-11-17 10:58:32 UTC (rev 1287) >> @@ -18,9 +18,11 @@ >> self.configs = ConfigReader(fn).read() >> >> def get_script_references(self, db): >> - stmt = "SELECT test_scripts.testable_id, test_scripts.id, test_scripts.filename, content_blobs.data " >> - stmt += "FROM test_scripts,content_blobs WHERE test_scripts.content_blob_id = content_blobs.id;" >> >> + stmt = "SELECT service_tests.service_id, service_tests.test_id, test_scripts.filename, content_blobs.data " >> + stmt += "FROM service_tests,test_scripts,content_blobs " >> + stmt += "WHERE service_tests.test_id =test_scripts.id AND service_tests.test_type ='TestScript' AND test_scripts.content_blob_id = content_blobs.id;" >> + >> results = db.execute(stmt) >> references = db.fetchall() >> return references >> @@ -61,7 +63,6 @@ >> fh.write(data) >> fh.close() >> >> - print "does this dir exist? = %s"%dir >> if self.is_zip(fname): >> os.chdir(dir) >> os.system("unzip %s"%fname ) >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> From ericnzuo at ebi.ac.uk Tue Nov 17 04:06:09 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 17 Nov 2009 09:06:09 +0000 Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern module in the BioCatalogue In-Reply-To: References:

Message-ID: <4B026781.3070307@ebi.ac.uk> Next week for me too Franck Tanoh wrote: > Hi guys, > Are you ok for Wed this week or Wed next week from 15.00 to 16.00? > > Cheers, > Franck > > 2009/11/13 Franck Tanoh > > > Finally back > > Franck > > Begin forwarded message: > >> *From: *"Michael Reich via RT" > > >> *Date: *13 November 2009 17:30:44 GMT >> *To: *ytanoh at cs.man.ac.uk >> *Subject: **[rt.broad #129246] GenePattern module in the >> BioCatalogue * >> *Reply-To: *gp-help at broadinstitute.org >> >> >> Franck, >> >> Apologies for dropping the ball on this! I'd love to revisit our >> plan to have a >> con call to discuss GenePattern and BioCatalogue. Please feel >> free to suggest >> some times next week when you are available. >> >> Best, >> Michael >> >> On Thu Sep 17 05:21:56 2009, ytanoh at cs.man.ac.uk >> wrote: >>> Hi Michael, >>> >>> Did you get my suggestion for possible date <<9/17 or 9/18 between >>> 13.00-15.00 GMT >>? We are OK for next week too if that better for >>> you. >>> >>> Regard, >>> Franck >>> >> > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From MAILER-DAEMON at ebi.ac.uk Tue Nov 17 11:31:02 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 17 Nov 2009 16:31:02 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911171631.nAHGV2t3032373@spike.ebi.ac.uk> The original message was received at Tue, 17 Nov 2009 16:29:24 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `name' for nil:NilClass" Date: Tue, 17 Nov 2009 16:29:24 +0000 Size: 9660 URL: From ytanoh at cs.man.ac.uk Tue Nov 17 12:03:16 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 17 Nov 2009 17:03:16 +0000 Subject: [BioCatalogue-developers] [rt.broad #129246] GenePattern module in the BioCatalogue In-Reply-To: References:

Message-ID: Hi Michael, >Apologies for dropping the ball on this! Good to hear from you >Please feel free to suggest some times next week when you are available. We are fine with next week Wednesday Nov 25 from 15.00 to 16.00 is that OK with you? Regards Franck 2009/11/13 Michael Reich via RT > Franck, > > Apologies for dropping the ball on this! I'd love to revisit our plan to > have a > con call to discuss GenePattern and BioCatalogue. Please feel free to > suggest > some times next week when you are available. > > Best, > Michael > > On Thu Sep 17 05:21:56 2009, ytanoh at cs.man.ac.uk wrote: > > Hi Michael, > > > > Did you get my suggestion for possible date <<9/17 or 9/18 between > > 13.00-15.00 GMT >>? We are OK for next week too if that better for > > you. > > > > Regard, > > Franck > > > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Nov 17 12:20:47 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 17 Nov 2009 17:20:47 +0000 Subject: [BioCatalogue-developers] [rt.broad #129246] GenePattern module in the BioCatalogue In-Reply-To: References:

Message-ID: I forgot to add that the time is GMT Franck On 17 Nov 2009, at 17:03, Franck Tanoh wrote: > Hi Michael, > > >Apologies for dropping the ball on this! > Good to hear from you > > >Please feel free to suggest some times next week when you are > available. > We are fine with next week Wednesday Nov 25 from 15.00 to 16.00 is > that OK with you? > > Regards > Franck > > 2009/11/13 Michael Reich via RT > Franck, > > Apologies for dropping the ball on this! I'd love to revisit our > plan to have a > con call to discuss GenePattern and BioCatalogue. Please feel free > to suggest > some times next week when you are available. > > Best, > Michael > > On Thu Sep 17 05:21:56 2009, ytanoh at cs.man.ac.uk wrote: > > Hi Michael, > > > > Did you get my suggestion for possible date <<9/17 or 9/18 between > > 13.00-15.00 GMT >>? We are OK for next week too if that better for > > you. > > > > Regard, > > Franck > > > > > > > -- > "Science knows no country, because knowledge belongs to humanity, > and is the torch which illuminates the world." - Louis Pasteur > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Nov 17 12:57:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Nov 2009 12:57:39 -0500 (EST) Subject: [BioCatalogue-developers] [1289] branches/rest-services-support/app/views: updated ui for better coherence Message-ID: <20091117175740.003631858323@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Tue Nov 17 13:05:04 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 17 Nov 2009 18:05:04 +0000 Subject: [BioCatalogue-developers] [1289] branches/rest-services-support/app/views: updated ui for better coherence In-Reply-To: <20091117175740.003631858323@rubyforge.org> References: <20091117175740.003631858323@rubyforge.org> Message-ID: <4B02E5D0.6030102@cs.man.ac.uk> Mannie, Please don't add custom processing like this: (controller.controller_name=="rest_services"? "50x7":"50x10") It's much harder to maintain. Does it really need to be a different size? If it really needs to be then apply a custom class or something or get the partial to take in an optional param for the height (see app/views/annotations/_descriptions.html.erb for examples of how to do optional params for partials). Cheers, Jits noreply at rubyforge.org wrote: > > Revision > 1289 > Author > mannie > Date > 2009-11-17 12:57:39 -0500 (Tue, 17 Nov 2009) > > > Log Message > > updated ui for better coherence > > > Modified Paths > > * branches/rest-services-support/app/views/annotations/_service_submission_fields.html.erb > <#branchesrestservicessupportappviewsannotations_service_submission_fieldshtmlerb> > * branches/rest-services-support/app/views/rest_services/_show_service_tabs.html.erb > <#branchesrestservicessupportappviewsrest_services_show_service_tabshtmlerb> > * branches/rest-services-support/app/views/rest_services/new.html.erb > <#branchesrestservicessupportappviewsrest_servicesnewhtmlerb> > * branches/rest-services-support/app/views/services/show.html.erb > <#branchesrestservicessupportappviewsservicesshowhtmlerb> > > > Diff > > > Modified: > branches/rest-services-support/app/views/annotations/_service_submission_fields.html.erb > (1288 => 1289) > > > --- branches/rest-services-support/app/views/annotations/_service_submission_fields.html.erb 2009-11-17 12:58:45 UTC (rev 1288) > +++ branches/rest-services-support/app/views/annotations/_service_submission_fields.html.erb 2009-11-17 17:57:39 UTC (rev 1289) > @@ -30,7 +30,7 @@ >

> Add a description of this service: >
> - <%= text_area_tag "annotations[description]", params[:annotations][:description], :disabled => fields_disabled, :size => "50x10", :style => "width: 99%;" %> > + <%= text_area_tag "annotations[description]", params[:annotations][:description], :disabled => fields_disabled, :size => (controller.controller_name=="rest_services"? "50x7":"50x10"), :style => "width: 99%;" %> >

> -

Resources (<%= resources.length -%>)

> +

Endpoints (<%= resources.length -%>)

> > >

> @@ -28,113 +28,111 @@ > > > <% resources.each do |resource| %> > - > - <%= content_tag(:a, h(resource.path), :href => "#rest_resource_#{resource.id}") -%> > - > + <% resource.rest_methods.each do |meth| %> > + > + <%= content_tag(:a, h("#{meth.method_type} #{resource.path}"), > + :href => "#rest_resource_#{resource.id}_#{meth.id}") -%> > + > + <% end %> > <% end %> >

> >

> > <% resources.each do |resource| %> > + <% resource.rest_methods.each do |method| %> > > -

> - > - > - > -

> - Resource Path: > - <%= h resource.path -%> > -

> - > -

> -

> - > -

> - <%= render :partial => "annotations/name_aliases", > - :locals => { :annotatable => resource } -%> > +

> + + name='<%=h "rest_resource_#{resource.id}_#{method.id}" -%>'> > + > +

> + Endpoint: > + > + <%= h "#{method.method_type} #{resource.path}" -%> > + > +

> + > +

> +

> + <%= render :partial => "annotations/name_aliases", > + :locals => { :annotatable => resource } -%> > +

> + > +

> + <%= render :partial => "annotations/descriptions", > + :locals => { :annotatable => resource } -%> > +

> + > + > +

> + <%= render :partial => "annotations/other_annotations", > + :locals => { :annotatable => resource } -%> > +

> + >

> > -

> - <%= render :partial => "annotations/descriptions", > +

> + <%= render :partial => "annotations/tags_box", > :locals => { :annotatable => resource } -%> > - >

> > -

> - <%= render :partial => "annotations/other_annotations", > - :locals => { :annotatable => resource } -%> > -

> - > + >

> > -

> - <%= render :partial => "annotations/tags_box", > - :locals => { :annotatable => resource } -%> > -

> +
> > - > -

> - > -
> - > - Methods: > -

> - <% resource.rest_methods.each do |method| %> > -

> -

> - Method: > - <%= h method.method_type.upcase -%> > + Parameters: > +

> + <% unless method.request_parameters.blank? %> > + <% method.request_parameters.each do |param| %> > +

> + <% uniq_id = "#{resource.id}M#{method.id}P#{param.id}" %> > + > + <%= link_to_function param.name, visual_effect( > + :toggle_blind, uniq_id, :duration => 0.5) %> > + > + > + <%= link_to_function image_tag("expand.png"), visual_effect( > + :toggle_blind, uniq_id, :duration => 0.5) %> > + > + > + >

> - > -

> - <%= render :partial => "annotations/name_aliases", > - :locals => { :annotatable => method } -%> > -

> - > -

> - Parameters: > - <% unless method.request_parameters.blank? %> > -

> - <%=h param.name %> > - <% unless param.default_value.blank? %> > - (<%=h (param.name + "=" + CGI.escape(param.default_value)) -%>) > - <% end %> > -

> - <% else %> > - unknown > - <% end %> > -

> - > - <%= render :partial => "annotations/descriptions", > - :locals => { :annotatable => method } -%> > - > - <%= render :partial => "annotations/examples", > - :locals => { :annotatable => method } -%> > - > - <%= render :partial => "annotations/other_annotations", > - :locals => { :annotatable => method } -%> > -

> -

> - <%= render :partial => "annotations/tags_box", > - :locals => { :annotatable => method } -%> > -

> + <% end %> > + <% else %> > + unknown > + <% end %> > + > > -

> - <% end %> > +

> + >

> - > -

> + > +

> Back to top >

> > + <% end %> > <% end %> > >

> > > Modified: > branches/rest-services-support/app/views/rest_services/new.html.erb > (1288 => 1289) > > > --- branches/rest-services-support/app/views/rest_services/new.html.erb 2009-11-17 12:58:45 UTC (rev 1288) > +++ branches/rest-services-support/app/views/rest_services/new.html.erb 2009-11-17 17:57:39 UTC (rev 1289) > @@ -12,95 +12,89 @@ > >

New REST Service

> > - > +

> > -

> + > +

> + Note: please do not specify parameterised URLs or URLs to specific > + functionality. Only provide the base URL to the REST service. > +

> + Example: > +
> +

Bad URL: http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/{db}/{id}
Good URL: http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/

> +

> > + > +

> + Note: these will be used for status checks so please ensure that > + the methods, resources and parameters all represent valid entities. > + > +

> + > + Example:
> +

http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/{db}/{id}?{params}
{method} http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/{db}/{id}

> +
Where: > +

{method} is an html method e.g. POST, PUT, DELETE, etc
{db} is an actual database name
{id} is an existing resource ID
{params} are the parameters given to the REST Service (if any)

> +

> + > + > <% form_for :rest_service, :url => { :action => :create } do |f| %> > <%= f.error_messages %> > > -

1. Specify the URL of the endpoint of the REST service (ie: the base URL):

> - > -

<%= text_field_tag "endpoint", params[:endpoint] || "http://", :style => "width: 100%;" -%>

> - > -

> - Note: please do not specify parameterised URLs or URLs to specific functionality. Only provide the base URL to the REST service. > - (In the future you will be able to describe the different functionality and parameters and so on). > -

> - Example: > -
> -

Bad URL: http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/{db}/{id}
Good URL: http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/

> -

> +

> + > +

> + 1. Specify the URL of the endpoint of the REST service (ie: the base URL): > +

> + > +

> + <%= text_field_tag "endpoint", params[:endpoint] || "http://", > + :style => "width: 99%" -%> > +

> + > + > +

2. Provide more information on the REST Service:

> + > +

> + What is the official or common name of this REST service? > + * > +
> + <%= text_field_tag "rest_service[name]", params[:rest_service] ? > + params[:rest_service][:name] : "", :style => "width: 99%;" %> > + > + <%= render :partial => 'annotations/service_submission_fields' -%> > +

> + > + > +

> + 3. List the methods (including resources and their parameters) provided > + by this REST service: > +

> > -

2. Provide more information on the REST Service:

> - > -

> - > - > - > - > - > - > -

> - > -

> - Methods provided by the REST Service > +

> > -

> - List the methods (including resources and their parameters) provided by this REST service:
> -

> - Note: these will be used for status checks so please ensure that the methods, resources and parameters > - all represent valid entities.

> - > - Example:
> -

http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/{db}/{id}?{params}
{method} http://www.ebi.ac.uk/Tools/webservices/rest/dbfetch/{db}/{id}

> -
Where: > -

{method} is an html method e.g. POST, PUT, DELETE, etc
{db} is an actual database name
{id} is an existing resource ID
{params} are the parameters given to the REST Service (if any)

> -

> - <%= text_area_tag "annotations[description]", params[:annotations][:description], :size => "50x10", :style => "width: 99%;" %> > -

> - > -

> -

> - More Information > - > - > -

> - What is the official or common name of this REST service? > - * > -
> - <%= text_field_tag "rest_service[name]", params[:rest_service] ? params[:rest_service][:name] : "", :style => "width: 99%;" %> > -

> - > - <%= render :partial => 'annotations/service_submission_fields' -%> > - > -

> - <%= f.submit "Submit", :disable_with => "Submitting..." -%> > -

> -

> + <%= text_area_tag "annotations[description]", params[:annotations][:description], > + :size => "50x7", :style => "width: 99%;" %> > +

> > - <% end %> > + > +

> + <%= f.submit "Submit", :disable_with => "Submitting..." -%> > +

> > +

> + > + <% end %> > + >

> > > Modified: > branches/rest-services-support/app/views/services/show.html.erb > (1288 => 1289) > > > --- branches/rest-services-support/app/views/services/show.html.erb 2009-11-17 12:58:45 UTC (rev 1288) > +++ branches/rest-services-support/app/views/services/show.html.erb 2009-11-17 17:57:39 UTC (rev 1289) > @@ -144,7 +144,7 @@ >

> >

> - Endpoint: > + Base Endpoint: >
> <% @latest_version.service_deployments.each do |s_d| -%> > <%= link_to(h(s_d.endpoint), s_d.endpoint, :popup => true) -%> > ------------------------------------------------------------------------ > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Tue Nov 17 13:38:03 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 17 Nov 2009 13:38:03 -0500 (EST) Subject: [BioCatalogue-developers] [1290] trunk: Initial work on some curation features: Message-ID: <20091117183803.CBF1E185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Tue Nov 17 15:05:33 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 17 Nov 2009 20:05:33 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911172005.nAHK5XvO023306@spike.ebi.ac.uk> The original message was received at Tue, 17 Nov 2009 20:03:59 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Tue, 17 Nov 2009 20:03:59 +0000 Size: 9459 URL: From MAILER-DAEMON at ebi.ac.uk Tue Nov 17 20:47:31 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 01:47:31 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911180147.nAI1lVe1016258@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 01:45:57 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `name' for nil:NilClass" Date: Wed, 18 Nov 2009 01:45:57 +0000 Size: 9579 URL: From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 02:45:37 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 07:45:37 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911180745.nAI7jbko010900@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 07:44:04 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Wed, 18 Nov 2009 07:44:03 +0000 Size: 9459 URL: From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 06:18:57 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 11:18:57 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911181118.nAIBIv7C005707@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 11:17:23 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Wed, 18 Nov 2009 11:17:23 +0000 Size: 11139 URL: From noreply at rubyforge.org Wed Nov 18 06:23:03 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 06:23:03 -0500 (EST) Subject: [BioCatalogue-developers] [1291] trunk: submit soaplab services in a background process and update of the about soaplab information Message-ID: <20091118112304.12B2018582CC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 18 06:44:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 06:44:45 -0500 (EST) Subject: [BioCatalogue-developers] [1292] trunk: Various style fixes and new main heading style (with Franck' s and Paul's help). Message-ID: <20091118114445.5A0FC1598078@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 09:19:01 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 14:19:01 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911181419.nAIEJ1k5025924@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 14:17:28 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `name' for nil:NilClass" Date: Wed, 18 Nov 2009 14:17:28 +0000 Size: 9580 URL: From noreply at rubyforge.org Wed Nov 18 10:55:49 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 10:55:49 -0500 (EST) Subject: [BioCatalogue-developers] [1293] branches/jerzy/app/controllers/application_controller.rb: activity logging for search by data Message-ID: <20091118155549.40B2A185831D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 18 11:20:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 11:20:11 -0500 (EST) Subject: [BioCatalogue-developers] [1294] branches/jerzy/app/views/search/by_data.html.erb: Minor UI updates Message-ID: <20091118162011.44A921858328@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Nov 18 12:30:37 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 18 Nov 2009 17:30:37 +0000 Subject: [BioCatalogue-developers] Fwd: [rt.broad #129246] GenePattern module in the BioCatalogue In-Reply-To: References: <4B031149.4070701@broadinstitute.org> Message-ID: ---------- Forwarded message ---------- From: Michael Reich via RT Date: 2009/11/17 Subject: Re: [BioCatalogue-developers] [rt.broad #129246] GenePattern module in the BioCatalogue To: ytanoh at cs.man.ac.uk Franck, That sounds great. We're looking forward to talking at 10 AM EST on 11/25. Michael Franck Tanoh via RT wrote: > > > I forgot to add that the time is GMT > > Franck > On 17 Nov 2009, at 17:03, Franck Tanoh wrote: > > >> Hi Michael, >> >> >>> Apologies for dropping the ball on this! >>> >> Good to hear from you >> >> >>> Please feel free to suggest some times next week when you are >>> >> available. >> We are fine with next week Wednesday Nov 25 from 15.00 to 16.00 is >> that OK with you? >> >> Regards >> Franck >> >> 2009/11/13 Michael Reich via RT >> Franck, >> >> Apologies for dropping the ball on this! I'd love to revisit our >> plan to have a >> con call to discuss GenePattern and BioCatalogue. Please feel free >> to suggest >> some times next week when you are available. >> >> Best, >> Michael >> >> On Thu Sep 17 05:21:56 2009, ytanoh at cs.man.ac.uk wrote: >> >>> Hi Michael, >>> >>> Did you get my suggestion for possible date <<9/17 or 9/18 between >>> 13.00-15.00 GMT >>? We are OK for next week too if that better for >>> you. >>> >>> Regard, >>> Franck >>> >>> >> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, >> and is the torch which illuminates the world." - Louis Pasteur >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > > -- __________________________________________________________ Michael Reich Director of Cancer Informatics Development Broad Institute of MIT and Harvard 7 Cambridge Center / Cambridge, MA 02142 USA Phone (617) 714-7467 http://www.broadinstitute.org/cancer -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 18 12:49:35 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 12:49:35 -0500 (EST) Subject: [BioCatalogue-developers] [1295] branches/rest-services-support: more ui updates + added functionality to delete individual parameters from each rest resource Message-ID: <20091118174935.4AE961858333@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 18 12:59:09 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 12:59:09 -0500 (EST) Subject: [BioCatalogue-developers] [1296] trunk: Further style tweaks, and a restyling of the top part of the Service show page. Message-ID: <20091118175909.B71F21858334@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 18 13:11:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 13:11:17 -0500 (EST) Subject: [BioCatalogue-developers] [1297] trunk/app/views/services/show.html.erb: Minor fix Message-ID: <20091118181117.34AD11858333@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 18 13:25:28 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 18 Nov 2009 13:25:28 -0500 (EST) Subject: [BioCatalogue-developers] [1298] trunk/app/views/services/show.html.erb: In the cases where a custom name has been provided the original specified name is now also shown . Message-ID: <20091118182528.AAF751858316@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Wed Nov 18 13:28:45 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Wed, 18 Nov 2009 18:28:45 +0000 Subject: [BioCatalogue-developers] Latest release Message-ID: <4B043CDD.9050107@cs.man.ac.uk> Hi Eric, I've just finished committing a load of various style updates (and a restyling of the top part of the service show page). Please could you update the test server at the earliest convenient time. And then if all goes well please could you go ahead and update the live site. The only custom steps I need are: db:migrate, and Set Franck to have role ID 1 I'm on leave tomorrow and Friday but I'll be checking my email a few times in case anything urgent comes up. It's very important we get the release done this week as next week I need to merge Jerzy's work in to trunk. Also, I'm sure you have stuff to be getting on with. Cheers, Jits From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 13:37:57 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 18:37:57 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911181837.nAIIbv9D021940@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 18:36:26 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to mx0.cs.man.ac.uk.: <<< 421 Too many concurrent SMTP connections; please try again later. ... while talking to mx1.cs.man.ac.uk.: <<< 421 mx1.cs.man.ac.uk: Too many concurrent SMTP connections; please try again later ... Deferred: 421 mx1.cs.man.ac.uk: Too many concurrent SMTP connections; please try again later ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Wed, 18 Nov 2009 18:36:26 +0000 Size: 9642 URL: From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 13:38:51 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 18:38:51 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911181838.nAIIcpGN022049@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 18:37:14 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to mx0.cs.man.ac.uk.: <<< 421 Too many concurrent SMTP connections; please try again later. ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Wed, 18 Nov 2009 18:37:14 +0000 Size: 9642 URL: From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 16:20:10 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Wed, 18 Nov 2009 21:20:10 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911182120.nAIKRkt6002936@spike.ebi.ac.uk> The original message was received at Wed, 18 Nov 2009 18:37:59 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] application#show (ActionView::TemplateError) "undefined method `display_name' for nil:NilClass" Date: Wed, 18 Nov 2009 18:37:59 +0000 Size: 9642 URL: From MAILER-DAEMON at ebi.ac.uk Wed Nov 18 22:05:55 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 03:05:55 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911190305.nAJ35tlc005408@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 03:04:21 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] users#rpx_update (NoMethodError) "undefined method `call' for nil:NilClass" Date: Thu, 19 Nov 2009 03:04:21 +0000 Size: 13876 URL: From ericnzuo at ebi.ac.uk Thu Nov 19 06:25:51 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Nov 2009 11:25:51 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B043CDD.9050107@cs.man.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> Message-ID: <4B052B3F.5080408@ebi.ac.uk> Hi Jits, I was at a seminar this morning. I will update the server now but it not clear me how this should be tested. I hope you have discussed with Franck. Eric Jiten Bhagat wrote: > Hi Eric, > > I've just finished committing a load of various style updates (and a > restyling of the top part of the service show page). > > Please could you update the test server at the earliest convenient time. > > And then if all goes well please could you go ahead and update the live > site. > > The only custom steps I need are: > > db:migrate, and > Set Franck to have role ID 1 > > I'm on leave tomorrow and Friday but I'll be checking my email a few > times in case anything urgent comes up. > > It's very important we get the release done this week as next week I > need to merge Jerzy's work in to trunk. Also, I'm sure you have stuff to > be getting on with. > > Cheers, > Jits > From ericnzuo at ebi.ac.uk Thu Nov 19 06:59:07 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Nov 2009 11:59:07 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B052B3F.5080408@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> Message-ID: <4B05330B.9010308@ebi.ac.uk> I have updated the test site. Jits could you please check that the updates have been correctly applied? Eric Eric Nzuobontane wrote: > Hi Jits, > I was at a seminar this morning. I will update the server now but it > not clear me how this should be tested. I hope you have discussed with > Franck. > > Eric > > > > Jiten Bhagat wrote: >> Hi Eric, >> >> I've just finished committing a load of various style updates (and a >> restyling of the top part of the service show page). >> >> Please could you update the test server at the earliest convenient time. >> >> And then if all goes well please could you go ahead and update the live >> site. >> >> The only custom steps I need are: >> >> db:migrate, and >> Set Franck to have role ID 1 >> >> I'm on leave tomorrow and Friday but I'll be checking my email a few >> times in case anything urgent comes up. >> >> It's very important we get the release done this week as next week I >> need to merge Jerzy's work in to trunk. Also, I'm sure you have stuff to >> be getting on with. >> >> Cheers, >> Jits >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From noreply at rubyforge.org Thu Nov 19 09:13:47 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Nov 2009 09:13:47 -0500 (EST) Subject: [BioCatalogue-developers] [1299] trunk: create display names for soaplab services and fix a migration script Message-ID: <20091119141348.02D0D197811E@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Nov 19 09:34:27 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 19 Nov 2009 14:34:27 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B05330B.9010308@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> Message-ID: finish testing .. nothing major to report except those issues: 1- the icon to promote alternative name to default name is barely visible .. 2- can't access thes services: http://test.biocatalogue.org/services/5-wsinterproscanservice_85990 http://test.biocatalogue.org/services/4-wsdbfetchserverlegacyservice_404849 http://test.biocatalogue.org/services/47-wsncbiblastservice_519650 http://test.biocatalogue.org/services/1-chebiwebserviceservice_755784 3-This service has a header in his description: http://test.biocatalogue.org/services/1932-search_826164 Franck 2009/11/19 Eric Nzuobontane > I have updated the test site. Jits could you please check that the updates > have been correctly applied? > > Eric > > > > Eric Nzuobontane wrote: > >> Hi Jits, >> I was at a seminar this morning. I will update the server now but it not >> clear me how this should be tested. I hope you have discussed with Franck. >> >> Eric >> >> >> >> Jiten Bhagat wrote: >> >>> Hi Eric, >>> >>> I've just finished committing a load of various style updates (and a >>> restyling of the top part of the service show page). >>> >>> Please could you update the test server at the earliest convenient time. >>> >>> And then if all goes well please could you go ahead and update the live >>> site. >>> >>> The only custom steps I need are: >>> >>> db:migrate, and >>> Set Franck to have role ID 1 >>> >>> I'm on leave tomorrow and Friday but I'll be checking my email a few >>> times in case anything urgent comes up. >>> >>> It's very important we get the release done this week as next week I >>> need to merge Jerzy's work in to trunk. Also, I'm sure you have stuff to >>> be getting on with. >>> >>> Cheers, >>> Jits >>> >>> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Thu Nov 19 09:57:57 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Nov 2009 14:57:57 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> Message-ID: <4B055CF5.6060502@ebi.ac.uk> > finish testing .. nothing major to report > except those issues: > > 1- the icon to promote alternative name to default name is barely > visible .. I hope Jits will have a look at this one. > 2- can't access thes services: > http://test.biocatalogue.org/services/5-wsinterproscanservice_85990 > http://test.biocatalogue.org/services/4-wsdbfetchserverlegacyservice_404849 > > http://test.biocatalogue.org/services/47-wsncbiblastservice_519650 > http://test.biocatalogue.org/services/1-chebiwebserviceservice_755784 I will investigate these > > 3-This service has a header in his description: > http://test.biocatalogue.org/services/1932-search_826164 > Weird! Eric > Franck > > > 2009/11/19 Eric Nzuobontane > > > I have updated the test site. Jits could you please check that the > updates have been correctly applied? > > Eric > > > > Eric Nzuobontane wrote: > > Hi Jits, > I was at a seminar this morning. I will update the server now > but it not clear me how this should be tested. I hope you have > discussed with Franck. > > Eric > > > > Jiten Bhagat wrote: > > Hi Eric, > > I've just finished committing a load of various style > updates (and a > restyling of the top part of the service show page). > > Please could you update the test server at the earliest > convenient time. > > And then if all goes well please could you go ahead and > update the live > site. > > The only custom steps I need are: > > db:migrate, and > Set Franck to have role ID 1 > > I'm on leave tomorrow and Friday but I'll be checking my > email a few > times in case anything urgent comes up. > > It's very important we get the release done this week as > next week I > need to merge Jerzy's work in to trunk. Also, I'm sure you > have stuff to > be getting on with. > > Cheers, > Jits > > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > > http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > > > > -- > "Science knows no country, because knowledge belongs to humanity, and > is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Thu Nov 19 10:28:04 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Nov 2009 10:28:04 -0500 (EST) Subject: [BioCatalogue-developers] [1300] trunk: Fixes: Message-ID: <20091119152804.EE3BB1598079@rubyforge.org> An HTML attachment was scrubbed... URL: From jits at cs.man.ac.uk Thu Nov 19 10:18:49 2009 From: jits at cs.man.ac.uk (jits at cs.man.ac.uk) Date: Thu, 19 Nov 2009 15:18:49 -0000 (UTC) Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B055CF5.6060502@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> <4B055CF5.6060502@ebi.ac.uk> Message-ID: <533825c7079edcc047714e03eb11362e.squirrel@webmail.cs.man.ac.uk> Hi guys, > >> finish testing .. nothing major to report >> except those issues: >> >> 1- the icon to promote alternative name to default name is barely >> visible .. > I hope Jits will have a look at this one. I'll make it darker. >> 2- can't access thes services: >> http://test.biocatalogue.org/services/5-wsinterproscanservice_85990 >> http://test.biocatalogue.org/services/4-wsdbfetchserverlegacyservice_404849 >> >> http://test.biocatalogue.org/services/47-wsncbiblastservice_519650 >> http://test.biocatalogue.org/services/1-chebiwebserviceservice_755784 > I will investigate these Looks like this is a bug in the code (good catch Eric)... I'll fix. >> >> 3-This service has a header in his description: >> http://test.biocatalogue.org/services/1932-search_826164 >> > Weird! Please could you add a task to the task list to create a custom stylesheet for the contents of annotations. Cheers, Jits > > Eric > >> Franck >> >> >> 2009/11/19 Eric Nzuobontane > > >> >> I have updated the test site. Jits could you please check that the >> updates have been correctly applied? >> >> Eric >> >> >> >> Eric Nzuobontane wrote: >> >> Hi Jits, >> I was at a seminar this morning. I will update the server now >> but it not clear me how this should be tested. I hope you have >> discussed with Franck. >> >> Eric >> >> >> >> Jiten Bhagat wrote: >> >> Hi Eric, >> >> I've just finished committing a load of various style >> updates (and a >> restyling of the top part of the service show page). >> >> Please could you update the test server at the earliest >> convenient time. >> >> And then if all goes well please could you go ahead and >> update the live >> site. >> >> The only custom steps I need are: >> >> db:migrate, and >> Set Franck to have role ID 1 >> >> I'm on leave tomorrow and Friday but I'll be checking my >> email a few >> times in case anything urgent comes up. >> >> It's very important we get the release done this week as >> next week I >> need to merge Jerzy's work in to trunk. Also, I'm sure you >> have stuff to >> be getting on with. >> >> Cheers, >> Jits >> >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> >> >> >> -- >> "Science knows no country, because knowledge belongs to humanity, and >> is the torch which illuminates the world." - Louis Pasteur > > From noreply at rubyforge.org Thu Nov 19 10:38:01 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 19 Nov 2009 10:38:01 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2842] add custom style sheet for annotation contents Message-ID: <20091119153801.5E34418582C1@rubyforge.org> Task #2842 has been updated. Project: BioCatalogue Subproject: Main Summary: add custom style sheet for annotation contents Complete: 0% Status: Open Description: Please could you add a task to the task list to create a custom stylesheet for the contents of annotations. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2842&group_id=6901&group_project_id=12540 From ericnzuo at ebi.ac.uk Thu Nov 19 10:43:49 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Thu, 19 Nov 2009 15:43:49 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B055CF5.6060502@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> <4B055CF5.6060502@ebi.ac.uk> Message-ID: <4B0567B5.5070105@ebi.ac.uk> > >> 2- can't access thes services: >> http://test.biocatalogue.org/services/5-wsinterproscanservice_85990 >> http://test.biocatalogue.org/services/4-wsdbfetchserverlegacyservice_404849 >> >> http://test.biocatalogue.org/services/47-wsncbiblastservice_519650 >> http://test.biocatalogue.org/services/1-chebiwebserviceservice_755784 Jits has committed a fix for this and the test server has been updated. From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 11:23:15 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 16:23:15 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191623.nAJGNFqQ017014@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:21:42 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:21:42 +0000 Size: 10257 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 11:24:53 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 16:24:53 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191624.nAJGOr7E017196@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:23:19 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:23:19 +0000 Size: 10261 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 11:29:04 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 16:29:04 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191629.nAJGT4it017603@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:27:31 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:27:31 +0000 Size: 10300 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 11:30:29 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 16:30:29 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191630.nAJGUTQI017750@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:28:55 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] service_providers#show (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:28:55 +0000 Size: 11685 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:13:09 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:13:09 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191713.nAJGRkIn017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:23:57 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#show (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:23:57 +0000 Size: 9747 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:18:10 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:18:10 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191718.nAJGRkIo017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:26:40 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] tags#show (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:26:40 +0000 Size: 10150 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:23:11 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:23:11 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191723.nAJGRkIp017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:26:10 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:26:10 +0000 Size: 10187 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:28:12 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:28:12 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191728.nAJGRkIq017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:24:20 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:24:20 +0000 Size: 10835 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:33:15 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:33:15 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191733.nAJGRkIr017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:24:34 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:24:34 +0000 Size: 11708 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:38:16 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:38:16 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191738.nAJGRkIs017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:25:42 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:25:42 +0000 Size: 11870 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:43:18 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:43:18 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191743.nAJGRkIt017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:25:20 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:25:20 +0000 Size: 11952 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 12:48:19 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 17:48:19 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191748.nAJGRkIu017630@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:25:01 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:25:01 +0000 Size: 11952 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:25:51 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:25:51 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191825.nAJHRk7x026140@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:27:56 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] tags#show (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:27:56 +0000 Size: 10156 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:30:52 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:30:52 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191830.nAJHRk80026140@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:27:47 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:27:47 +0000 Size: 10187 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:35:53 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:35:53 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191835.nAJHRk81026140@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:29:14 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:29:14 +0000 Size: 10332 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:37:26 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:37:26 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191837.nAJIRk2P001411@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:30:26 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:30:26 +0000 Size: 10373 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:41:00 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:41:00 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191841.nAJHRk82026140@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:29:49 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#show (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:29:49 +0000 Size: 11111 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:42:27 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:42:27 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191842.nAJIRk2Q001411@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:29:55 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] service_providers#show (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:29:55 +0000 Size: 11675 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:46:01 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:46:01 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191846.nAJHRk83026140@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:30:59 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:30:59 +0000 Size: 11871 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 19 13:47:28 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 19 Nov 2009 18:47:28 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911191847.nAJIRk2R001411@spike.ebi.ac.uk> The original message was received at Thu, 19 Nov 2009 16:30:53 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `all_name_annotations_for_service' for #" Date: Thu, 19 Nov 2009 16:30:53 +0000 Size: 11968 URL: From ericnzuo at ebi.ac.uk Fri Nov 20 04:59:59 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 20 Nov 2009 09:59:59 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B0567B5.5070105@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> <4B055CF5.6060502@ebi.ac.uk> <4B0567B5.5070105@ebi.ac.uk> Message-ID: <4B06689F.3090005@ebi.ac.uk> I have now put the latest code into production. This went live last night. Franck, an important thing would be for you to resubmit your soaplab servers that were not completely submitted. Could you also gently ask Paul to resubmit his soaplab server? Eric > Jits has committed a fix for this and the test server has been updated. > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ytanoh at cs.man.ac.uk Fri Nov 20 06:28:13 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 20 Nov 2009 11:28:13 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B06689F.3090005@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> <4B055CF5.6060502@ebi.ac.uk> <4B0567B5.5070105@ebi.ac.uk> <4B06689F.3090005@ebi.ac.uk> Message-ID: Hi Eric, > I have now put the latest code into production Well done! 1 thing I came across, services are not deletable anymore. > Could you also gently ask Paul to resubmit his soaplab server? I've asked him Can you add to the following list the new features so that i can send it to the friend list ? - Possibility to promote service alternative name set by users as default service name - User interface tweaks and bug fixes. Franck > I have now put the latest code into production. This went live last > night. Franck, an important thing would be for you to resubmit your > soaplab servers that were not completely submitted. Could you also > gently ask Paul to resubmit his soaplab server? > > Eric > >> Jits has committed a fix for this and the test server has been >> updated. >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From ericnzuo at ebi.ac.uk Fri Nov 20 07:50:37 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 20 Nov 2009 12:50:37 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> <4B055CF5.6060502@ebi.ac.uk> <4B0567B5.5070105@ebi.ac.uk> <4B06689F.3090005@ebi.ac.uk> Message-ID: <4B06909D.5050307@ebi.ac.uk> > 1 thing I came across, services are not deletable anymore. I think it because I have not given you admin privileges. I will do that now. Eric > > >> Could you also gently ask Paul to resubmit his soaplab server? > I've asked him > > Can you add to the following list the new features so that i can send > it to the friend list ? > - Possibility to promote service alternative name set by users as > default service name > - User interface tweaks and bug fixes. > > Franck > > > >> I have now put the latest code into production. This went live last >> night. Franck, an important thing would be for you to resubmit your >> soaplab servers that were not completely submitted. Could you also >> gently ask Paul to resubmit his soaplab server? >> >> Eric >> >>> Jits has committed a fix for this and the test server has been updated. >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> From ytanoh at cs.man.ac.uk Fri Nov 20 08:15:30 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Fri, 20 Nov 2009 13:15:30 +0000 Subject: [BioCatalogue-developers] Latest release In-Reply-To: <4B06909D.5050307@ebi.ac.uk> References: <4B043CDD.9050107@cs.man.ac.uk> <4B052B3F.5080408@ebi.ac.uk> <4B05330B.9010308@ebi.ac.uk> <4B055CF5.6060502@ebi.ac.uk> <4B0567B5.5070105@ebi.ac.uk> <4B06689F.3090005@ebi.ac.uk> <4B06909D.5050307@ebi.ac.uk> Message-ID: > I think it because I have not given you admin privileges. I will do > that now. ok The promote alternative name to default name is behaving very strangely. I tried to promote the alternative name of that service: http://www.biocatalogue.org/services/116-soapservice_986196 the alternative name has disappeared, no where to be found. I had the same problem with that one: http://www.biocatalogue.org/services/70-tfmodellerserviceservice_146264 to solve the problem I created another alternative name and promote it... that worked fine. Franck On 20 Nov 2009, at 12:50, Eric Nzuobontane wrote: > >> 1 thing I came across, services are not deletable anymore. > I think it because I have not given you admin privileges. I will do > that now. > > Eric > >> >> >>> Could you also gently ask Paul to resubmit his soaplab server? >> I've asked him >> >> Can you add to the following list the new features so that i can >> send it to the friend list ? >> - Possibility to promote service alternative name set by users as >> default service name >> - User interface tweaks and bug fixes. >> >> Franck >> >> >> >>> I have now put the latest code into production. This went live >>> last night. Franck, an important thing would be for you to >>> resubmit your soaplab servers that were not completely submitted. >>> Could you also gently ask Paul to resubmit his soaplab server? >>> >>> Eric >>> >>>> Jits has committed a fix for this and the test server has been >>>> updated. >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > From noreply at rubyforge.org Fri Nov 20 08:50:56 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 20 Nov 2009 08:50:56 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2801] Test UI users Message-ID: <20091120135056.412FB18582FF@rubyforge.org> Task #2801 has been updated. Project: BioCatalogue Subproject: Main Summary: Test UI users Complete: 100% Status: Closed Description: Only activated users should show up in the UI. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2801&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Nov 20 08:53:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 20 Nov 2009 08:53:17 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2568] unable to submit some services Message-ID: <20091120135317.F135518582FE@rubyforge.org> Task #2568 has been updated. Project: BioCatalogue Subproject: Main Summary: unable to submit some services Complete: 100% Status: Closed Description: The registry treats these services as the same; so I can only register one of them. But in reality they are doing different things: http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl and http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1_ws0.wsdl http://www.cbs.dtu.dk/ws/RNAmmer/RNAmmer_1_2_ws0.wsdl and http://www.cbs.dtu.dk/ws/BLASTatlas/BLASTatlas_1_0_ws2.wsdl http://www.cbs.dtu.dk/ws/NetGlycate/NetGlycate_1_0.wsdl and http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl http://www.cbs.dtu.dk/ws/NetNGlyc/NetNGlyc_1_0a_ws0.wsdl and http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl ?.. The provider: http://www.cbs.dtu.dk/ws/ Follow-Ups: ------------------------------------------------------- Date: 2009-11-20 13:53 By: ebontane Comment: new parser solves this problems ------------------------------------------------------- Date: 2009-06-16 13:44 By: ebontane Comment: http://www.cbs.dtu.dk/ws/MaxAlign/MaxAlign_1_1_ws0.wsdl http://www.cbs.dtu.dk/ws/SIDDbase/SIDDbase_1_0.wsdl http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl need to still be verified for parse error. The rest have been tested to parse properly ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2568&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Nov 20 11:52:37 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 20 Nov 2009 11:52:37 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2843] soaplab warning message when submission too long Message-ID: <20091120165237.5F1F11858302@rubyforge.org> Task #2843 has been updated. Project: BioCatalogue Subproject: Main Summary: soaplab warning message when submission too long Complete: 0% Status: Open Description: Paul submitted his soaplab service. When he got back to the browse page the service weren't there like for normal soap service. He then said 'it doesn't work'. Actually it does work. Soaplab submission takes a while and it is processed in the background. The problem is that we don't tell user what is happening...so they expect the submission to be as normal SOAP service. Can we have sensible messages to warn user that their soaplab submission may take longer than usual and we will notify them (e.g by email) when the process is completed? OR if technically possible, the process need to be made shorter. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2843&group_id=6901&group_project_id=12540 From MAILER-DAEMON at ebi.ac.uk Sat Nov 21 03:51:13 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Sat, 21 Nov 2009 08:51:13 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911210851.nAL8pDrn023359@spike.ebi.ac.uk> The original message was received at Sat, 21 Nov 2009 08:49:40 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] sessions#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Sat, 21 Nov 2009 08:49:40 +0000 Size: 12620 URL: From MAILER-DAEMON at ebi.ac.uk Sat Nov 21 03:51:37 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Sat, 21 Nov 2009 08:51:37 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911210851.nAL8pbnE023424@spike.ebi.ac.uk> The original message was received at Sat, 21 Nov 2009 08:50:04 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] sessions#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Sat, 21 Nov 2009 08:50:04 +0000 Size: 12356 URL: From MAILER-DAEMON at ebi.ac.uk Sat Nov 21 04:35:09 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Sat, 21 Nov 2009 09:35:09 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911210935.nAL9Rk0u030953@spike.ebi.ac.uk> The original message was received at Sat, 21 Nov 2009 08:50:22 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] sessions#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Sat, 21 Nov 2009 08:50:22 +0000 Size: 12783 URL: From ericnzuo at ebi.ac.uk Mon Nov 23 04:43:16 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 23 Nov 2009 09:43:16 +0000 Subject: [BioCatalogue-developers] delayed job workers! Message-ID: <4B0A5934.8090602@ebi.ac.uk> Hi Guys, The monitoring failed to run for 2 days and I do not see any pending monitoring jobs in the queue. I am investigating... Eric From jits at cs.man.ac.uk Mon Nov 23 04:52:30 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 23 Nov 2009 09:52:30 +0000 Subject: [BioCatalogue-developers] delayed job workers! In-Reply-To: <4B0A5934.8090602@ebi.ac.uk> References: <4B0A5934.8090602@ebi.ac.uk> Message-ID: <4B0A5B5E.1060103@cs.man.ac.uk> Thanks Eric. Did you restart the script/worker(s) when you did the live update? Jits Eric Nzuobontane wrote: > Hi Guys, > The monitoring failed to run for 2 days and I do not see any pending > monitoring jobs in the queue. I am investigating... > > Eric > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Mon Nov 23 04:55:20 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 23 Nov 2009 09:55:20 +0000 Subject: [BioCatalogue-developers] delayed job workers! In-Reply-To: <4B0A5B5E.1060103@cs.man.ac.uk> References: <4B0A5934.8090602@ebi.ac.uk> <4B0A5B5E.1060103@cs.man.ac.uk> Message-ID: <4B0A5C08.7040808@ebi.ac.uk> YES!! Jiten Bhagat wrote: > Thanks Eric. > > Did you restart the script/worker(s) when you did the live update? > > Jits > > > Eric Nzuobontane wrote: > >> Hi Guys, >> The monitoring failed to run for 2 days and I do not see any pending >> monitoring jobs in the queue. I am investigating... >> >> Eric >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> From ericnzuo at ebi.ac.uk Mon Nov 23 05:00:52 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 23 Nov 2009 10:00:52 +0000 Subject: [BioCatalogue-developers] delayed job workers! In-Reply-To: <4B0A5B5E.1060103@cs.man.ac.uk> References: <4B0A5934.8090602@ebi.ac.uk> <4B0A5B5E.1060103@cs.man.ac.uk> Message-ID: <4B0A5D54.6040809@ebi.ac.uk> In fact, I stopped them before the update and restarted them afterwards. I have just checked on the machines and do not see an any worker daemon process running! Eric Jiten Bhagat wrote: > Thanks Eric. > > Did you restart the script/worker(s) when you did the live update? > > Jits > > > Eric Nzuobontane wrote: > >> Hi Guys, >> The monitoring failed to run for 2 days and I do not see any pending >> monitoring jobs in the queue. I am investigating... >> >> Eric >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> From ericnzuo at ebi.ac.uk Mon Nov 23 05:28:30 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 23 Nov 2009 10:28:30 +0000 Subject: [BioCatalogue-developers] delayed job workers! In-Reply-To: <4B0A5C08.7040808@ebi.ac.uk> References: <4B0A5934.8090602@ebi.ac.uk> <4B0A5B5E.1060103@cs.man.ac.uk> <4B0A5C08.7040808@ebi.ac.uk> Message-ID: <4B0A63CE.8090709@ebi.ac.uk> Unfortunately the workers died, while tweeting the creation of new services from the soaplab server submission. I have just looked at the queue and there is a pending soaplab server submission. However, since this has a job worker id is associated with items in the job queue, I believe restarting the workers will not run this job in the queue. I think this will need to be remove manually. Do you agree, Jits? Eric 1 jobs processed at 0.0294 j/s, 0 failed ... I AM TWEETING! I AM TWEETING! I AM TWEETING! I AM TWEETING! I AM TWEETING! 1 jobs processed at 0.0052 j/s, 0 failed ... /ebi/www/plive/ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:146:in `select': time interval must be positive (ArgumentError) from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:146:in `do_select' from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:62:in `initialize' from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:61:in `new' from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:61:in `initialize' from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:48:in `synchronize' from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:48:in `initialize' from lib/ruby/1.8/singleton.rb:95:in `new' from lib/ruby/1.8/singleton.rb:95:in `instance' ... 53 levels... from ruby/gems/gems/daemons-1.0.10/lib/daemons/cmdline.rb:105:in `call' from ruby/gems/gems/daemons-1.0.10/lib/daemons/cmdline.rb:105:in `catch_exceptions' from ruby/gems/gems/daemons-1.0.10/lib/daemons.rb:187:in `run_proc' from script/worker:19 Eric Nzuobontane wrote: > YES!! > > > > Jiten Bhagat wrote: >> Thanks Eric. >> >> Did you restart the script/worker(s) when you did the live update? >> >> Jits >> >> >> Eric Nzuobontane wrote: >> >>> Hi Guys, >>> The monitoring failed to run for 2 days and I do not see any pending >>> monitoring jobs in the queue. I am investigating... >>> >>> Eric >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Mon Nov 23 05:42:50 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 23 Nov 2009 10:42:50 +0000 Subject: [BioCatalogue-developers] delayed job workers! In-Reply-To: <4B0A63CE.8090709@ebi.ac.uk> References: <4B0A5934.8090602@ebi.ac.uk> <4B0A5B5E.1060103@cs.man.ac.uk> <4B0A5C08.7040808@ebi.ac.uk> <4B0A63CE.8090709@ebi.ac.uk> Message-ID: <4B0A672A.8030506@ebi.ac.uk> I have restarted the workers. Eric Eric Nzuobontane wrote: > Unfortunately the workers died, while tweeting the creation of new > services from the soaplab server submission. I have just looked at the > queue and there is a pending soaplab server submission. However, since > this has a job worker id is associated with items in the job queue, I > believe restarting the workers will not run this job in the queue. I > think this will need to be remove manually. Do you agree, Jits? > > Eric > > 1 jobs processed at 0.0294 j/s, 0 failed ... > I AM TWEETING! > I AM TWEETING! > I AM TWEETING! > I AM TWEETING! > I AM TWEETING! > 1 jobs processed at 0.0052 j/s, 0 failed ... > /ebi/www/plive/ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:146:in > `select': time interval must be positive (ArgumentError) > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:146:in > `do_select' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:62:in > `initialize' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:61:in > `new' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:61:in > `initialize' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:48:in > `synchronize' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:48:in > `initialize' > from lib/ruby/1.8/singleton.rb:95:in `new' > from lib/ruby/1.8/singleton.rb:95:in `instance' > ... 53 levels... > from ruby/gems/gems/daemons-1.0.10/lib/daemons/cmdline.rb:105:in > `call' > from ruby/gems/gems/daemons-1.0.10/lib/daemons/cmdline.rb:105:in > `catch_exceptions' > from ruby/gems/gems/daemons-1.0.10/lib/daemons.rb:187:in `run_proc' > from script/worker:19 > > > > > Eric Nzuobontane wrote: >> YES!! >> >> >> >> Jiten Bhagat wrote: >>> Thanks Eric. >>> >>> Did you restart the script/worker(s) when you did the live update? >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> Hi Guys, >>>> The monitoring failed to run for 2 days and I do not see any pending >>>> monitoring jobs in the queue. I am investigating... >>>> >>>> Eric >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From jits at cs.man.ac.uk Mon Nov 23 05:49:18 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Mon, 23 Nov 2009 10:49:18 +0000 Subject: [BioCatalogue-developers] delayed job workers! In-Reply-To: <4B0A63CE.8090709@ebi.ac.uk> References: <4B0A5934.8090602@ebi.ac.uk> <4B0A5B5E.1060103@cs.man.ac.uk> <4B0A5C08.7040808@ebi.ac.uk> <4B0A63CE.8090709@ebi.ac.uk> Message-ID: <4B0A68AE.5050308@cs.man.ac.uk> Eric Nzuobontane wrote: > Unfortunately the workers died, while tweeting the creation of new > services from the soaplab server submission. I have just looked at the > queue and there is a pending soaplab server submission. However, since > this has a job worker id is associated with items in the job queue, I > believe restarting the workers will not run this job in the queue. I > think this will need to be remove manually. Do you agree, Jits? Let's take this on Skype. Jits > > Eric > > 1 jobs processed at 0.0294 j/s, 0 failed ... > I AM TWEETING! > I AM TWEETING! > I AM TWEETING! > I AM TWEETING! > I AM TWEETING! > 1 jobs processed at 0.0052 j/s, 0 failed ... > /ebi/www/plive/ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:146:in > `select': time interval must be positive (ArgumentError) > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:146:in > `do_select' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:62:in > `initialize' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:61:in > `new' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:61:in > `initialize' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:48:in > `synchronize' > from ruby/gems/gems/Dnsruby-1.0/lib/Dnsruby/select_thread.rb:48:in > `initialize' > from lib/ruby/1.8/singleton.rb:95:in `new' > from lib/ruby/1.8/singleton.rb:95:in `instance' > ... 53 levels... > from ruby/gems/gems/daemons-1.0.10/lib/daemons/cmdline.rb:105:in > `call' > from ruby/gems/gems/daemons-1.0.10/lib/daemons/cmdline.rb:105:in > `catch_exceptions' > from ruby/gems/gems/daemons-1.0.10/lib/daemons.rb:187:in `run_proc' > from script/worker:19 > > > > > Eric Nzuobontane wrote: >> YES!! >> >> >> >> Jiten Bhagat wrote: >>> Thanks Eric. >>> >>> Did you restart the script/worker(s) when you did the live update? >>> >>> Jits >>> >>> >>> Eric Nzuobontane wrote: >>> >>>> Hi Guys, >>>> The monitoring failed to run for 2 days and I do not see any pending >>>> monitoring jobs in the queue. I am investigating... >>>> >>>> Eric >>>> _______________________________________________ >>>> BioCatalogue-developers mailing list >>>> BioCatalogue-developers at rubyforge.org >>>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >>>> >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > From noreply at rubyforge.org Mon Nov 23 06:18:42 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 06:18:42 -0500 (EST) Subject: [BioCatalogue-developers] [1301] branches/jerzy/data/regex.txt: Message-ID: <20091123111842.8DEDD1858317@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Nov 23 08:53:51 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 08:53:51 -0500 (EST) Subject: [BioCatalogue-developers] [1302] trunk: Merged Jerzy's (aka George) work on the Search By Data branch , from revision 1171:1301 of 'jerzy' branch. Message-ID: <20091123135351.C8453185830D@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Nov 23 09:00:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 09:00:29 -0500 (EST) Subject: [BioCatalogue-developers] [1303] trunk/public/stylesheets/styles.css: Added a very slight green border to the H1 style to make it stand out more as a heading . Message-ID: <20091123140029.AF77B18582C5@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Nov 23 09:06:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 09:06:40 -0500 (EST) Subject: [BioCatalogue-developers] [1304] trunk/public/stylesheets/styles.css: Added a rounded border effect on H1 titles. Message-ID: <20091123140640.B7D1D185830D@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Nov 23 09:12:59 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 23 Nov 2009 14:12:59 +0000 Subject: [BioCatalogue-developers] [rt.broad #129246] GenePattern module in the BioCatalogue In-Reply-To: References: <4B031149.4070701@broadinstitute.org> Message-ID: Hi Michael, I've set up a telecon for the meeting this Wednesday, here are the details: Tel: +49 1803 002 070 Pin : 877295 my SKYPE id is ytanoh just in case you are having any connection problem. The aim of the meeting is to discuss how to bring GenePattern Modules in the BioCatalogue (http://www.biocatalogue.org/) Regards, Franck 2009/11/17 Michael Reich via RT > Franck, > > That sounds great. We're looking forward to talking at 10 AM EST on 11/25. > > Michael > > Franck Tanoh via RT wrote: > > > > > > I forgot to add that the time is GMT > > > > Franck > > On 17 Nov 2009, at 17:03, Franck Tanoh wrote: > > > > > >> Hi Michael, > >> > >> > >>> Apologies for dropping the ball on this! > >>> > >> Good to hear from you > >> > >> > >>> Please feel free to suggest some times next week when you are > >>> > >> available. > >> We are fine with next week Wednesday Nov 25 from 15.00 to 16.00 is > >> that OK with you? > >> > >> Regards > >> Franck > >> > >> 2009/11/13 Michael Reich via RT > >> Franck, > >> > >> Apologies for dropping the ball on this! I'd love to revisit our > >> plan to have a > >> con call to discuss GenePattern and BioCatalogue. Please feel free > >> to suggest > >> some times next week when you are available. > >> > >> Best, > >> Michael > >> > >> On Thu Sep 17 05:21:56 2009, ytanoh at cs.man.ac.uk wrote: > >> > >>> Hi Michael, > >>> > >>> Did you get my suggestion for possible date <<9/17 or 9/18 between > >>> 13.00-15.00 GMT >>? We are OK for next week too if that better for > >>> you. > >>> > >>> Regard, > >>> Franck > >>> > >>> > >> > >> > >> -- > >> "Science knows no country, because knowledge belongs to humanity, > >> and is the torch which illuminates the world." - Louis Pasteur > >> _______________________________________________ > >> BioCatalogue-developers mailing list > >> BioCatalogue-developers at rubyforge.org > >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > >> > > > > > > > > -- > __________________________________________________________ > > Michael Reich > Director of Cancer Informatics Development > Broad Institute of MIT and Harvard > 7 Cambridge Center / Cambridge, MA 02142 USA > Phone (617) 714-7467 > http://www.broadinstitute.org/cancer > > > -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur -------------- next part -------------- An HTML attachment was scrubbed... URL: From twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com Mon Nov 23 09:15:09 2009 From: twitter-follow-biocatalogue-developers=rubyforge.org at postmaster.twitter.com (Twitter) Date: Mon, 23 Nov 2009 14:15:09 +0000 Subject: [BioCatalogue-developers] Jiten Bhagat is now following you on Twitter! Message-ID: <4b0a98ed1e208_2fa3d1fbaa0931280@mx003.twitter.com.tmail> Hi, BioCatalogue Test (biocat_test). Jiten Bhagat (jitenbhagat) is now following your tweets on Twitter. Check out Jiten Bhagat's profile here: http://twitter.com/jitenbhagat You may follow Jiten Bhagat as well by clicking on the "follow" button. Jiten Bhagat may not appear in your follower list. Jiten Bhagat may have decided to stop following you, or the account may have been suspended for a Terms of Service violation. If you believe Jiten Bhagat is engaging in abusive behavior on Twitter, you may report Jiten Bhagat for spam (http://twitter.com/user_spam_reports/confirm/19420634?utm_source=follow&utm_campaign=twitter20080331162631&utm_medium=email). Best, Twitter -- If you'd rather not receive follow notification emails from Twitter, you can unsubscribe immediately. To resubscribe or change other Twitter email preferences, visit your account settings to manage email notices. Unsubscribe: http://twitter.com/account/unsubscribe?utm_source=follow&code=YSlaCzjGdvoZcrlfVh97oa%2BYGDfTIfHzHvSuGoY7f508V9Q3yhtvdw%3D%3D&utm_campaign=twitter20080331162631&utm_medium=email&t=follow -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Nov 23 09:40:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 09:40:58 -0500 (EST) Subject: [BioCatalogue-developers] [1305] trunk/app/models/annotation.rb: Minor cleanup Message-ID: <20091123144058.67603185830A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Nov 23 12:24:01 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 12:24:01 -0500 (EST) Subject: [BioCatalogue-developers] [1306] trunk: Moved the service create tweeting process into a background job so it doesn 't affect the main submission of a service. Message-ID: <20091123172401.87E56185830A@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Mon Nov 23 12:24:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 12:24:31 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2718] Move tweets to a delayed job Message-ID: <20091123172432.0955E185830A@rubyforge.org> Task #2718 has been updated. Project: BioCatalogue Subproject: Main Summary: Move tweets to a delayed job Complete: 100% Status: Closed Description: (as per title) Follow-Ups: ------------------------------------------------------- Date: 2009-11-23 17:24 By: jits Comment: Done, revision 1306 ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2718&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Nov 23 12:26:40 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 12:26:40 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2844] Add more tweets! Message-ID: <20091123172640.C4979185830D@rubyforge.org> Task #2844 has been updated. Project: BioCatalogue Subproject: Main Summary: Add more tweets! Complete: 0% Status: Open Description: Start tweeting more events, with more useful info shown ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2844&group_id=6901&group_project_id=12540 From jerzyo at genesilico.pl Mon Nov 23 13:14:47 2009 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Mon, 23 Nov 2009 18:14:47 +0000 Subject: [BioCatalogue-developers] NAR article TODO list In-Reply-To: <20091123144058.67603185830A@rubyforge.org> References: <20091123144058.67603185830A@rubyforge.org> Message-ID: <4B0AD117.3060908@genesilico.pl> Hi Here are the points from NAR requirements. The only missing think is help pages. See below: _____ REQUIREMENTS FOR WEB SERVICES ____ Web Services. This section will include short papers describing websites that implement useful web services, that is, multiple task, automated analyses that are accessed programmatically rather than through manual interaction with a web server. To be considered, a website must: * Implement a large collection of web services. These services may be for general bioinformatics use, or focused on a single data domain, such as microarray data. More or less OK * Provide a help page which contains a comprehensive list of the web services available along with a clear description and the access url of each. Needs to be done - should we do it on wiki or on the site? * Provide a template program in perl, or another commonly used programming language, that can be run to access several of the web services and parse the output data. The goal is to give the user (and the reviewers) a working template for web services access. Ideally, the program should be easily modifiable so that it can be used for all of the web services available. Can we do it out of our test scripts? * Provide a prominent link to the template program on the home page. How about: "REST API" link ____ REQUIREMENTS FOR THE SUMMARY _______ * Authors must contact Dr. Gary Benson at narwbsrv at bu.edu to check the suitability of their proposed submission by 31 December, 2009 at the latest. A maximum one page summary should be submitted for this purpose. Proposals sent in before 30 November 2009 will not be reviewed until after that date. Write the summary - George for middle of december Review the Summary - Rodrigo - can You do it? * The WEB SERVER MUST BE FUNCTIONAL on the date of the proposal submission. Access to the server must be through a web browser. Non-server application programs will only be considered for high-throughput data (see above). DONE * The website MUST include a simple mechanism to try out sample data provided by the authors, for example, a button for automatic loading of the data. Accession for REST - to be done in help pages with (example GET and POST queries) * The website MUST contain help pages or a tutorial with links to sample output that performs interactively in the same way as real output. To be done on help pages * The output MUST be primarily web-based and viewable on the website. Use of browser plugins for data visualization is encouraged. DONE * If the website is not able to return results immediately, it MUST provide a web link to the results, at the time of data submission, which the user can then bookmark and access at a later time. Ideally, this link will report the status of the job (queued, running, or finished). Do not assume that users will provide an email address for results notification. ADD note on waiting when submitting Soaplab services * The one page summary MUST contain, at the top, the following affirmative statement. "This website is free and open to all users and there is no login requirement." OK * The one page summary MUST include the website address; website name; and the names, affiliations, and email addresses of all authors. OK, I have to be provided with these in the proper order with affiliations * The one page summary MUST provide descriptions of the input data, the output, and the processing method; complete citations for previous publications of the method or the web server; and two to four keywords. Additionally, authors must indicate how long the server has been running, the number of inputs analyzed during testing, and an estimate of the number of individuals outside of the authors' group who have been involved in the testing. OK - we'll take it from report data * The one page summary MUST include a notification if this is an update from a previous publication in the Web Server issue, and in that case, include an estimate of the number of users and the number of citations. Not relevant * IF THE WEB SERVER IS PREDICTIVE, authors must include, within the summary, details on validation of predictions from new data not used in training. N-fold cross validation studies will not be considered sufficient. Details should include size and composition of the validation data set (number of positive and negative cases), and several measures of predictive performance, including sensitivity, specificity, and precision. Not relevant From noreply at rubyforge.org Mon Nov 23 14:34:56 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 14:34:56 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2845] Tags should only be allowed on top level service container Message-ID: <20091123193456.8A9A9185830D@rubyforge.org> Task #2845 has been updated. Project: BioCatalogue Subproject: Main Summary: Tags should only be allowed on top level service container Complete: 0% Status: Open Description: Currently, the tags box for a service combines all tags on the Service, ServiceDeployments, ServiceVersions and SoapService/RestService. This adds significant processing overheads to things! Need to consolidate this to only allow 'tag' annotations on the top level Service object. This will also make things like ServiceProvider#tags_from_services more accurate! ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2845&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Nov 23 15:27:27 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 23 Nov 2009 15:27:27 -0500 (EST) Subject: [BioCatalogue-developers] [1307] trunk: Initial work on richer Service Provider profiles: Message-ID: <20091123202727.9ACB51858316@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Nov 24 08:24:12 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Nov 2009 08:24:12 -0500 (EST) Subject: [BioCatalogue-developers] [1308] branches/rest-services-support: wrote the skeleton logic to mine the user input for resources and params Message-ID: <20091124132412.EB9A715B8025@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Tue Nov 24 09:52:46 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 24 Nov 2009 14:52:46 +0000 Subject: [BioCatalogue-developers] Mail to Friends Message-ID: <4B0BF33E.5090708@ebi.ac.uk> Please comment on the mail below intended for the friend's list. Dear All, There was an update of the BioCatalogue on Friday November 21, 2009. With this update, it is now possible for submitters or curators to set an alternative name as the preferred display name of a service. This is a feature that has been requested by many users. With this feature you can show more descriptive names for your services. Also included in this update are some user experience improvements for the submission of Soaplab servers. For example, if you add new tools to your existing Soaplab server, you can simply resubmit in the usual way and BioCatalogue will register the new tools to the existing Soaplab entry in BioCatalogue. For Soaplab services, BioCatalogue also sets altenative display names automatically. Please do not hesitate to give us feedback on these and any other features of BioCatalogue The BioCatalogue Team From jits at cs.man.ac.uk Tue Nov 24 10:24:34 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Tue, 24 Nov 2009 15:24:34 +0000 Subject: [BioCatalogue-developers] Mail to Friends In-Reply-To: <4B0BF33E.5090708@ebi.ac.uk> References: <4B0BF33E.5090708@ebi.ac.uk> Message-ID: <4B0BFAB2.9030306@cs.man.ac.uk> Hi Eric, Looks good to me. Few minor points: - I wouldn't put the exact date of the update. - "For Soaplab services, BioCatalogue also sets altenative display names automatically. " should say "... preferred display names... ". Cheers, Jits Eric Nzuobontane wrote: > Please comment on the mail below intended for the friend's list. > > Dear All, > > There was an update of the BioCatalogue on Friday November 21, 2009. > With this update, it is now possible for submitters or curators to set > an alternative name as the preferred display name of a service. This > is a feature that has been requested by many users. With this feature > you can show more descriptive names for your services. Also included > in this update are some user experience improvements for the > submission of Soaplab servers. For example, if you add new tools to > your existing Soaplab server, you can simply resubmit in the usual way > and BioCatalogue will register the new tools to the existing Soaplab > entry in BioCatalogue. For Soaplab services, BioCatalogue also sets > altenative display names automatically. > > Please do not hesitate to give us feedback on these and any other > features of BioCatalogue > > The BioCatalogue Team > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ytanoh at cs.man.ac.uk Tue Nov 24 10:32:51 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 24 Nov 2009 15:32:51 +0000 Subject: [BioCatalogue-developers] Mail to Friends In-Reply-To: <4B0BFAB2.9030306@cs.man.ac.uk> References: <4B0BF33E.5090708@ebi.ac.uk> <4B0BFAB2.9030306@cs.man.ac.uk> Message-ID: <928794D7-28CF-48C8-BA1D-75681E2E6333@cs.man.ac.uk> I would prefer the features as bullet points... makes it clear and easy to read. There were some UI tweaks as well. Franck Franck On 24 Nov 2009, at 15:24, Jiten Bhagat wrote: > Hi Eric, > > Looks good to me. Few minor points: > - I wouldn't put the exact date of the update. > - "For Soaplab services, BioCatalogue also sets altenative display > names > automatically. " should say "... preferred display names... ". > > Cheers, > Jits > > > Eric Nzuobontane wrote: >> Please comment on the mail below intended for the friend's list. >> >> Dear All, >> >> There was an update of the BioCatalogue on Friday November 21, 2009. >> With this update, it is now possible for submitters or curators to >> set >> an alternative name as the preferred display name of a service. This >> is a feature that has been requested by many users. With this >> feature >> you can show more descriptive names for your services. Also included >> in this update are some user experience improvements for the >> submission of Soaplab servers. For example, if you add new tools to >> your existing Soaplab server, you can simply resubmit in the usual >> way >> and BioCatalogue will register the new tools to the existing Soaplab >> entry in BioCatalogue. For Soaplab services, BioCatalogue also sets >> altenative display names automatically. >> >> Please do not hesitate to give us feedback on these and any other >> features of BioCatalogue >> >> The BioCatalogue Team >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Tue Nov 24 10:40:44 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 24 Nov 2009 15:40:44 +0000 Subject: [BioCatalogue-developers] Mail to Friends In-Reply-To: <928794D7-28CF-48C8-BA1D-75681E2E6333@cs.man.ac.uk> References: <4B0BF33E.5090708@ebi.ac.uk> <4B0BFAB2.9030306@cs.man.ac.uk> <928794D7-28CF-48C8-BA1D-75681E2E6333@cs.man.ac.uk> Message-ID: <4B0BFE7C.9070007@ebi.ac.uk> Thank you guys for the comments. Franck, the reason I avoided bullet points is because I thought it would make it look a bit thin. But I am not sure if that is a good or a bad thing. Eric Franck Tanoh wrote: > I would prefer the features as bullet points... makes it clear and > easy to read. > There were some UI tweaks as well. > > Franck > > Franck > On 24 Nov 2009, at 15:24, Jiten Bhagat wrote: > >> Hi Eric, >> >> Looks good to me. Few minor points: >> - I wouldn't put the exact date of the update. >> - "For Soaplab services, BioCatalogue also sets altenative display names >> automatically. " should say "... preferred display names... ". >> >> Cheers, >> Jits >> >> >> Eric Nzuobontane wrote: >>> Please comment on the mail below intended for the friend's list. >>> >>> Dear All, >>> >>> There was an update of the BioCatalogue on Friday November 21, 2009. >>> With this update, it is now possible for submitters or curators to set >>> an alternative name as the preferred display name of a service. This >>> is a feature that has been requested by many users. With this feature >>> you can show more descriptive names for your services. Also included >>> in this update are some user experience improvements for the >>> submission of Soaplab servers. For example, if you add new tools to >>> your existing Soaplab server, you can simply resubmit in the usual way >>> and BioCatalogue will register the new tools to the existing Soaplab >>> entry in BioCatalogue. For Soaplab services, BioCatalogue also sets >>> altenative display names automatically. >>> >>> Please do not hesitate to give us feedback on these and any other >>> features of BioCatalogue >>> >>> The BioCatalogue Team >>> _______________________________________________ >>> BioCatalogue-developers mailing list >>> BioCatalogue-developers at rubyforge.org >>> http://rubyforge.org/mailman/listinfo/biocatalogue-developers >> >> _______________________________________________ >> BioCatalogue-developers mailing list >> BioCatalogue-developers at rubyforge.org >> http://rubyforge.org/mailman/listinfo/biocatalogue-developers From ericnzuo at ebi.ac.uk Tue Nov 24 10:57:38 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Tue, 24 Nov 2009 15:57:38 +0000 Subject: [BioCatalogue-developers] Mail to BIoCatalogue Friends Message-ID: <4B0C0272.1090203@ebi.ac.uk> Following your comment, this is what I am going to send... Dear All, We recently made an update to BioCatalogue (http://www.biocatalogue.org). With this update: - submitters or curators can set an alternative name as the preferred display name of a service. This is a feature that has been requested by many users. With this feature you can show more descriptive names for your services. - are improvements to the user experience for the submission of Soaplab servers. For example, if you add new tools to your existing Soaplab server, you can simply resubmit in the usual way and BioCatalogue will register the new tools to the existing Soaplab entry in BioCatalogue. For Soaplab services, BioCatalogue also sets preferred display names automatically. Please do not hesitate to give us feedback on these and any other features of BioCatalogue Thanks! The BioCatalogue Team From noreply at rubyforge.org Tue Nov 24 11:31:32 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Nov 2009 11:31:32 -0500 (EST) Subject: [BioCatalogue-developers] [1309] branches/rest-services-support/app: integrated the functionality to mine for resources into the rest resource controller Message-ID: <20091124163132.E3F701598079@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Nov 24 11:37:08 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Nov 2009 11:37:08 -0500 (EST) Subject: [BioCatalogue-developers] [1310] trunk: Substantial improvements to the header and the core navigation links (aka: 'action bar'). Message-ID: <20091124163708.2CFCC1598079@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Tue Nov 24 13:09:36 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Tue, 24 Nov 2009 18:09:36 +0000 Subject: [BioCatalogue-developers] Genepattern meeting Message-ID: <2CE7368B-E8BE-4AF0-A603-CDF92AC65D85@cs.man.ac.uk> Hi guys, A reminder that we have a telecom with the genepattern team from 3.00 to 4.00pm. Telecom details: phone: 0844 473 7458 PIN: 877295 Franck -------------- next part -------------- An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Tue Nov 24 13:41:49 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Tue, 24 Nov 2009 18:41:49 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911241841.nAOIfnsK026305@spike.ebi.ac.uk> The original message was received at Tue, 24 Nov 2009 18:40:16 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] sessions#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Tue, 24 Nov 2009 18:40:16 +0000 Size: 12429 URL: From noreply at rubyforge.org Tue Nov 24 14:45:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Nov 2009 14:45:30 -0500 (EST) Subject: [BioCatalogue-developers] [1311] trunk: Added a dropdown menu next to the search box to provide the option for " Search by Data". Message-ID: <20091124194531.019861598079@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Tue Nov 24 15:12:56 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Tue, 24 Nov 2009 15:12:56 -0500 (EST) Subject: [BioCatalogue-developers] [1312] trunk: Moved the various actions in the show pages into a dropdown actions menu, using the dropdown menu mechanism from the previous commit. Message-ID: <20091124201256.3601215B8025@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 25 07:25:37 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 07:25:37 -0500 (EST) Subject: [BioCatalogue-developers] [1313] trunk: Improvements for the Search by Data feature: Message-ID: <20091125122537.66A9018582AC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 25 07:40:23 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 07:40:23 -0500 (EST) Subject: [BioCatalogue-developers] [1314] trunk/app/views: Added "format" annotations field to input and output ports, under the heading " Data Format(s)". Message-ID: <20091125124023.3B14918582C1@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 25 11:39:03 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 11:39:03 -0500 (EST) Subject: [BioCatalogue-developers] [1315] trunk: Further changes to header design and other styles, based on feedback from Paul and Franck. Message-ID: <20091125163904.0B9B718582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Wed Nov 25 12:15:02 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Wed, 25 Nov 2009 17:15:02 +0000 Subject: [BioCatalogue-developers] link for the website Message-ID: Hi Jits, the only link i have in mind for now is the soaplab one... We could say something like: Turn your command line application into Web Services: http://soaplab.sourceforge.net/soaplab2/StepByStep.html Eric, and George please send Jits any interesting links you may have. Cheers, Franck -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Wed Nov 25 17:18:41 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 17:18:41 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2846] Need a rich text editor Message-ID: <20091125221841.D6A921858289@rubyforge.org> Task #2846 has been updated. Project: BioCatalogue Subproject: Main Summary: Need a rich text editor Complete: 0% Status: Open Description: ... for things like the announcement text box and annotations. CKEditor and TinyMCE are both copyleft licenced, so try something like: http://github.com/80beans/wysihat-engine|wysihat-engine ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2846&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Wed Nov 25 18:57:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 18:57:58 -0500 (EST) Subject: [BioCatalogue-developers] [1316] trunk: Latest work on a brand new homepage and brand new announcements system! This commit also includes many various style tweaks in other places . Message-ID: <20091125235759.170B11858282@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 25 22:56:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 22:56:38 -0500 (EST) Subject: [BioCatalogue-developers] [1317] trunk: Implemented the news feed. Message-ID: <20091126035638.9288F3C803E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Wed Nov 25 23:30:15 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Wed, 25 Nov 2009 23:30:15 -0500 (EST) Subject: [BioCatalogue-developers] [1318] trunk/app: Bugfixes for the ordering of the activity/news feed Message-ID: <20091126043016.146FD3C803E@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 06:32:41 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 06:32:41 -0500 (EST) Subject: [BioCatalogue-developers] [1319] trunk: Initial attempt at having a fallback for the homepage. Message-ID: <20091126113241.2251918582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 06:40:33 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 06:40:33 -0500 (EST) Subject: [BioCatalogue-developers] [1320] trunk/app/helpers/activity_feeds_helper.rb: Removed some debug code Message-ID: <20091126114033.EAF3818582C9@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 06:45:46 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 06:45:46 -0500 (EST) Subject: [BioCatalogue-developers] [1321] trunk/app/helpers/activity_feeds_helper.rb: Added some check code for the objects that might not exist anymore, for the activity feed. Message-ID: <20091126114546.4BB9F15B8027@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 08:21:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 08:21:31 -0500 (EST) Subject: [BioCatalogue-developers] [1322] trunk/app: Further changes and fixes to the new homepage, based on feedback. Message-ID: <20091126132132.2332218582CB@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Nov 26 09:51:24 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 26 Nov 2009 14:51:24 +0000 Subject: [BioCatalogue-developers] notes from testing ... Message-ID: Hi guys, I've told you about issues 1 and 3 ... pls look at issue 2 1-Was unable to access the home page after i submitted a service. 2- a typo in the message users get when they first register: currently we have <> not 'as' but 'has'. 3-in the search by data can ..should be able to upload file. Franck "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Thu Nov 26 09:53:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 09:53:24 -0500 (EST) Subject: [BioCatalogue-developers] [1323] trunk/app/controllers/users_controller.rb: Fixed typo Message-ID: <20091126145324.4973118582CB@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 26 09:58:02 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 26 Nov 2009 14:58:02 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911261458.nAQEw2oC011186@spike.ebi.ac.uk> The original message was received at Thu, 26 Nov 2009 14:56:31 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to mx0.cs.man.ac.uk.: <<< 421 Too many concurrent SMTP connections; please try again later. ... while talking to mx1.cs.man.ac.uk.: <<< 421 mx1.cs.man.ac.uk: Too many concurrent SMTP connections; please try again later ... Deferred: 421 mx1.cs.man.ac.uk: Too many concurrent SMTP connections; please try again later ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Thu, 26 Nov 2009 14:56:31 +0000 Size: 13500 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 26 09:58:09 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 26 Nov 2009 14:58:09 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911261458.nAQEw9sB011144@spike.ebi.ac.uk> The original message was received at Thu, 26 Nov 2009 14:56:06 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to mx0.cs.man.ac.uk.: <<< 421 mx0.cs.man.ac.uk: Too many concurrent SMTP connections; please try again later ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Thu, 26 Nov 2009 14:56:06 +0000 Size: 13147 URL: From noreply at rubyforge.org Thu Nov 26 10:04:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 10:04:24 -0500 (EST) Subject: [BioCatalogue-developers] [1324] trunk/app/views/layouts/_flashes.html.erb: Minor layout fix. Message-ID: <20091126150424.AA9F218582CA@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 10:29:41 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 10:29:41 -0500 (EST) Subject: [BioCatalogue-developers] [1325] trunk/lib/bio_catalogue/filtering.rb: Bugfix for service provider filter options - the new display name mechanism was not taking effect . Message-ID: <20091126152941.6939518582BC@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 10:31:04 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 10:31:04 -0500 (EST) Subject: [BioCatalogue-developers] [1326] trunk/app/helpers/activity_feeds_helper.rb: Reduced the max number of activity items to show, to reduce perf hit. Message-ID: <20091126153104.E056B18582C3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 10:36:48 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 10:36:48 -0500 (EST) Subject: [BioCatalogue-developers] [1327] branches/rest-services-support: minor ui tweaks Message-ID: <20091126153648.2012718582C3@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Thu Nov 26 10:51:26 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Thu, 26 Nov 2009 15:51:26 +0000 Subject: [BioCatalogue-developers] Fwd: WS-VLAM link References: <4B0E9EFA.2090702@uva.nl> Message-ID: Begin forwarded message: > From: Marco Roos > Date: 26 November 2009 15:30:02 GMT > To: Franck Tanoh > Subject: WS-VLAM link > > Hello Franck, > > Here is the link to WS-VLAM, the grid enabled workflow system from > Amsterdam: > http://staff.science.uva.nl/~gvlam/wsvlam/ > This page refers to myExperiment as well, so kind-of nice to link > back. > > Btw, if I understood Edgar correctly, then these cross-links can > raise the Google rank, so the more the better. Are you cross > referencing to/from the myGrid page as well? > > Cheers, > Marco. > > -- > Marco Roos (PhD) > BioSemantics group, Human Genetics department, Leiden University > Medical Centre > Albinusdreef 2 (Building 2, room R-04-003) > 2333 ZA Leiden > Tel. +31 (0) 71 526 9415 > Adaptive Information Disclosure group, Informatics Institute, > University of Amsterdam > Kruislaan 403 ( room N2.30) 1098 SJ Amsterdam > Tel. +31 (0) 20 525 7522 > Communities: > Professional: LinkedIn, myExperiment Personal: Hyves -------------- next part -------------- An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 11:29:11 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 11:29:11 -0500 (EST) Subject: [BioCatalogue-developers] [1328] trunk/app/views: Added 'description' annotations for Service Providers. Message-ID: <20091126162911.6602F16782B4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 11:34:58 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 11:34:58 -0500 (EST) Subject: [BioCatalogue-developers] [1329] trunk: Updates and fixes to the homepage: Message-ID: <20091126163458.172B116782B3@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 26 11:37:41 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 26 Nov 2009 16:37:41 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911261637.nAQGbfSr023671@spike.ebi.ac.uk> The original message was received at Thu, 26 Nov 2009 16:36:08 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Thu, 26 Nov 2009 16:36:08 +0000 Size: 13147 URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 26 11:38:03 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 26 Nov 2009 16:38:03 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911261638.nAQGc3Tr023720@spike.ebi.ac.uk> The original message was received at Thu, 26 Nov 2009 16:36:29 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Thu, 26 Nov 2009 16:36:29 +0000 Size: 13500 URL: From noreply at rubyforge.org Thu Nov 26 12:22:39 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 12:22:39 -0500 (EST) Subject: [BioCatalogue-developers] [1330] branches/rest-services-support: and example url is added base on the one supplied by the user on service submission Message-ID: <20091126172239.3BEFF16782B3@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Thu Nov 26 12:26:03 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Thu, 26 Nov 2009 17:26:03 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911261726.nAQGRkJE022740@spike.ebi.ac.uk> The original message was received at Thu, 26 Nov 2009 14:56:33 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] contact#create (ActionController::InvalidAuthenticityToken) "ActionController::InvalidAuthenticityToken" Date: Thu, 26 Nov 2009 14:56:33 +0000 Size: 13499 URL: From noreply at rubyforge.org Thu Nov 26 13:15:29 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 13:15:29 -0500 (EST) Subject: [BioCatalogue-developers] [1331] trunk: Revamped design of the homepage focusing on making it simpler and easier to understand . Message-ID: <20091126181529.AA61318582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 13:22:54 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 13:22:54 -0500 (EST) Subject: [BioCatalogue-developers] [1332] trunk/app/views/home/_info_boxes.html.erb: Minor layout fix Message-ID: <20091126182254.3452A18582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 13:27:37 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 13:27:37 -0500 (EST) Subject: [BioCatalogue-developers] [1333] trunk/public/stylesheets/styles.css: Increased min width of page Message-ID: <20091126182737.7476518582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 14:09:30 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 14:09:30 -0500 (EST) Subject: [BioCatalogue-developers] [1334] trunk: Layout fixes for minimum width, which would affect most screens that aren't high resolution. Message-ID: <20091126190930.52E1716782B3@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 14:11:19 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 14:11:19 -0500 (EST) Subject: [BioCatalogue-developers] [1335] trunk/public/stylesheets/styles.css: minor tweak Message-ID: <20091126191119.DF84B18582CE@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Thu Nov 26 14:13:23 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Thu, 26 Nov 2009 14:13:23 -0500 (EST) Subject: [BioCatalogue-developers] [1336] trunk/public/stylesheets/styles.css: Minor text style change Message-ID: <20091126191323.6126418582CE@rubyforge.org> An HTML attachment was scrubbed... URL: From ericnzuo at ebi.ac.uk Fri Nov 27 04:22:47 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Fri, 27 Nov 2009 09:22:47 +0000 Subject: [BioCatalogue-developers] link for the website In-Reply-To: References: Message-ID: <4B0F9A67.9060408@ebi.ac.uk> OK, this might sound like self promotion but hey, it is a very valuable page for bioinformaticians... http://www.ebi.ac.uk/Tools/webservices/ As other resources, though not exactly 'web services', we could add links as such if we are allowed to : http://www.wwpdb.org/ http://www.pdb.org/pdb/home/home.do http://sw-tools.pdb.org/ ... Eric Franck Tanoh wrote: > Hi Jits, > > the only link i have in mind for now is the soaplab one... > We could say something like: > Turn your command line application into Web Services: > http://soaplab.sourceforge.net/soaplab2/StepByStep.html > > Eric, and George please send Jits any interesting links you may have. > > Cheers, > Franck > > > From jits at cs.man.ac.uk Fri Nov 27 04:29:53 2009 From: jits at cs.man.ac.uk (Jiten Bhagat) Date: Fri, 27 Nov 2009 09:29:53 +0000 Subject: [BioCatalogue-developers] link for the website In-Reply-To: <4B0F9A67.9060408@ebi.ac.uk> References: <4B0F9A67.9060408@ebi.ac.uk> Message-ID: <4B0F9C11.8080708@cs.man.ac.uk> Great, thanks Eric. Franck - please could you compile these into a list so I can add these into the next release. Cheers, Jits Eric Nzuobontane wrote: > OK, this might sound like self promotion but hey, it is a very > valuable page for bioinformaticians... > http://www.ebi.ac.uk/Tools/webservices/ > > As other resources, though not exactly 'web services', we could add > links as such if we are allowed to : > http://www.wwpdb.org/ > http://www.pdb.org/pdb/home/home.do > http://sw-tools.pdb.org/ > ... > > Eric > > > > Franck Tanoh wrote: >> Hi Jits, >> >> the only link i have in mind for now is the soaplab one... >> We could say something like: >> Turn your command line application into Web Services: >> http://soaplab.sourceforge.net/soaplab2/StepByStep.html >> >> Eric, and George please send Jits any interesting links you may have. >> >> Cheers, >> Franck >> >> >> > > _______________________________________________ > BioCatalogue-developers mailing list > BioCatalogue-developers at rubyforge.org > http://rubyforge.org/mailman/listinfo/biocatalogue-developers From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 04:27:24 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 09:27:24 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911270927.nAR9ROEL031845@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:25:52 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:25:52 +0000 Size: 11039 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 04:28:05 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 09:28:05 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911270928.nAR9S5xP031897@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:26:31 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:26:31 +0000 Size: 11050 URL: From noreply at rubyforge.org Fri Nov 27 04:33:48 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 04:33:48 -0500 (EST) Subject: [BioCatalogue-developers] [1337] trunk/app/helpers/application_helper.rb: Minor textual change Message-ID: <20091127093348.8AC0A18582D4@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Nov 27 04:38:03 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 04:38:03 -0500 (EST) Subject: [BioCatalogue-developers] [1338] trunk/app/views/announcements/index.atom.builder: Fix for blank announcements feed Message-ID: <20091127093803.D10E918582DE@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 04:34:31 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 09:34:31 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911270934.nAR9YVfX032482@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:32:57 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:32:57 +0000 Size: 11037 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 04:35:13 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 09:35:13 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911270935.nAR9ZDEd032550@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:33:39 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:33:39 +0000 Size: 11039 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 05:12:58 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 10:12:58 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271012.nAR9Rkb6032010@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:25:25 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:25:25 +0000 Size: 10630 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 05:17:59 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 10:17:59 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271017.nAR9Rkb7032010@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:26:52 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:26:52 +0000 Size: 11042 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 05:23:01 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 10:23:01 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271023.nAR9Rkb8032010@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:26:57 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:26:57 +0000 Size: 11043 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 05:28:02 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 10:28:02 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271028.nAR9Rkb9032010@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:26:37 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:26:37 +0000 Size: 11043 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 05:33:04 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 10:33:04 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271033.nAR9RkbA032010@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:26:47 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:26:47 +0000 Size: 11044 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 05:38:05 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 10:38:05 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271038.nAR9RkbB032010@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:26:33 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:26:33 +0000 Size: 11050 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 06:18:32 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 11:18:32 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271118.nARARkZT005779@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:35:13 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:35:13 +0000 Size: 10745 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 06:23:33 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 11:23:33 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271123.nARARkZU005779@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:35:42 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:35:42 +0000 Size: 10753 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 06:28:34 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 11:28:34 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271128.nARARkZV005779@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 09:29:10 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] announcements#index (ActionView::TemplateError) "undefined method `updated_at' for nil:NilClass" Date: Fri, 27 Nov 2009 09:29:10 +0000 Size: 10957 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 06:41:36 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 11:41:36 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271141.nARBfaES012674@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 11:39:59 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: =?utf-8?Q?=5BProduction_ERROR=5D_annotations=23create=5Finline_=28ActiveRecord=3A=3AStatementInvalid=29_=22Mysql=3A=3AError=3A_Illegal_mix_of_collations_=28latin=31=5Fswedish=5Fci=2CIMPLICIT=29_and_=28utf=38=5Fgeneral=5Fci=2CCOERCIBLE=29_for_operation_=27=3D=27=3A_SELECT_=60annotations=60=2E=2A_FROM_=60annotations=60___INNER_JOIN_=60annotation=5Fattributes=60_ON_=60annotation=5Fattributes=60=2Eid_=3D_=60annotations=60=2Eattribute=5Fid__WHERE_=28=60annotations=60=2E=60annotatable=5Fid=60_=3D_=32=31=32=32_AND_=60annotations=60=2E=60value=60_=3D_=27The_services_should_only_be_used_for_non=2Dcommercial_purposes=2E_Please_see_COPASI_Non=2DCommercial_License_for_details=2E=5C=5Cn=5C=5Cn=2D=2D=5C=5Cn=5C=5CnCopasi_Non=E2=88=92Commercial_Purpose_License=5C=5Cn=5C=5Cn=5C=5CnCopyright_=C2=A9_=32=30=30=35_by_Pedro_Mendes=2C_Virginia_Tech_Intellectual=5C=5CnProperties=2C_Inc=2E_and_EML_Research=2C_gGmbH=2E=5C=5CnAll_rights_reserved=2E=5C=5Cn=5C=5CnVirginia_Tech_Intellectual_Prop! erties=2C 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cannot_be_terminated_by=5C=5Cn_______any_other_mechanism_or_for_any_other_reason_than_those_stated=5C=5Cn_______herein=2E=5C=5Cn=5C=5Cn___Use_of_Names=5C=5Cn_______Users_will_not_use_the_name_of_the_Virginia_Polytechnic=5C=5Cn_______Institute_and_State_University=2C_Virginia_Bioinformatics=5C=5Cn_______Institute=2C_Virginia_Tech_Intellectual_Properties=2C_Inc=2E=2C_EML=5C=5Cn_______Research=2C_and_COPASI_nor_any_adaptation_thereof_in_any=5C=5Cn_______publicity_or_advertising=2C_without_the_prior_written_consent=5C=5Cn_______from_VTIP_and_EML_Research=2C_gGmbH_in_each_case=2E=5C=5Cn=5C=5Cn=5C=5Cn=36=29_Export_License=5C=5Cn=5C=5Cn___Export_of_this_software_from_the_United_States_may_require_a=5C=5Cn___specific_license_from_the_United_States_Government=2E__It_is_the=5C=5Cn___responsibility_of_any_person_or_organization_contemplating_export=5C=5Cn___to_obtain_such_a_license_before_exporting=2E=5C=5Cn=5C=5Cn=5C=5Cn=37=29_END_OF_TERMS_AND_CONDITIONS=5C=5Cn=5C=5Cn___Address_all_co rrespondence_regarding_this_license_to_electronic_mail=5C=5Cn___address=3A__license=40copasi=2Eorg=27_AND_=60annotations=60=2E=60annotatable=5Ftype=60_=3D_=27SoapService=27_AND_=60annotation=5Fattributes=60=2E=60name=60_=3D_=27license=27=29_=22?= Date: Fri, 27 Nov 2009 11:39:58 +0000 Size: 60672 URL: From noreply at rubyforge.org Fri Nov 27 06:47:06 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 06:47:06 -0500 (EST) Subject: [BioCatalogue-developers] [1339] trunk/lib/bio_catalogue/annotations.rb: Updated list of "known" annotation attributes Message-ID: <20091127114707.008CA18582D3@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 06:47:09 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 11:47:09 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271147.nARBl9P3013216@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 11:45:31 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: =?utf-8?Q?=5BProduction_ERROR=5D_annotations=23create=5Finline_=28ActiveRecord=3A=3AStatementInvalid=29_=22Mysql=3A=3AError=3A_Illegal_mix_of_collations_=28latin=31=5Fswedish=5Fci=2CIMPLICIT=29_and_=28utf=38=5Fgeneral=5Fci=2CCOERCIBLE=29_for_operation_=27=3D=27=3A_SELECT_=60annotations=60=2E=2A_FROM_=60annotations=60___INNER_JOIN_=60annotation=5Fattributes=60_ON_=60annotation=5Fattributes=60=2Eid_=3D_=60annotations=60=2Eattribute=5Fid__WHERE_=28=60annotations=60=2E=60annotatable=5Fid=60_=3D_=32=31=32=32_AND_=60annotations=60=2E=60value=60_=3D_=27The_services_should_only_be_used_for_non=2Dcommercial_purposes=2E_Please_see_COPASI_Non=2DCommercial_License_for_details=2E=5C=5Cn=5C=5Cn=2D=2D=5C=5Cn=5C=5CnCOPASI_Non=E2=88=92Commercial_Purpose_License=5C=5Cn=5C=5Cn=5C=5CnCopyright_=C2=A9_=32=30=30=35_by_Pedro_Mendes=2C_Virginia_Tech_Intellectual=5C=5CnProperties=2C_Inc=2E_and_EML_Research=2C_gGmbH=2E=5C=5CnAll_rights_reserved=2E=5C=5Cn=5C=5CnVirginia_Tech_Intellectual_Prop! erties=2C _Inc_=28VTIP=29_and_EML_Research_=5C=5CngGmbH_=28EML=29_own_the_COPASI_software_and_its_associated_documentation_=5C=5Cn=28=5C=5C=5C=22Software=5C=5C=5C=22=29=2E__You_should_carefully_read_the_following_terms_and_=5C=5Cnconditions_before_using_this_software=2E__Your_use_of_this_Software_=5C=5Cnindicates_your_acceptance_of_this_license_agreement_and_all_terms_and_=5C=5Cnconditions=2E=5C=5Cn=5C=5CnThe_main_authors_of_COPASI_are_Pedro_Mendes=2C_Stefan_Hoops=2C_Sven_Sahle=2C_=5C=5CnRalph_Gauges=2C_and_Ursula_Kummer=2E_This_software_has_been_made_possible=5C=5Cnwith_the_dedicated_support_of_a_large_number_of_graduate_students_at=5C=5CnVBI_and_EML=2E=5C=5Cn=5C=5CnYou_are_hereby_granted_a_non=2Dexclusive_and_non=2Dtransferable_license_to=5C=5Cnuse_and_distribute_the_Software_in_both_source_and_binary_form=5C=5Cnaccording_to_the_following_terms_and_conditions=2E__This_license_is_to=5C=5Cnuse_the_Software_for_Non=E2=88=92Commercial_Purpose_only=2E__Non=E2=88=92Commercial=5C=5CnPurpos e_means_the_use_of_the_Software_solely_for_internal=5C=5Cnnon=2Dcommercial_research_and_academic_purposes=2E__Non=E2=88=92Commercial_Purpose=5C=5Cnexcludes=2C_without_limitation=2C_any_use_of_the_Software=2C_as_part_of=2C_or=5C=5Cnin_any_way_in_connection_with_a_product_or_service_which_is_sold=2C=5C=5Cnoffered_for_sale=2C_licensed=2C_leased=2C_loaned=2C_or_rented=2E__Permission_to=5C=5Cnuse=2C_copy=2C_modify=2C_and_distribute_this_compilation_for_Non=E2=88=92Commercial=5C=5CnPurpose_is_hereby_granted_without_fee=2C_subject_to_the_following_terms=5C=5Cnof_this_license=2E__Only_verbatim=2C_complete=2C_and_unmodified_versions_of=5C=5Cnthis_software_=28in_either_binary_or_source_code_form=29_are_permitted_to=5C=5Cnbe_redistributed_under_this_license=2E=5C=5Cn=5C=5Cn=5C=5Cn=31=29_Copies_and_Modifications=5C=5Cn=5C=5Cn___You_must_include_the_above_copyright_notice_and_this_license_on=5C=5Cn___any_copy_or_modification_of_this_compilation=2E__Each_time_you=5C=5Cn___redistribute_thi s_Software=2C_the_recipient_automatically_receives_a=5C=5Cn___license_to_copy=2C_distribute_or_modify_the_Software_subject_to=5C=5Cn___these_terms_and_conditions=2E__You_may_not_impose_any_further=5C=5Cn___restrictions_on_this_Software_or_any_derivative_works_beyond_those=5C=5Cn___restrictions_herein=2E=5C=5Cn=5C=5Cn___Any_inquiries_and_comments_regarding_bugs=2C_bug_fixes=2C_enhancements=2C=5C=5Cn___modifications_or_any_other_similar_issues_should_be_directed_to=3A=5C=5Cn___bugs=40copasi=2Eorg=2E=5C=5Cn=5C=5Cn=32=29_Commercial_Use=5C=5Cn=5C=5Cn___If_you_desire_to_use_the_software_for_profit=2Dmaking_or_commercial=5C=5Cn___purposes=2C_you_agree_to_negotiate_in_good_faith_a_license_with_VTIP=5C=5Cn___and_EML_prior_to_such_profit=2Dmaking_or_commercial_use=2E__VTIP_and=5C=5Cn___EML_shall_have_no_obligation_to_grant_such_license_to_you=2C_and_may=5C=5Cn___grant_exclusive_or_non=2Dexclusive_licenses_to_others=2E_You_agree_to=5C=5Cn___notify_VTIP_and_EML_of_any_inquiries_you_have _for_commercial_use=5C=5Cn___of_the_Software_and=2For_its_modifications=2E_You_may_contact_the=5C=5Cn___following_email_to_discuss_commercial_use=3A_license=40copasi=2Eorg=5C=5Cn=5C=5Cn=5C=5Cn=33=29_Governing_Law=5C=5Cn=5C=5Cn___This_agreement_shall_be_governed_by_the_laws_of_the_Commonwealth_of=5C=5Cn___Virginia=2E=5C=5Cn=5C=5Cn=5C=5Cn=34=29_Disclaimer_of_Warranty=5C=5Cn=5C=5Cn___Because_this_software_is_licensed_free_of_charge=2C_there_is_no=5C=5Cn___warranty_for_the_program=2E__VTIP_and_EML_make_no_warranty_or=5C=5Cn___representation_that_the_operation_of_the_software_in_this=5C=5Cn___compilation_will_be_error=2Dfree=2C_and_VTIP_and_EML_are_under_no=5C=5Cn___obligation_to_provide_any_services=2C_by_way_of_maintenance=2C_update=2C=5C=5Cn___or_otherwise=2E=5C=5Cn=5C=5Cn___THIS_SOFTWARE_AND_THE_ACCOMPANYING_FILES_ARE_LICENSED_=5C=5C=5C=22AS_IS=5C=5C=5C=22_AND=5C=5Cn___WITHOUT_WARRANTIES_AS_TO_PERFORMANCE_OR_MERCHANTABILITY_OR_ANY=5C=5Cn___OTHER_WARRANTIES_WHETHER_EXPRESSED_O R_IMPLIED=2E__NO_WARRANTY_OF=5C=5Cn___FITNESS_FOR_A_PARTICULAR_PURPOSE_IS_OFFERED=2E__THE_ENTIRE_RISK_AS=5C=5Cn___TO_THE_QUALITY_AND_PERFORMANCE_OF_THE_PROGRAM_IS_WITH_YOU=2E__SHOULD=5C=5Cn___THE_PROGRAM_PROVE_DEFECTIVE=2C_YOU_ASSUME_THE_COST_OF_ALL_NECESSARY=5C=5Cn___SERVICING=2C_REPAIR_OR_CORRECTION=2E=5C=5Cn=5C=5Cn=5C=5Cn=35=29_Limitation_of_Liability=5C=5Cn=5C=5Cn___IN_NO_EVENT_WILL_VTIP_AND_EML_RESEARCH=2C_OR_ANY_OTHER_PARTY_WHO_MAY=5C=5Cn___MODIFY_AND=2FOR_REDISTRIBUTE_THE_PROGRAM_AS_PERMITTED_ABOVE=2C_BE=5C=5Cn___LIABLE_TO_YOU_FOR_DAMAGES=2C_INCLUDING_ANY_GENERAL=2C_SPECIAL=2C=5C=5Cn___INCIDENTAL_OR_CONSEQUENTIAL_DAMAGES_ARISING_OUT_OF_THE_USE_OR=5C=5Cn___INABILITY_TO_USE_THE_PROGRAM_=28INCLUDING_BUT_NOT_LIMITED_TO_LOSS_OF=5C=5Cn___DATA_OR_DATA_BEING_RENDERED_INACCURATE_OR_LOSSES_SUSTAINED_BY_YOU=5C=5Cn___OR_THIRD_PARTIES_OR_A_FAILURE_OF_THE_PROGRAM_TO_OPERATE_WITH_ANY=5C=5Cn___OTHER_PROGRAMS=29=2C_EVEN_IF_VTIP_AND_EML_RESEARCH_OR_OTHER_PARTY_HAS=5C=5Cn___BEEN_ADVISED _OF_THE_POSSIBILITY_OF_SUCH_DAMAGES=2E=5C=5Cn=5C=5Cn___Termination=5C=5Cn_______This_agreement_is_effective_until_terminated=2E__You_may=5C=5Cn_______terminate_this_agreement_at_any_time_by_destroying_all_copies=5C=5Cn_______of_the_software_and_other_associated_materials_=28e=2Eg=2E=2C=5C=5Cn_______documentation=29_in_your_possession=2E__This_agreement_will=5C=5Cn_______terminate_immediately_without_notice_from_VTIP_and_EML=5C=5Cn_______Research_if_you_fail_to_comply_with_any_of_the_terms_and=5C=5Cn_______conditions_of_this_license=2E__Upon_termination=2C_you_must=5C=5Cn_______destroy_all_copies_of_the_software_and_other_associated=5C=5Cn_______materials=2E__This_agreement_will_also_terminate_immediately=5C=5Cn_______with_out_notice_from_VTIP_and_EML_if_it_is_found_to_implement=5C=5Cn_______patented_algorithms_or_contain_copyrighted_code_not_owned_or=5C=5Cn_______licensed_to_VTIP_and_EML_for_the_purpose_of_its_inclusion_in=5C=5Cn_______the_COPASI_software=2E__This_agreement_ cannot_be_terminated_by=5C=5Cn_______any_other_mechanism_or_for_any_other_reason_than_those_stated=5C=5Cn_______herein=2E=5C=5Cn=5C=5Cn___Use_of_Names=5C=5Cn_______Users_will_not_use_the_name_of_the_Virginia_Polytechnic=5C=5Cn_______Institute_and_State_University=2C_Virginia_Bioinformatics=5C=5Cn_______Institute=2C_Virginia_Tech_Intellectual_Properties=2C_Inc=2E=2C_EML=5C=5Cn_______Research=2C_and_COPASI_nor_any_adaptation_thereof_in_any=5C=5Cn_______publicity_or_advertising=2C_without_the_prior_written_consent=5C=5Cn_______from_VTIP_and_EML_Research=2C_gGmbH_in_each_case=2E=5C=5Cn=5C=5Cn=5C=5Cn=36=29_Export_License=5C=5Cn=5C=5Cn___Export_of_this_software_from_the_United_States_may_require_a=5C=5Cn___specific_license_from_the_United_States_Government=2E__It_is_the=5C=5Cn___responsibility_of_any_person_or_organization_contemplating_export=5C=5Cn___to_obtain_such_a_license_before_exporting=2E=5C=5Cn=5C=5Cn=5C=5Cn=37=29_END_OF_TERMS_AND_CONDITIONS=5C=5Cn=5C=5Cn___Address_all_co rrespondence_regarding_this_license_to_electronic_mail=5C=5Cn___address=3A__license=40copasi=2Eorg=27_AND_=60annotations=60=2E=60annotatable=5Ftype=60_=3D_=27SoapService=27_AND_=60annotation=5Fattributes=60=2E=60name=60_=3D_=27license=27=29_=22?= Date: Fri, 27 Nov 2009 11:45:31 +0000 Size: 60625 URL: From noreply at rubyforge.org Fri Nov 27 07:05:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 07:05:45 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2847] WSDL URL search doesn't work for some URLs Message-ID: <20091127120545.84E6518582C7@rubyforge.org> Task #2847 has been updated. Project: BioCatalogue Subproject: Main Summary: WSDL URL search doesn't work for some URLs Complete: 0% Status: Open Description: eg: http://www.comp-sys-bio.org/CopasiWS/services/ModelProcessorService?wsdl ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2847&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Fri Nov 27 07:27:24 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 07:27:24 -0500 (EST) Subject: [BioCatalogue-developers] [1340] trunk/db/migrate/20081102202410_add_activity_logs_table.rb: Removed explicit charset setting in activity logs migration. Message-ID: <20091127122724.333CA18582D4@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 07:58:47 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 12:58:47 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271258.nARCwlJA021000@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 12:57:13 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] services#index (ActionView::TemplateError) "undefined method `name' for nil:NilClass" Date: Fri, 27 Nov 2009 12:57:13 +0000 Size: 11622 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:02:36 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:02:36 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271402.nARE2abQ028180@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:01:00 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_input_url' for #" Date: Fri, 27 Nov 2009 14:01:00 +0000 Size: 15743 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:02:39 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:02:39 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271402.nARE2dOq028196@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:01:06 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (ActiveRecord::RecordInvalid) "Validation failed: This annotation already exists and is not allowed to be created again." Date: Fri, 27 Nov 2009 14:01:06 +0000 Size: 15541 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:07:52 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:07:52 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271407.nARE7q2V028749@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:06:18 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_input_url' for #" Date: Fri, 27 Nov 2009 14:06:18 +0000 Size: 15718 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:08:30 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:08:30 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271408.nARE8UOh028827@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:06:56 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (ActiveRecord::RecordInvalid) "Validation failed: This annotation already exists and is not allowed to be created again." Date: Fri, 27 Nov 2009 14:06:56 +0000 Size: 15557 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:13:02 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:13:02 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271413.nARED2hk029293@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:11:28 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_input_url' for #" Date: Fri, 27 Nov 2009 14:11:28 +0000 Size: 15588 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:22:01 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:22:01 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271422.nAREM1Ow030424@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:20:09 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_output_url' for #" Date: Fri, 27 Nov 2009 14:20:09 +0000 Size: 17481 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:27:04 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:27:04 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271427.nARER4Kv030877@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:25:30 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_input_url' for #" Date: Fri, 27 Nov 2009 14:25:30 +0000 Size: 15700 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:33:15 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:33:15 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271433.nAREXFj7031419@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:30:40 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_operation_url' for #" Date: Fri, 27 Nov 2009 14:30:39 +0000 Size: 15701 URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 09:37:14 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 14:37:14 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271437.nAREbEDc031910@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:35:40 GMT from pweb-3b.ebi.ac.uk [172.18.1.108] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_input_url' for #" Date: Fri, 27 Nov 2009 14:35:40 +0000 Size: 15696 URL: From noreply at rubyforge.org Fri Nov 27 09:44:38 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 09:44:38 -0500 (EST) Subject: [BioCatalogue-developers] [1341] trunk/app: Fixes for annotations: Message-ID: <20091127144438.5CA5418582AC@rubyforge.org> An HTML attachment was scrubbed... URL: From MAILER-DAEMON at ebi.ac.uk Fri Nov 27 10:48:06 2009 From: MAILER-DAEMON at ebi.ac.uk (Mail Delivery Subsystem) Date: Fri, 27 Nov 2009 15:48:06 GMT Subject: [BioCatalogue-developers] Returned mail: see transcript for details Message-ID: <200911271548.nARFRken004768@spike.ebi.ac.uk> The original message was received at Fri, 27 Nov 2009 14:35:46 GMT from pweb-4a.ebi.ac.uk [172.18.1.109] ----- The following addresses had permanent fatal errors ----- (reason: 550 5.7.1 : Sender address rejected: Mail server in loopback network) ----- Transcript of session follows ----- ... while talking to rubyforge.org.: >>> DATA <<< 550 5.7.1 : Sender address rejected: Mail server in loopback network 550 5.1.1 ... User unknown <<< 554 5.5.1 Error: no valid recipients -------------- next part -------------- An embedded message was scrubbed... From: BioCatalogue Errors Subject: [Production ERROR] annotations#create_inline (NoMethodError) "undefined method `soap_input_url' for #" Date: Fri, 27 Nov 2009 14:35:46 +0000 Size: 16275 URL: From noreply at rubyforge.org Fri Nov 27 11:01:41 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 11:01:41 -0500 (EST) Subject: [BioCatalogue-developers] [1342] trunk/config/initializers/biocat_main.rb: Allow tables in annotation values Message-ID: <20091127160141.16CE118582C7@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Fri Nov 27 11:52:45 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Fri, 27 Nov 2009 11:52:45 -0500 (EST) Subject: [BioCatalogue-developers] [1343] branches/test-scripts: test scripts integration work Message-ID: <20091127165245.EC40B1588061@rubyforge.org> An HTML attachment was scrubbed... URL: From noreply at rubyforge.org Sun Nov 29 12:20:19 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 29 Nov 2009 12:20:19 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2848] add "import file" button in search by data Message-ID: <20091129172019.9D724185830F@rubyforge.org> Task #2848 has been updated. Project: BioCatalogue Subproject: Main Summary: add "import file" button in search by data Complete: 0% Status: Open Description: note to check if the file is binary and change encoding to unicode if needed. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2848&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Sun Nov 29 12:24:14 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Sun, 29 Nov 2009 12:24:14 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2849] Make Biocatologue a scientific jurnal Message-ID: <20091129172414.4FF9D185830E@rubyforge.org> Task #2849 has been updated. Project: BioCatalogue Subproject: Main Summary: Make Biocatologue a scientific jurnal Complete: 0% Status: Open Description: With (if chosen by provider) - peer-reviewing of the services - pdf genation - DOI - affiliations, references citations etc. ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2849&group_id=6901&group_project_id=12540 From noreply at rubyforge.org Mon Nov 30 03:50:17 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 30 Nov 2009 03:50:17 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2850] Add disclaimer on /search/by_data Message-ID: <20091130085018.3BB4118582C1@rubyforge.org> Task #2850 has been updated. Project: BioCatalogue Subproject: Main Summary: Add disclaimer on /search/by_data Complete: 0% Status: Open Description: Something like: "Your searches might be logged and used for annotation of services in the future. Therefore do not use any secure or confidential data." ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2850&group_id=6901&group_project_id=12540 From ericnzuo at ebi.ac.uk Mon Nov 30 04:38:42 2009 From: ericnzuo at ebi.ac.uk (Eric Nzuobontane) Date: Mon, 30 Nov 2009 09:38:42 +0000 Subject: [BioCatalogue-developers] updated test scripts Message-ID: <4B1392A2.8030602@ebi.ac.uk> Hi Steve, I understand Mahmut already updated the soaplab test scripts in the EMBRACE registry. I would like run of those in my test environment but for that I need a dump of to the EMBRACE database. Would it be possible for you to provide me with a dump or arrange for someone to do so? cheers, Eric From noreply at rubyforge.org Mon Nov 30 04:56:08 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 30 Nov 2009 04:56:08 -0500 (EST) Subject: [BioCatalogue-developers] [Task #2851] Add search/by_data to stats Message-ID: <20091130095608.6FABB18582C3@rubyforge.org> Task #2851 has been updated. Project: BioCatalogue Subproject: Main Summary: Add search/by_data to stats Complete: 0% Status: Open Description: Show number of search_by data queries (preferably by month) ------------------------------------------------------- For more info, visit: http://rubyforge.org/pm/task.php?func=detailtask&project_task_id=2851&group_id=6901&group_project_id=12540 From jerzyo at genesilico.pl Mon Nov 30 10:04:49 2009 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Mon, 30 Nov 2009 15:04:49 +0000 Subject: [BioCatalogue-developers] SoapServlet logs from Annotation Jumboree Message-ID: <4B13DF11.5090902@genesilico.pl> We got more than 100 examples collected (attached) -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: all.txt URL: From noreply at rubyforge.org Mon Nov 30 11:37:41 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 30 Nov 2009 11:37:41 -0500 (EST) Subject: [BioCatalogue-developers] [1344] trunk: Bugfixes for the metadata counts, and a bugfix for displaying the computational type of input/output ports. Message-ID: <20091130163741.C4BD6185828D@rubyforge.org> An HTML attachment was scrubbed... URL: From ytanoh at cs.man.ac.uk Mon Nov 30 11:42:24 2009 From: ytanoh at cs.man.ac.uk (Franck Tanoh) Date: Mon, 30 Nov 2009 16:42:24 +0000 Subject: [BioCatalogue-developers] Fwd: BioCatalogue: Usage Conditions In-Reply-To: References: Message-ID: some ideas from Pieter.... ---------- Forwarded message ---------- From: Pieter Neerincx Date: 2009/11/30 Subject: BioCatalogue: Usage Conditions To: Franck Tanoh Hi Franck, It's been a great pleasure to visit the BioCatalogue Annotation Jamboree! While I was traveling back I thought a bit more about usage conditions. With regard to throttling to prevent overloading servers it would be great if that part of the "usage conditions" could be fetched automatically from the BioCatalogue when you add a service to a workflow in Taverna. By automatically inserting limits users can spend more time on the interesting parts of designing a workflow and don't have to worry about accidentally overloading a service and getting their University blacklisted. The latter can happen quite easily and I still remember the day Wageningen University got completely disconnected from the NCBI, because one of my former colleagues enthusiastically scripted PubMed record retrieval from the NCBI site for a text mining pilot... Services can have many different usage conditions, which probably explains the current "free text" field, but after thinking about this for a while I think the limits on the load you are allowed to generate can be captured in two generic fields: ?1. The amount of jobs you can submit per unit of time. ?2. The amount of jobs you can process in parallel. For many services the first parameter will be enough, but if the time it takes to process a job is a lot longer than the time between submitting jobs based on the first parameter, the second parameter may be useful. Simple example: ?1. Max 2 jobs per minute with an average job processing time of 30 seconds. ?2. Not necessary to specify param 2 as the amount of simultaneously running jobs will be around 2. Especially for asynchronous services the second parameter my be useful as submitting a job will be fast, but processing it may take a lot longer. For example: ?1. Max 20 jobs per minute with an average job processing time of 30 minutes. ?2. Max 100 jobs "processed" in parallel. (processed here = submitted to web service and apart from a job ID or ticket number we have not gotten any results back.) In this case the first param prevents us from getting a denial of service attack on the web server hosting the service, which may happen if 100 jobs would be submitted in a split second. Maybe on the serverside the jobs are dispatched to a small grid using the Sun Grid Engine or PBS or a similar queueing mechanism and only 10 jobs are really running at the same time. Other jobs will have to wait in a queue. The second parameter will now prevent a client from overloading the queue. It will probably require quite some extra work to add this functionality to Taverna, but adding two fields to the BioCatalogue and adding API support to the Biocatalogue so workflow management systems can automatically retrieve this kind of info from the BioCatalogue in the near future should be straight forward... Cheers, Pi ------------------------------------------------------------- Biomolecular Mass Spectrometry and Proteomics Group Faculty of Science Utrecht University Visiting address: H.R. Kruyt building room O607 Padualaan 8 3584 CH Utrecht The Netherlands Mail address: P.O. box 80.082 3508 TB Utrecht The Netherlands phone: +31 (0)6-143 66 783 email: pieter.neerincx at gmail.com skype: pieter.online ------------------------------------------------------------- -- "Science knows no country, because knowledge belongs to humanity, and is the torch which illuminates the world." - Louis Pasteur From noreply at rubyforge.org Mon Nov 30 11:52:31 2009 From: noreply at rubyforge.org (noreply at rubyforge.org) Date: Mon, 30 Nov 2009 11:52:31 -0500 (EST) Subject: [BioCatalogue-developers] [1345] trunk/app/helpers/activity_feeds_helper.rb: Bugfix for activity feed where someone has added a category annotation and the category ID was being shown instead of the category name . Message-ID: <20091130165231.18C02159807F@rubyforge.org> An HTML attachment was scrubbed... URL: From philip.mcdermott at manchester.ac.uk Mon Nov 30 05:09:50 2009 From: philip.mcdermott at manchester.ac.uk (Philip McDermott) Date: Mon, 30 Nov 2009 10:09:50 +0000 Subject: [BioCatalogue-developers] updated test scripts In-Reply-To: <4B1392A2.8030602@ebi.ac.uk> References: <4B1392A2.8030602@ebi.ac.uk> Message-ID: <31C14402-0E21-40E0-B12C-04B17C814743@manchester.ac.uk> Hi Eric, Sorry your last request got lost in a sea of email in a rather busy period we're going through. I've just uploaded the latest dump as a tarball to drropbox. File sizes indicate that there are possibly no new services since the last dump (1st Nov.). Cheers Phil On 30 Nov 2009, at 09:38, Eric Nzuobontane wrote: > Hi Steve, > > I understand Mahmut already updated the soaplab test scripts in the > EMBRACE registry. I would like run of those in my test environment > but for that I need a dump of to the EMBRACE database. Would it be > possible for you to provide me with a dump or arrange for someone to > do so? > > cheers, > > Eric > > From jerzyo at genesilico.pl Mon Nov 30 15:00:50 2009 From: jerzyo at genesilico.pl (Jerzy Orlowski) Date: Mon, 30 Nov 2009 21:00:50 +0100 Subject: [BioCatalogue-developers] Biocatalogue help Message-ID: <20091130210050.14702njcnsls1lrm@horde.genesilico.pl> Jits Here is the plan of bicatalogue help pages: 1. Getting Started - main help page 2. Using Biocatalogue a) How can you search for web services, what fields can you search for, how can one make complicated queries. How does sysnonyms search work? a') How can I use search by data? What input should I use? How does it work? I found no correct results - what is the reason? b) What does it mean to register a web service? Who can register a service - Can I register a service someone alse has made? How to register a service - step by step tutorial. c) What does it mean to annotate a service? How to annotate web services? Who can annotate? Can I annotate a service of someone else? Why should I annptate services? Which annotations are the most important? Examples of well annotated servicves d) What does it mean to monitor a service? How services are monitored by biocatalogue. 3. General info on web services. a) What is this? What are different types of services? Why are they useful? b) I have a piece of code - how can I make it a web service - different solutions in different languages c) I found a nice service - how can I execute it? - Web, GUI and client code in different languages Jurek