galaxy-commits April 2014

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261 discussions

commit/galaxy-central: davebgx: Merge fix from stable.
by commits-noreply＠bitbucket.org 19 Apr '14

19 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e2dd42ca0708/ Changeset: e2dd42ca0708 User: davebgx Date: 2014-04-18 20:58:04 Summary: Merge fix from stable. Affected #: 3 files diff -r 1d5f72128929f5ee2f982dd26ff94f7cc4f33610 -r e2dd42ca0708315efffd55479e68a81954b9c931 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1713,9 +1713,11 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) - # We aren't concerned with repository's of type tool_dependency_definition here if a repository_metadata record is not returned - # because repositories of this type will never have repository dependencies. - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + # We aren't concerned with repositories of type tool_dependency_definition here if a repository_metadata record is not returned + # because repositories of this type will never have repository dependencies. However, if a readme file is uploaded, or some other + # change is made that does not create a new downloadable changeset revision but updates the existing one, we still want to be able + # to get repository dependencies. + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans, repository, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: Charts: Update nvd3
by commits-noreply＠bitbucket.org 19 Apr '14

19 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d5f72128929/ Changeset: 1d5f72128929 User: guerler Date: 2014-04-18 20:53:48 Summary: Charts: Update nvd3 Affected #: 1 file This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: davebgx: If a tool shed repository was updated after a tool migration without a new installable changeset revision being generated, for example by adding or removing a readme file, the migration install framework would be unable to find repository dependencies. This changeset resolves that.
by commits-noreply＠bitbucket.org 19 Apr '14

19 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e6876f691854/ Changeset: e6876f691854 Branch: stable User: davebgx Date: 2014-04-18 19:58:51 Summary: If a tool shed repository was updated after a tool migration without a new installable changeset revision being generated, for example by adding or removing a readme file, the migration install framework would be unable to find repository dependencies. This changeset resolves that. Affected #: 1 file diff -r 5fd196b5d1760d1a8180184f8e5450e0957b37c2 -r e6876f6918548a0805fa0cc5306ba1ced6fb184a lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1700,9 +1700,11 @@ changeset_revision = kwd.get( 'changeset_revision', None ) repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_id = trans.security.encode_id( repository.id ) - # We aren't concerned with repository's of type tool_dependency_definition here if a repository_metadata record is not returned - # because repositories of this type will never have repository dependencies. - repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + # We aren't concerned with repositories of type tool_dependency_definition here if a repository_metadata record is not returned + # because repositories of this type will never have repository dependencies. However, if a readme file is uploaded, or some other + # change is made that does not create a new downloadable changeset revision but updates the existing one, we still want to be able + # to get repository dependencies. + repository_metadata = suc.get_current_repository_metadata_for_changeset_revision( trans, repository, changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: QA, metrics logger: test metrics post
by commits-noreply＠bitbucket.org 19 Apr '14

19 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f5bfac95df59/ Changeset: f5bfac95df59 User: carlfeberhard Date: 2014-04-18 20:42:26 Summary: QA, metrics logger: test metrics post Affected #: 1 file diff -r 4603eccf8a589d5f0b77e1484cf42c1420c75c57 -r f5bfac95df59c8dd436deae60d6bb9fc7593f4da test/qunit/tests/metrics-logger.js --- a/test/qunit/tests/metrics-logger.js +++ b/test/qunit/tests/metrics-logger.js @@ -23,7 +23,6 @@ }; module( "Metrics logger tests" ); - // ======================================================================== MetricsLogger test( "logger construction/initializiation defaults", function() { var logger = new metrics.MetricsLogger({}); @@ -95,7 +94,84 @@ logger.emit( 'metric', 'test', [{ window: window }] ); equal( logger.cache.length(), 0 ); }); - + + function metricsFromRequestBody( request ){ + // assumes 'metrics' is only entry in requestBody + return JSON.parse( decodeURIComponent( request.requestBody.replace( 'metrics=', '' ) ) ); + } + + test( "_postCache success", function () { + var callback = sinon.spy(), + logger = new metrics.MetricsLogger({ + logLevel : 'metric', + onServerResponse : function( response ){ callback(); } + }); + + var server = sinon.fakeServer.create(), + metricsOnServer; + server.respondWith( 'POST', '/api/metrics', function( request ){ + metricsOnServer = metricsFromRequestBody( request ); + request.respond( + 200, + { "Content-Type": "application/json" }, + JSON.stringify({ + fakeResponse: 'yes' + }) + ); + }); + + logger.emit( 'metric', 'test', [ 1, 2, { three: 3 }] ); + logger._postCache(); + server.respond(); + ok( callback.calledOnce, 'onServerResponse was called' ); + equal( logger.cache.length(), 0, 'should have emptied cache (on success)' ); + equal( logger._postSize, 1000, '_postSize still at default' ); + + // metrics were in proper form on server + equal( metricsOnServer.length, 1 ); + var metric = metricsOnServer[0]; + equal( metric.level, metrics.MetricsLogger.METRIC ); + equal( metric.namespace, 'client.test' ); + equal( metric.args.length, 3 ); + equal( metric.args[2].three, 3 ); + ok( typeof metric.time === 'string' ); + ok( metric.time === new Date( metric.time ).toISOString() ); + + server.restore(); + }); + + test( "_postCache failure", function () { + var callback = sinon.spy(), + logger = new metrics.MetricsLogger({ + logLevel : 'metric', + onServerResponse : function( response ){ callback(); } + }); + + var server = sinon.fakeServer.create(); + server.respondWith( 'POST', '/api/metrics', function( request ){ + request.respond( + 500, + { "Content-Type": "application/json" }, + JSON.stringify({ + err_msg: 'NoooOPE!' + }) + ); + }); + + logger.emit( 'metric', 'test', [ 1, 2, { three: 3 }] ); + logger._postCache(); + server.respond(); + //TODO: is the following what we want? + ok( !callback.calledOnce, 'onServerResponse was NOT called' ); + equal( logger.cache.length(), 1, 'should NOT have emptied cache' ); + equal( logger._postSize, logger.options.maxCacheSize, '_postSize changed to max' ); + + //TODO: still doesn't solve the problem that when cache == max, post will be tried on every emit + + server.restore(); + }); + + // ======================================================================== LoggingCache test( "cache construction/initializiation defaults", function() { var cache = new metrics.LoggingCache(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update NGS read simulator to use job working directory.
by commits-noreply＠bitbucket.org 18 Apr '14

18 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4603eccf8a58/ Changeset: 4603eccf8a58 User: dan Date: 2014-04-18 19:31:13 Summary: Update NGS read simulator to use job working directory. Affected #: 1 file diff -r 2edb06612c92b7e259e710f63b5cd15d4805c490 -r 4603eccf8a589d5f0b77e1484cf42c1420c75c57 tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -7,7 +7,7 @@ --input="${in_type.genome.fields.path}" --genome=$in_type.genome #else - --input=$in_type.input1 + --input="${ in_type.input1 }" #end if --read_len=$read_len --avg_coverage=$avg_coverage @@ -15,10 +15,10 @@ --num_sims=$num_sims --polymorphism=$polymorphism --detection_thresh=$detection_thresh - --output_png=$output_png + --output_png="${ output_png }" --summary_out=$summary_out - --output_summary=$output_summary - --new_file_path=$__new_file_path__ + --output_summary="${ output_summary }" + --new_file_path="." </command><!-- If want to include all simulation results file sim_results=$sim_results Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update MAF to BED to use job working directory and built-in primary dataset collection.
by commits-noreply＠bitbucket.org 18 Apr '14

18 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2edb06612c92/ Changeset: 2edb06612c92 User: dan Date: 2014-04-18 19:23:38 Summary: Update MAF to BED to use job working directory and built-in primary dataset collection. Affected #: 3 files diff -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 -r 2edb06612c92b7e259e710f63b5cd15d4805c490 tools/maf/maf_to_bed.py --- a/tools/maf/maf_to_bed.py +++ b/tools/maf/maf_to_bed.py @@ -19,6 +19,7 @@ species = sys.argv[3].split(',') partial = sys.argv[4] + output_id = sys.argv[6] out_files = {} primary_spec = None @@ -47,10 +48,7 @@ out_files[spec] = open( output_filename, 'w' ) primary_spec = spec else: - out_files[spec] = tempfile.NamedTemporaryFile( mode = 'w', dir = database_tmp_dir, suffix = '.maf_to_bed' ) - filename = out_files[spec].name - out_files[spec].close() - out_files[spec] = open( filename, 'w' ) + out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_bed_%s' % ( output_id, spec, spec ) ), 'wb+' ) num_species = len( species ) print "Restricted to species:", ",".join( species ) @@ -71,10 +69,7 @@ if not spec or not chrom: spec = chrom = c.src if spec not in out_files.keys(): - out_files[spec] = tempfile.NamedTemporaryFile( mode='w', dir = database_tmp_dir, suffix = '.maf_to_bed' ) - filename = out_files[spec].name - out_files[spec].close() - out_files[spec] = open( filename, 'w' ) + out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_bed_%s' % ( output_id, spec, spec ) ), 'wb+' ) if c.strand == "-": out_files[spec].write( chrom + "\t" + str( c.src_size - c.end ) + "\t" + str( c.src_size - c.start ) + "\t" + spec + "_" + str( block_num ) + "\t" + "0\t" + c.strand + "\n" ) @@ -85,10 +80,6 @@ for file_out in out_files.keys(): out_files[file_out].close() - for spec in out_files.keys(): - if spec != primary_spec: - print "#FILE\t" + spec + "\t" + os.path.join( database_tmp_dir, os.path.split( out_files[spec].name )[1] ) - else: - print "#FILE1\t" + spec + "\t" + out_files[spec].name + print "#FILE1_DBKEY\t%s" % ( primary_spec ) if __name__ == "__main__": __main__() diff -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 -r 2edb06612c92b7e259e710f63b5cd15d4805c490 tools/maf/maf_to_bed.xml --- a/tools/maf/maf_to_bed.xml +++ b/tools/maf/maf_to_bed.xml @@ -1,6 +1,6 @@ -<tool id="MAF_To_BED1" name="Maf to BED" force_history_refresh="True"> +<tool id="MAF_To_BED1" name="MAF to BED" force_history_refresh="True"><description>Converts a MAF formatted file to the BED format</description> - <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks $__new_file_path__</command> + <command interpreter="python">maf_to_bed.py "${ input1 }" "${ out_file1 }" "${ species }" "${ complete_blocks }" "." "${ out_file1.id }"</command><inputs><param format="maf" name="input1" type="data" label="MAF file to convert"/><param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species"> diff -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 -r 2edb06612c92b7e259e710f63b5cd15d4805c490 tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py +++ b/tools/maf/maf_to_bed_code.py @@ -6,56 +6,20 @@ def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): output_data = out_data.items()[0][1] - history = output_data.history - if history == None: - print "unknown history!" - return new_stdout = "" split_stdout = stdout.split("\n") - basic_name = output_data.name - output_data_list = [] for line in split_stdout: if line.startswith("#FILE1"): fields = line.split("\t") dbkey = fields[1] - filepath = fields[2] output_data.dbkey = dbkey - output_data.name = basic_name + " (" + dbkey + ")" + output_data.name = "%s (%s)" % ( output_data.name, dbkey ) app.model.context.add( output_data ) app.model.context.flush() - output_data_list.append(output_data) - elif line.startswith("#FILE"): - fields = line.split("\t") - dbkey = fields[1] - filepath = fields[2] - newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) - newdata.set_size() - newdata.extension = "bed" - newdata.name = basic_name + " (" + dbkey + ")" - app.model.context.add( newdata ) - app.model.context.flush() - history.add_dataset( newdata ) - app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset ) - app.model.context.add( history ) - app.model.context.flush() - try: - app.object_store.update_from_file( newdata.dataset, file_name=filepath, create=True ) - os.unlink( filepath ) - newdata.info = newdata.name - newdata.state = newdata.states.OK - except: - newdata.info = "The requested file is missing from the system." - newdata.state = newdata.states.ERROR - newdata.dbkey = dbkey - newdata.init_meta() - newdata.set_meta() - newdata.set_peek() - app.model.context.flush() - output_data_list.append(newdata) else: - new_stdout = new_stdout + line - for data in output_data_list: - if data.state == data.states.OK: - data.info = new_stdout - app.model.context.add( data ) - app.model.context.flush() + new_stdout = "%s\n%s" % ( new_stdout, line ) + for data in output_data.creating_job.output_datasets: + data = data.dataset + data.info = new_stdout + app.model.context.add( data ) + app.model.context.flush() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: QA: more testing of metrics logger
by commits-noreply＠bitbucket.org 18 Apr '14

18 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc34e6a879f7/ Changeset: bc34e6a879f7 User: carlfeberhard Date: 2014-04-18 18:58:20 Summary: QA: more testing of metrics logger Affected #: 4 files diff -r 47285f0d20f4cbcb150a894f343fd8cbf1bed4a7 -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 static/scripts/packed/galaxy-app-base.js --- a/static/scripts/packed/galaxy-app-base.js +++ b/static/scripts/packed/galaxy-app-base.js @@ -1,1 +1,1 @@ -define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization","bootstrapped-data"],function(b,d,g,e,a){function h(n){var m=this;return m._init(n||{})}g(h,"GalaxyApp");h.prototype.defaultOptions={patchExisting:true,root:"/"};h.prototype._init=function k(n){var m=this;_.extend(m,Backbone.Events);m._processOptions(n);m.debug("GalaxyApp.options: ",m.options);m._patchGalaxy(window.Galaxy);m.debug("GalaxyApp.options: ",m.options);m._initLogger(n.loggerOptions||{});m.debug("GalaxyApp.logger: ",m.logger);m._initLocale();m.debug("GalaxyApp.localize: ",m.localize);m.config=n.config||a.config||{};m.debug("GalaxyApp.config: ",m.config);m._initUser(n.user||a.user||{});m.debug("GalaxyApp.user: ",m.user);m.trigger("ready",m);return m};h.prototype._processOptions=function f(o){var n=this,p=n.defaultOptions;n.debug("_processOptions: ",o);n.options={};for(var m in p){if(p.hasOwnProperty(m)){n.options[m]=(o.hasOwnProperty(m))?(o[m]):(p[m])}}return n};h.prototype._patchGalaxy=function f(m){var o=this;if(o.options.patchExisting&&m){o.debug("found existing Galaxy object:",m);for(var n in m){if(m.hasOwnProperty(n)){o.debug("\t patching in "+n+" to Galaxy");o[n]=m[n]}}}};h.prototype._initLogger=function l(n){var m=this;m.debug("_initLogger:",n);m.logger=new d.MetricsLogger(n);return m};h.prototype._initLocale=function j(n){var m=this;m.debug("_initLocale:",n);m.localize=e;window._l=m.localize;return m};h.prototype._initUser=function i(n){var m=this;m.debug("_initUser:",n);m.user=new b.User(n);m.currUser=m.user;return m};h.prototype.toString=function c(){var m=this.user.get("email")||"(anonymous)";return"GalaxyApp("+m+")"};return{GalaxyApp:h}}); \ No newline at end of file +define(["mvc/user/user-model","utils/metrics-logger","utils/add-logging","utils/localization","bootstrapped-data"],function(b,d,g,e,a){function h(n){var m=this;return m._init(n||{})}g(h,"GalaxyApp");h.prototype.defaultOptions={patchExisting:true,root:"/"};h.prototype._init=function k(n){var m=this;_.extend(m,Backbone.Events);m._processOptions(n);m.debug("GalaxyApp.options: ",m.options);m._patchGalaxy(window.Galaxy);m._initLogger(n.loggerOptions||{});m.debug("GalaxyApp.logger: ",m.logger);m._initLocale();m.debug("GalaxyApp.localize: ",m.localize);m.config=n.config||a.config||{};m.debug("GalaxyApp.config: ",m.config);m._initUser(n.user||a.user||{});m.debug("GalaxyApp.user: ",m.user);m.trigger("ready",m);return m};h.prototype._processOptions=function f(o){var n=this,p=n.defaultOptions;n.debug("_processOptions: ",o);n.options={};for(var m in p){if(p.hasOwnProperty(m)){n.options[m]=(o.hasOwnProperty(m))?(o[m]):(p[m])}}return n};h.prototype._patchGalaxy=function f(m){var o=this;if(o.options.patchExisting&&m){o.debug("found existing Galaxy object:",m);for(var n in m){if(m.hasOwnProperty(n)){o.debug("\t patching in "+n+" to Galaxy");o[n]=m[n]}}}};h.prototype._initLogger=function l(n){var m=this;m.debug("_initLogger:",n);m.logger=new d.MetricsLogger(n);return m};h.prototype._initLocale=function j(n){var m=this;m.debug("_initLocale:",n);m.localize=e;window._l=m.localize;return m};h.prototype._initUser=function i(n){var m=this;m.debug("_initUser:",n);m.user=new b.User(n);m.currUser=m.user;return m};h.prototype.toString=function c(){var m=this.user.get("email")||"(anonymous)";return"GalaxyApp("+m+")"};return{GalaxyApp:h}}); \ No newline at end of file diff -r 47285f0d20f4cbcb150a894f343fd8cbf1bed4a7 -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 static/scripts/packed/utils/metrics-logger.js --- a/static/scripts/packed/utils/metrics-logger.js +++ b/static/scripts/packed/utils/metrics-logger.js @@ -1,1 +1,1 @@ -define([],function(){function h(z){z=z||{};var y=this;y.consoleLogger=z.consoleLogger||null;y._init(z);return y}h.ALL=0;h.DEBUG=10;h.INFO=20;h.WARN=30;h.ERROR=40;h.METRIC=50;h.NONE=100;h.defaultOptions={logLevel:h.NONE,consoleLevel:h.NONE,defaultNamespace:"Galaxy",clientPrefix:"client.",maxCacheSize:3000,postSize:1000,addTime:true,postUrl:"/api/metrics",getPingData:undefined,onServerResponse:undefined};h.prototype._init=function i(A){var z=this;z.options={};for(var y in h.defaultOptions){if(h.defaultOptions.hasOwnProperty(y)){z.options[y]=(A.hasOwnProperty(y))?(A[y]):(h.defaultOptions[y])}}z.options.logLevel=z._parseLevel(z.options.logLevel);z.options.consoleLevel=z._parseLevel(z.options.consoleLevel);z._sending=false;z._postSize=z.options.postSize;z._initCache();return z};h.prototype._initCache=function a(){this.cache=new w({maxSize:this.options.maxCacheSize})};h.prototype._parseLevel=function j(A){var z=typeof A;if(z==="number"){return A}if(z==="string"){var y=A.toUpperCase();if(h.hasOwnProperty(y)){return h[y]}}throw new Error("Unknown log level: "+A)};h.prototype.emit=function m(B,A,z){var y=this;A=A||y.options.defaultNamespace;if(!B||!z){return y}B=y._parseLevel(B);if(B>=y.options.logLevel){y._addToCache(B,A,z)}if(y.consoleLogger&&B>=y.options.consoleLevel){y._emitToConsole(B,A,z)}return y};h.prototype._addToCache=function b(D,A,z){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var y=this;try{var C=y.cache.add(y._buildEntry(D,A,z));if(C>=y._postSize){y._postCache()}}catch(B){if(y.options.consoleLevel<=h.WARN){console.warn("Metrics logger could not stringify logArguments:",A,z);console.error(B)}}return y};h.prototype._buildEntry=function r(B,z,y){this._emitToConsole("debug","MetricsLogger",["_buildEntry:",arguments]);var A={level:B,namespace:this.options.clientPrefix+z,args:y};if(this.options.addTime){A.time=new Date().toISOString()}return A};h.prototype._postCache=function s(B){B=B||{};this._emitToConsole("info","MetricsLogger",["_postCache",B,this._postSize]);if(!this.options.postUrl||this._sending){return jQuery.when({})}var A=this,D=B.count||A._postSize,y=A.cache.get(D),C=y.length,z=(typeof A.options.getPingData==="function")?(A.options.getPingData()):({});z.metrics=A._preprocessCache(y);A._sending=true;return jQuery.post(A.options.postUrl,z).always(function(){A._sending=false}).fail(function(){A._postSize=A.options.maxCacheSize}).done(function(E){if(typeof A.options.onServerResponse==="function"){A.options.onServerResponse(E)}A.cache.remove(C);console.debug("removed entries:",C,"size now:",A.cache.length());A._postSize=A.options.postSize})};h.prototype._preprocessCache=function f(y){return["[",(y.join(",\n")),"]"].join("\n")};h.prototype._emitToConsole=function c(C,B,A){var y=this;if(!y.consoleLogger){return y}var z=Array.prototype.slice.call(A,0);z.unshift(B);if(C>=h.METRIC&&typeof(y.consoleLogger.info)==="function"){return y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.ERROR&&typeof(y.consoleLogger.error)==="function"){return y.consoleLogger.error.apply(y.consoleLogger,z)}else{if(C>=h.WARN&&typeof(y.consoleLogger.warn)==="function"){y.consoleLogger.warn.apply(y.consoleLogger,z)}else{if(C>=h.INFO&&typeof(y.consoleLogger.info)==="function"){y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.DEBUG&&typeof(y.consoleLogger.debug)==="function"){y.consoleLogger.debug.apply(y.consoleLogger,z)}else{if(typeof(y.consoleLogger.log)==="function"){y.consoleLogger.log.apply(y.consoleLogger,z)}}}}}}return y};h.prototype.debug=function l(){this.emit(h.DEBUG,this.options.defaultNamespace,arguments)};h.prototype.log=function g(){this.emit(1,this.options.defaultNamespace,arguments)};h.prototype.info=function u(){this.emit(h.INFO,this.options.defaultNamespace,arguments)};h.prototype.warn=function t(){this.emit(h.WARN,this.options.defaultNamespace,arguments)};h.prototype.error=function p(){this.emit(h.ERROR,this.options.defaultNamespace,arguments)};h.prototype.metric=function n(){this.emit(h.METRIC,this.options.defaultNamespace,arguments)};function w(z){var y=this;y._cache=[];return y._init(z||{})}w.defaultOptions={maxSize:5000};w.prototype._init=function i(y){this.maxSize=y.maxSize||w.defaultOptions.maxSize;return this};w.prototype.add=function k(A){var z=this,y=(z.length()+1)-z.maxSize;if(y>0){z.remove(y)}z._cache.push(z._preprocessEntry(A));return z.length()};w.prototype._preprocessEntry=function q(y){return JSON.stringify(y)};w.prototype.length=function e(){return this._cache.length};w.prototype.get=function v(y){return this._cache.slice(0,y)};w.prototype.remove=function x(y){return this._cache.splice(0,y)};w.prototype.stringify=function o(y){return["[",(this.get(y).join(",\n")),"]"].join("\n")};w.prototype.print=function d(){this._cache.forEach(function(y){console.log(y)})};return{MetricsLogger:h,LoggingCache:w}}); \ No newline at end of file +define([],function(){function h(z){z=z||{};var y=this;y.consoleLogger=z.consoleLogger||null;y._init(z);return y}h.ALL=0;h.DEBUG=10;h.INFO=20;h.WARN=30;h.ERROR=40;h.METRIC=50;h.NONE=100;h.defaultOptions={logLevel:h.NONE,consoleLevel:h.NONE,defaultNamespace:"Galaxy",clientPrefix:"client.",maxCacheSize:3000,postSize:1000,addTime:true,postUrl:"/api/metrics",getPingData:undefined,onServerResponse:undefined};h.prototype._init=function i(A){var z=this;z.options={};for(var y in h.defaultOptions){if(h.defaultOptions.hasOwnProperty(y)){z.options[y]=(A.hasOwnProperty(y))?(A[y]):(h.defaultOptions[y])}}z.options.logLevel=z._parseLevel(z.options.logLevel);z.options.consoleLevel=z._parseLevel(z.options.consoleLevel);z._sending=false;z._postSize=z.options.postSize;z._initCache();return z};h.prototype._initCache=function a(){this.cache=new w({maxSize:this.options.maxCacheSize})};h.prototype._parseLevel=function j(A){var z=typeof A;if(z==="number"){return A}if(z==="string"){var y=A.toUpperCase();if(h.hasOwnProperty(y)){return h[y]}}throw new Error("Unknown log level: "+A)};h.prototype.emit=function m(B,A,z){var y=this;A=A||y.options.defaultNamespace;if(!B||!z){return y}B=y._parseLevel(B);if(B>=y.options.logLevel){y._addToCache(B,A,z)}if(y.consoleLogger&&B>=y.options.consoleLevel){y._emitToConsole(B,A,z)}return y};h.prototype._addToCache=function b(D,A,z){this._emitToConsole("debug","MetricsLogger",["_addToCache:",arguments,this.options.addTime,this.cache.length()]);var y=this;try{var C=y.cache.add(y._buildEntry(D,A,z));if(C>=y._postSize){y._postCache()}}catch(B){if(y.options.consoleLevel<=h.WARN){console.warn("Metrics logger could not stringify logArguments:",A,z);console.error(B)}}return y};h.prototype._buildEntry=function r(B,z,y){this._emitToConsole("debug","MetricsLogger",["_buildEntry:",arguments]);var A={level:B,namespace:this.options.clientPrefix+z,args:y};if(this.options.addTime){A.time=new Date().toISOString()}return A};h.prototype._postCache=function s(B){B=B||{};this._emitToConsole("info","MetricsLogger",["_postCache",B,this._postSize]);if(!this.options.postUrl||this._sending){return jQuery.when({})}var A=this,D=B.count||A._postSize,y=A.cache.get(D),C=y.length,z=(typeof A.options.getPingData==="function")?(A.options.getPingData()):({});z.metrics=A._preprocessCache(y);A._sending=true;return jQuery.post(A.options.postUrl,z).always(function(){A._sending=false}).fail(function(){A._postSize=A.options.maxCacheSize}).done(function(E){if(typeof A.options.onServerResponse==="function"){A.options.onServerResponse(E)}A.cache.remove(C);A._postSize=A.options.postSize})};h.prototype._preprocessCache=function f(y){return["[",(y.join(",\n")),"]"].join("\n")};h.prototype._emitToConsole=function c(C,B,A){var y=this;if(!y.consoleLogger){return y}var z=Array.prototype.slice.call(A,0);z.unshift(B);if(C>=h.METRIC&&typeof(y.consoleLogger.info)==="function"){return y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.ERROR&&typeof(y.consoleLogger.error)==="function"){return y.consoleLogger.error.apply(y.consoleLogger,z)}else{if(C>=h.WARN&&typeof(y.consoleLogger.warn)==="function"){y.consoleLogger.warn.apply(y.consoleLogger,z)}else{if(C>=h.INFO&&typeof(y.consoleLogger.info)==="function"){y.consoleLogger.info.apply(y.consoleLogger,z)}else{if(C>=h.DEBUG&&typeof(y.consoleLogger.debug)==="function"){y.consoleLogger.debug.apply(y.consoleLogger,z)}else{if(typeof(y.consoleLogger.log)==="function"){y.consoleLogger.log.apply(y.consoleLogger,z)}}}}}}return y};h.prototype.debug=function l(){this.emit(h.DEBUG,this.options.defaultNamespace,arguments)};h.prototype.log=function g(){this.emit(1,this.options.defaultNamespace,arguments)};h.prototype.info=function u(){this.emit(h.INFO,this.options.defaultNamespace,arguments)};h.prototype.warn=function t(){this.emit(h.WARN,this.options.defaultNamespace,arguments)};h.prototype.error=function p(){this.emit(h.ERROR,this.options.defaultNamespace,arguments)};h.prototype.metric=function n(){this.emit(h.METRIC,this.options.defaultNamespace,arguments)};function w(z){var y=this;y._cache=[];return y._init(z||{})}w.defaultOptions={maxSize:5000};w.prototype._init=function i(y){this.maxSize=y.maxSize||w.defaultOptions.maxSize;return this};w.prototype.add=function k(A){var z=this,y=(z.length()+1)-z.maxSize;if(y>0){z.remove(y)}z._cache.push(z._preprocessEntry(A));return z.length()};w.prototype._preprocessEntry=function q(y){return JSON.stringify(y)};w.prototype.length=function e(){return this._cache.length};w.prototype.get=function v(y){return this._cache.slice(0,y)};w.prototype.remove=function x(y){return this._cache.splice(0,y)};w.prototype.stringify=function o(y){return["[",(this.get(y).join(",\n")),"]"].join("\n")};w.prototype.print=function d(){this._cache.forEach(function(y){console.log(y)})};return{MetricsLogger:h,LoggingCache:w}}); \ No newline at end of file diff -r 47285f0d20f4cbcb150a894f343fd8cbf1bed4a7 -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 static/scripts/utils/metrics-logger.js --- a/static/scripts/utils/metrics-logger.js +++ b/static/scripts/utils/metrics-logger.js @@ -224,7 +224,7 @@ } // only remove if post successful self.cache.remove( entriesLength ); - console.debug( 'removed entries:', entriesLength, 'size now:', self.cache.length() ); + //console.debug( 'removed entries:', entriesLength, 'size now:', self.cache.length() ); // if we succeeded, reset the post target to the normal num of entries self._postSize = self.options.postSize; }); diff -r 47285f0d20f4cbcb150a894f343fd8cbf1bed4a7 -r bc34e6a879f7ec7a4e63e9a2cd858b89dda16761 test/qunit/tests/metrics-logger.js --- a/test/qunit/tests/metrics-logger.js +++ b/test/qunit/tests/metrics-logger.js @@ -9,11 +9,22 @@ $, sinon ){ - /*globals equal test module expect deepEqual strictEqual throws */ + /*globals equal test module expect deepEqual strictEqual throws ok */ "use strict"; + var MockConsole = function(){ + var self = this; + self.lastMessage = null; + [ 'log', 'debug', 'info', 'warn', 'error' ].forEach( function( fnName ){ + self[ fnName ] = function(){ + self.lastMessage = { level: fnName, args: Array.prototype.slice.call( arguments, 0 ) }; + }; + }); + }; + module( "Metrics logger tests" ); + // ======================================================================== MetricsLogger test( "logger construction/initializiation defaults", function() { var logger = new metrics.MetricsLogger({}); equal( logger.consoleLogger, null ); @@ -24,6 +35,9 @@ equal( logger.options.postSize, 1000 ); equal( logger.options.maxCacheSize, 3000 ); equal( logger.options.addTime, true ); + equal( logger.options.postUrl, '/api/metrics' ); + equal( logger.options.getPingData, undefined ); + equal( logger.options.onServerResponse, undefined ); equal( logger._postSize, 1000 ); equal( logger.cache.constructor, metrics.LoggingCache ); @@ -47,10 +61,105 @@ logger._parseLevel( 'nope' ); }, /Unknown log level/, 'Unknown log level throws error' ); }); + + // ------------------------------------------------------------------------ Emit to cache + test( "emit to cache at level", function() { + var logger = new metrics.MetricsLogger({ + logLevel : 'metric' + }); + equal( logger.options.logLevel, metrics.MetricsLogger.METRIC ); + logger.emit( 'metric', 'test', [ 1, 2, { three: 3 }] ); + equal( logger.cache.length(), 1 ); + + var cached = JSON.parse( logger.cache.get( 1 ) ); + equal( cached.level, metrics.MetricsLogger.METRIC ); + equal( cached.namespace, 'client.test' ); + equal( cached.args.length, 3 ); + equal( cached.args[2].three, 3 ); + ok( typeof cached.time === 'string' ); + ok( cached.time === new Date( cached.time ).toISOString() ); + }); + + test( "emit to cache below does not cache", function() { + var logger = new metrics.MetricsLogger({ + logLevel : 'metric' + }); + logger.emit( 'error', 'test', [ 1, 2, { three: 3 }] ); + equal( logger.cache.length(), 0 ); + }); + + test( "emit to cache (silently) drops non-parsable", function() { + var logger = new metrics.MetricsLogger({ + logLevel : 'metric' + }); + logger.emit( 'metric', 'test', [{ window: window }] ); + equal( logger.cache.length(), 0 ); + }); + // ======================================================================== LoggingCache test( "cache construction/initializiation defaults", function() { var cache = new metrics.LoggingCache(); equal( cache.maxSize, 5000 ); equal( $.type( cache._cache ), 'array' ); }); + + test( "cache construction/initializiation setting max cache size", function() { + var cache = new metrics.LoggingCache({ + maxSize : 5 + }); + equal( cache.maxSize, 5 ); + }); + + test( "cache plays well with no data", function() { + var cache = new metrics.LoggingCache(); + + equal( cache._cache.length, 0 ); + equal( cache.length(), 0 ); + var get = cache.get( 10 ); + ok( jQuery.type( get ) === 'array' && get.length === 0 ); + var remove = cache.remove( 10 ); + ok( jQuery.type( remove ) === 'array' && remove.length === 0 ); + equal( cache.length(), 0 ); + }); + + test( "cache add properly adds and removes data", function() { + var cache = new metrics.LoggingCache({ + maxSize : 5 + }); + var entry1 = [{ one: 1 }, 'two' ]; + cache.add( entry1 ); + + equal( cache._cache.length, 1 ); + equal( cache.length(), 1 ); + equal( cache._cache[0], JSON.stringify( entry1 ) ); + equal( cache.get( 1 ), JSON.stringify( entry1 ) ); + + var entry2 = { blah: { one: 1 }, bler: [ 'three', { two: 2 } ] }; + cache.add( entry2 ); + equal( cache.length(), 2 ); + equal( cache.stringify( 2 ), '[\n' + JSON.stringify( entry1 ) + ',\n' + JSON.stringify( entry2 ) + '\n]' ); + + // FIFO + var returned = cache.remove( 1 ); + equal( cache.length(), 1 ); + ok( jQuery.type( returned ) === 'array' && returned.length === 1 ); + var returned0 = returned[0]; + ok( jQuery.type( returned0 ) === 'string' && returned0 === JSON.stringify( entry1 ) ); + }); + + test( "cache past max loses oldest", function() { + var cache = new metrics.LoggingCache({ + maxSize : 5 + }); + for( var i=0; i<10; i+=1 ){ + cache.add({ index: i }); + } + equal( cache.length(), 5 ); + var get = cache.get( 5 ); + ok( JSON.parse( get[0] ).index === 5 ); + ok( JSON.parse( get[1] ).index === 6 ); + ok( JSON.parse( get[2] ).index === 7 ); + ok( JSON.parse( get[3] ).index === 8 ); + ok( JSON.parse( get[4] ).index === 9 ); + }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Update MAF to interval to use job working directory instead of __new_file_path__.
by commits-noreply＠bitbucket.org 18 Apr '14

18 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/47285f0d20f4/ Changeset: 47285f0d20f4 User: dan Date: 2014-04-18 18:34:08 Summary: Update MAF to interval to use job working directory instead of __new_file_path__. Affected #: 1 file diff -r a7e0eb001bc4c20ef69815c11c0098366b0bfb4d -r 47285f0d20f4cbcb150a894f343fd8cbf1bed4a7 tools/maf/maf_to_interval.xml --- a/tools/maf/maf_to_interval.xml +++ b/tools/maf/maf_to_interval.xml @@ -1,6 +1,6 @@ <tool id="MAF_To_Interval1" name="MAF to Interval" force_history_refresh="True"><description>Converts a MAF formatted file to the Interval format</description> - <command interpreter="python">maf_to_interval.py $input1 $out_file1 $out_file1.id $__new_file_path__ $input1.dbkey $species $input1.metadata.species $complete_blocks $remove_gaps</command> + <command interpreter="python">maf_to_interval.py "${ input1 }" "${ out_file1 }" "${ out_file1.id }" "." "${ input1.dbkey }" "${ species }" "${ input1.metadata.species }" "${ complete_blocks }" "${ remove_gaps }"</command><inputs><param format="maf" name="input1" type="data" label="MAF file to convert"/><param name="species" type="select" label="Select additional species" display="checkboxes" multiple="true" help="The species matching the dbkey of the alignment is always included. A separate history item will be created for each species."> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: QA: add login info to api-hda-tests.js (unable to repro failure shown on buildbot)
by commits-noreply＠bitbucket.org 18 Apr '14

18 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a7e0eb001bc4/ Changeset: a7e0eb001bc4 User: carlfeberhard Date: 2014-04-18 17:02:17 Summary: QA: add login info to api-hda-tests.js (unable to repro failure shown on buildbot) Affected #: 1 file diff -r ffaadbe7fbc29efe93b712e8ae158af28d09f4be -r a7e0eb001bc4c20ef69815c11c0098366b0bfb4d test/casperjs/api-hda-tests.js --- a/test/casperjs/api-hda-tests.js +++ b/test/casperjs/api-hda-tests.js @@ -17,6 +17,7 @@ spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.test.comment( '(logged in as ' + this.user.loggedInAs() + ')' ); this.api.tools.thenUpload( spaceghost.api.histories.show( 'current' ).id, { filepath: '../../test-data/1.sam' }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: QA: add login info to api-history-permission-tests (unable to repro failure shown on buildbot), use API to check loggedInAs
by commits-noreply＠bitbucket.org 18 Apr '14

18 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ffaadbe7fbc2/ Changeset: ffaadbe7fbc2 User: carlfeberhard Date: 2014-04-18 16:59:35 Summary: QA: add login info to api-history-permission-tests (unable to repro failure shown on buildbot), use API to check loggedInAs Affected #: 2 files diff -r 47860aa3f96d9d1276e08f0590506d5cf1c15fc7 -r ffaadbe7fbc29efe93b712e8ae158af28d09f4be test/casperjs/api-history-permission-tests.js --- a/test/casperjs/api-history-permission-tests.js +++ b/test/casperjs/api-history-permission-tests.js @@ -30,6 +30,7 @@ //// ------------------------------------------------------------------------------------------- create 3 histories spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + this.test.comment( '(logged in as ' + this.user.loggedInAs() + ')' ); // create three histories: make the 2nd importable (via the API), and the third published this.test.comment( 'importable, slug, and published should all be returned by show and initially off' ); @@ -216,6 +217,7 @@ spaceghost.user.loginOrRegisterUser( email2, password2 ); spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + this.test.comment( '(logged in as ' + this.user.loggedInAs() + ')' ); testInaccessible.call( spaceghost, inaccessibleHistory, inaccessibleHdas ); testAccessible.call( spaceghost, accessibleHistory, accessibleHdas ); testAccessible.call( spaceghost, publishedHistory, publishedHdas ); @@ -226,6 +228,7 @@ //// ------------------------------------------------------------------------------------------- user1 revoke perms spaceghost.user.loginOrRegisterUser( email, password ); spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + this.test.comment( '(logged in as ' + this.user.loggedInAs() + ')' ); this.test.comment( 'revoking perms should prevent access' ); this.api.histories.update( accessibleHistory.id, { importable : false @@ -250,6 +253,7 @@ //// ------------------------------------------------------------------------------------------- user2 retry perms spaceghost.user.loginOrRegisterUser( email2, password2 ); spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + this.test.comment( '(logged in as ' + this.user.loggedInAs() + ')' ); testInaccessible.call( spaceghost, accessibleHistory, accessibleHdas ); testInaccessible.call( spaceghost, publishedHistory, publishedHdas ); }); diff -r 47860aa3f96d9d1276e08f0590506d5cf1c15fc7 -r ffaadbe7fbc29efe93b712e8ae158af28d09f4be test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -163,19 +163,24 @@ * @returns {String} email of currently logged in user or '' if no one logged in */ User.prototype.loggedInAs = function loggedInAs(){ - return this.spaceghost.jumpToTop( function(){ - var userEmail = ''; - try { - var emailSelector = xpath( this.data.selectors.masthead.userMenu.userEmail_xpath ), - loggedInInfo = this.elementInfoOrNull( emailSelector ); - if( loggedInInfo !== null ){ - userEmail = loggedInInfo.text.replace( 'Logged in as ', '' ); - } - } catch( err ){ - this.warn( err ); - } - return userEmail; - }); + var currUser = this.spaceghost.api.users.show( 'current' ); + //this.spaceghost.debug( this.spaceghost.jsonStr( currUser ) ); + return currUser.email; +//TODO: due to late rendering of masthead this is no longer reliable - need a wait for in the main page + //return this.spaceghost.jumpToTop( function(){ + // var userEmail = ''; + // try { + // var emailSelector = xpath( this.data.selectors.masthead.userMenu.userEmail_xpath ), + // loggedInInfo = this.elementInfoOrNull( emailSelector ); + // this.debug( '\n\n' + this.jsonStr( loggedInInfo ) + '\n' ); + // if( loggedInInfo !== null ){ + // userEmail = loggedInInfo.text.replace( 'Logged in as ', '' ); + // } + // } catch( err ){ + // this.warn( err ); + // } + // return userEmail; + //}); }; /** Log out the current user Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits April 2014