3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0119b0d6befb/ Changeset: 0119b0d6befb User: jmchilton Date: 2014-09-05 21:19:18 Summary: More discovered dataset testing tweaks. Affected #: 2 files diff -r 77e633e926043524691dcc193f3e7d59809d06a8 -r 0119b0d6befbb77f7ae177ccf036109d97fa53f1 lib/galaxy/tools/parameters/output_collect.py --- a/lib/galaxy/tools/parameters/output_collect.py +++ b/lib/galaxy/tools/parameters/output_collect.py @@ -186,7 +186,8 @@ return self.pattern.replace( DATASET_ID_TOKEN, token_replacement ) def match( self, dataset_instance, filename ): - re_match = re.match( self.pattern_for_dataset( dataset_instance ), filename ) + pattern = self.pattern_for_dataset( dataset_instance ) + re_match = re.match( pattern, filename ) match_object = None if re_match: match_object = CollectedDatasetMatch( re_match, self ) diff -r 77e633e926043524691dcc193f3e7d59809d06a8 -r 0119b0d6befbb77f7ae177ccf036109d97fa53f1 test/functional/tools/multi_output_configured.xml --- a/test/functional/tools/multi_output_configured.xml +++ b/test/functional/tools/multi_output_configured.xml @@ -1,4 +1,4 @@ -<tool id="multi_output_configured" name="Multi_Output_Configured" description="multi_output_configured" force_history_refresh="True" version="0.1.0"> +<tool id="multi_output_configured" name="Multi_Output_Configured" description="multi_output_configured" version="0.1.0"><command> echo "Hello" > $report; mkdir subdir1; @@ -12,6 +12,9 @@ echo "Foo" > subdir3/Foo; echo "mapped reads" > split_bam_.MAPPED.bam; echo "unmapped reads" > split_bam_.UNMAPPED.bam; + echo "1" > sample1.report.tsv; + echo "2" > sample2.report.tsv; + echo "3" > sample3.report.tsv; </command><inputs><param name="num_param" type="integer" value="7" /> @@ -23,6 +26,7 @@ <discover_datasets pattern="CUSTOM_(?P<designation>.+)\.(?P<ext>.+)" directory="subdir2" visible="true" /><discover_datasets pattern="__designation__" directory="subdir3" ext="input" visible="true" /><discover_datasets pattern="split_bam_\.(?P<designation>([A-Z-])\w+)\.bam" ext="txt" visible="true" /> + <discover_datasets pattern="(?P<designation>.+)\.report\.tsv" ext="tabular" visible="true" /></data></outputs><tests> @@ -54,6 +58,9 @@ <discovered_dataset designation="UNMAPPED" ftype="txt"><assert_contents><has_line line="unmapped reads" /></assert_contents></discovered_dataset> + <discovered_dataset designation="sample1" ftype="tabular"> + <assert_contents><has_line line="1" /></assert_contents> + </discovered_dataset></output></test></tests> https://bitbucket.org/galaxy/galaxy-central/commits/8b450e9886e1/ Changeset: 8b450e9886e1 User: jmchilton Date: 2014-09-05 21:19:18 Summary: Switch default test interactor to API. Has dozens of advantages and the main tool shed is now running tests against the API and no one has complained. If you find regressions in test cases as part of this switch, please report them and set interactor="twill" on your test cases to revert to the old runner until the problem is being fixed. Eventually the twill interactor for tool functional tests will be eliminated all together. Affected #: 1 file diff -r 0119b0d6befbb77f7ae177ccf036109d97fa53f1 -r 8b450e9886e1e8d62201bf307d79e2f8e3458fbd lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py +++ b/lib/galaxy/tools/test.py @@ -14,7 +14,7 @@ DEFAULT_FTYPE = 'auto' DEFAULT_DBKEY = 'hg17' -DEFAULT_INTERACTOR = "twill" # Default mechanism test code uses for interacting with Galaxy instance. +DEFAULT_INTERACTOR = "api" # Default mechanism test code uses for interacting with Galaxy instance. DEFAULT_MAX_SECS = 120 https://bitbucket.org/galaxy/galaxy-central/commits/92238b01c946/ Changeset: 92238b01c946 User: jmchilton Date: 2014-09-05 21:19:18 Summary: Add another example tool - to illustrate three ways to collect files for concatenation. Affected #: 3 files diff -r 8b450e9886e1e8d62201bf307d79e2f8e3458fbd -r 92238b01c946c03b93f4b77d0729b24684940c89 test/functional/tools/for_workflows/cat_collection.xml --- /dev/null +++ b/test/functional/tools/for_workflows/cat_collection.xml @@ -0,0 +1,16 @@ +<tool id="cat_collection" name="Concatenate dataset collection (for test workflows)"> + <description>tail-to-head</description> + <command> + cat #for $q in $input1# $q #end for# > $out_file1 + </command> + <inputs> + <param name="input1" type="data_collection" label="Concatenate Dataset" collection_type="paired" /> + </inputs> + <outputs> + <data name="out_file1" format="input" /> + </outputs> + <tests> + </tests> + <help> + </help> +</tool> diff -r 8b450e9886e1e8d62201bf307d79e2f8e3458fbd -r 92238b01c946c03b93f4b77d0729b24684940c89 test/functional/tools/for_workflows/cat_list.xml --- a/test/functional/tools/for_workflows/cat_list.xml +++ b/test/functional/tools/for_workflows/cat_list.xml @@ -1,4 +1,4 @@ -<tool id="cat_list" name="Concatenate dataset list (for test workflows)"> +<tool id="cat_list" name="Concatenate multiple datasets (for test workflows)"><description>tail-to-head</description><command> cat #for $q in $input1# $q #end for# > $out_file1 diff -r 8b450e9886e1e8d62201bf307d79e2f8e3458fbd -r 92238b01c946c03b93f4b77d0729b24684940c89 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -28,8 +28,13 @@ <tool file="collection_optional_param.xml" /><!-- Tools interesting only for building up test workflows. --> + + <!-- Next three tools demonstrate concatenating multiple datasets + with a repeat, multiple datasets with a multiple input data + parameter, and multiple datasets from a collection. --><tool file="for_workflows/cat.xml" /><tool file="for_workflows/cat_list.xml" /> + <tool file="for_workflows/cat_collection.xml" /><tool file="for_workflows/head.xml" /></toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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