galaxy-commits July 2013

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commit/galaxy-central: carlfeberhard: Visualizations registry: turned off by default in main .ini
by commits-noreply＠bitbucket.org 18 Jul '13

18 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d9fe5bea5a43/ Changeset: d9fe5bea5a43 User: carlfeberhard Date: 2013-07-18 22:27:38 Summary: Visualizations registry: turned off by default in main .ini Affected #: 1 file diff -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa -r d9fe5bea5a43c4c4645408a9035ad818d89d012c universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -177,7 +177,7 @@ # Visualizations config directory, where to look for individual visualization # xml configuration files. Those files define how visualizations apply to # particular data and how to pass them the necessary parameters -visualizations_config_directory = config/visualizations +#visualizations_config_directory = config/visualizations # Each job is given a unique empty directory as its current working directory. # This option defines in what parent directory those directories will be 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: Visualizations registry: move built-in vis config files to sample, copying them over on registry start; add vis xml files to .hgignore; fix test data in scatterplot.xml
by commits-noreply＠bitbucket.org 18 Jul '13

18 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6781bf1f3de1/ Changeset: 6781bf1f3de1 User: carlfeberhard Date: 2013-07-18 22:24:18 Summary: Visualizations registry: move built-in vis config files to sample, copying them over on registry start; add vis xml files to .hgignore; fix test data in scatterplot.xml Affected #: 13 files diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa .hgignore --- a/.hgignore +++ b/.hgignore @@ -60,7 +60,7 @@ job_conf.xml data_manager_conf.xml shed_data_manager_conf.xml -visualizations_conf.xml +config/visualizations/*.xml static/welcome.html.* static/welcome.html diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/circster.xml --- a/config/visualizations/circster.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE visualization SYSTEM "visualization.dtd"> -<visualization name="circster"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="hda">hda_ldda</to_param> - </data_source> - <data_source> - <model_class>LibraryDatasetDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="ldda">hda_ldda</to_param> - </data_source> - </data_sources> - <params> - <param type="visualization">id</param> - <param type="hda_or_ldda">dataset_id</param> - <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> - <param type="dbkey">dbkey</param> - </params> - <template>circster.mako</template> - <render_location>_top</render_location> -</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/circster.xml.sample --- /dev/null +++ b/config/visualizations/circster.xml.sample @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="circster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="hda_or_ldda">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + <param type="dbkey">dbkey</param> + </params> + <template>circster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/example.xml.example --- a/config/visualizations/example.xml.example +++ /dev/null @@ -1,30 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE visualization SYSTEM "visualization.dtd"> -<visualization name="test"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="bler">string</to_param> - <to_param assign="False">boolean</to_param> - <to_param assign="-5">integer</to_param> - <to_param assign="3.14">float</to_param> - <to_param assign="{}">json</to_param> - </data_source> - </data_sources> - <params> - <param>default</param> - <param type="str">string</param> - <param type="bool">boolean</param> - <param type="int">integer</param> - <param type="float">float</param> - <param type="json">json</param> - <param type="str" required="true">string</param> - <param type="visualization" var_name_in_template="visualization">visualization_id</param> - <param type="dataset" var_name_in_template="dataset">dataset_id</param> - <param type="hda_or_ldda">dataset_instance</param> - <param_modifier type="str" modifies="dataset_instance">hda_ldda</param_modifier> - </params> - <template>v_fwork_test.mako</template> -</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/phyloviz.xml --- a/config/visualizations/phyloviz.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE visualization SYSTEM "visualization.dtd"> -<visualization name="phyloviz"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test> - <to_param param_attr="id">dataset_id</to_param> - </data_source> - </data_sources> - <params> - <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> - <param type="integer" default="0">tree_index</param> - </params> - <template>phyloviz.mako</template> - <render_location>_top</render_location> -</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/phyloviz.xml.sample --- /dev/null +++ b/config/visualizations/phyloviz.xml.sample @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="phyloviz"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + <param type="integer" default="0">tree_index</param> + </params> + <template>phyloviz.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/scatterplot.xml --- a/config/visualizations/scatterplot.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE visualization SYSTEM "visualization.dtd"> -<visualization name="scatterplot"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> - <to_param param_attr="id">dataset_id</to_param> - </data_source> - </data_sources> - <params> - <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> - <param required="true">bler</param> - </params> - <template>scatterplot.mako</template> -</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/scatterplot.xml.sample --- /dev/null +++ b/config/visualizations/scatterplot.xml.sample @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="scatterplot"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>scatterplot.mako</template> +</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/sweepster.xml --- a/config/visualizations/sweepster.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE visualization SYSTEM "visualization.dtd"> -<visualization name="sweepster"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="hda">hda_ldda</to_param> - </data_source> - <data_source> - <model_class>LibraryDatasetDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="ldda">hda_ldda</to_param> - </data_source> - </data_sources> - <params> - <param type="visualization" var_name_in_template="viz">visualization</param> - <param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param> - <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> - </params> - <template>sweepster.mako</template> - <render_location>_top</render_location> -</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/sweepster.xml.sample --- /dev/null +++ b/config/visualizations/sweepster.xml.sample @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="sweepster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization" var_name_in_template="viz">visualization</param> + <param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + </params> + <template>sweepster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/trackster.xml --- a/config/visualizations/trackster.xml +++ /dev/null @@ -1,29 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE visualization SYSTEM "visualization.dtd"> -<visualization name="trackster"> -  - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="hda">hda_ldda</to_param> - <to_param param_attr="dbkey">dbkey</to_param> - </data_source> - <data_source> - <model_class>LibraryDatasetDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="ldda">hda_ldda</to_param> - </data_source> - </data_sources> - <params> - <param type="visualization">id</param> - <param type="dataset">dataset_id</param> - <param type="genome_region">genome_region</param> - <param type="dbkey">dbkey</param> - </params> - <template_root>tracks</template_root> - <template>browser.mako</template> - <render_location>_top</render_location> -</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa config/visualizations/trackster.xml.sample --- /dev/null +++ b/config/visualizations/trackster.xml.sample @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="trackster"> +  + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + <to_param param_attr="dbkey">dbkey</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="dataset">dataset_id</param> + <param type="genome_region">genome_region</param> + <param type="dbkey">dbkey</param> + </params> + <template_root>tracks</template_root> + <template>browser.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 -r 6781bf1f3de1514967d62b6cf4fe4910cf9ec0aa lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -67,6 +67,7 @@ # load the registry from the xml files located in configuration_filepath using the given parser configuration_filepath = os.path.join( galaxy_root, configuration_filepath ) self.configuration_filepath = self.check_conf_filepath( configuration_filepath ) + self.move_sample_conf_files() self.load() # what to use to parse query strings into resources/vars for the template @@ -82,6 +83,20 @@ raise IOError( 'visualization configuration directory (%s) not found' %( configuration_filepath ) ) return configuration_filepath + def move_sample_conf_files( self ): + """ + Copies any `*.xml.sample` files in `configuration_filepath` to + `.xml` files of the same names if no file with that name already exists. + + :returns: a list of the files moved + """ + files_moved = [] + for sample_file in glob.glob( os.path.join( self.configuration_filepath, '*.sample' ) ): + new_name = os.path.splitext( sample_file )[0] + if not os.path.exists( new_name ): + shutil.copy2( sample_file, new_name ) + files_moved.append( new_name ) + def load( self ): """ Builds the registry by parsing the xml in `self.configuration_filepath` Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Visualizations registry: break visualizations_conf.xml into one xml file per visualization and place in config/visualizations
by commits-noreply＠bitbucket.org 18 Jul '13

18 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/91de48b4fd3b/ Changeset: 91de48b4fd3b User: carlfeberhard Date: 2013-07-18 21:52:38 Summary: Visualizations registry: break visualizations_conf.xml into one xml file per visualization and place in config/visualizations Affected #: 12 files diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/circster.xml --- /dev/null +++ b/config/visualizations/circster.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="circster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="hda_or_ldda">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + <param type="dbkey">dbkey</param> + </params> + <template>circster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/example.xml.example --- /dev/null +++ b/config/visualizations/example.xml.example @@ -0,0 +1,30 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="test"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="bler">string</to_param> + <to_param assign="False">boolean</to_param> + <to_param assign="-5">integer</to_param> + <to_param assign="3.14">float</to_param> + <to_param assign="{}">json</to_param> + </data_source> + </data_sources> + <params> + <param>default</param> + <param type="str">string</param> + <param type="bool">boolean</param> + <param type="int">integer</param> + <param type="float">float</param> + <param type="json">json</param> + <param type="str" required="true">string</param> + <param type="visualization" var_name_in_template="visualization">visualization_id</param> + <param type="dataset" var_name_in_template="dataset">dataset_id</param> + <param type="hda_or_ldda">dataset_instance</param> + <param_modifier type="str" modifies="dataset_instance">hda_ldda</param_modifier> + </params> + <template>v_fwork_test.mako</template> +</visualization> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/phyloviz.xml --- /dev/null +++ b/config/visualizations/phyloviz.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="phyloviz"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + <param type="integer" default="0">tree_index</param> + </params> + <template>phyloviz.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/scatterplot.xml --- /dev/null +++ b/config/visualizations/scatterplot.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="scatterplot"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + <param required="true">bler</param> + </params> + <template>scatterplot.mako</template> +</visualization> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/sweepster.xml --- /dev/null +++ b/config/visualizations/sweepster.xml @@ -0,0 +1,25 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="sweepster"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization" var_name_in_template="viz">visualization</param> + <param type="hda_or_ldda" var_name_in_template="dataset">dataset_id</param> + <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> + </params> + <template>sweepster.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/trackster.xml --- /dev/null +++ b/config/visualizations/trackster.xml @@ -0,0 +1,29 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "visualization.dtd"> +<visualization name="trackster"> +  + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="hda">hda_ldda</to_param> + <to_param param_attr="dbkey">dbkey</to_param> + </data_source> + <data_source> + <model_class>LibraryDatasetDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> + <to_param param_attr="id">dataset_id</to_param> + <to_param assign="ldda">hda_ldda</to_param> + </data_source> + </data_sources> + <params> + <param type="visualization">id</param> + <param type="dataset">dataset_id</param> + <param type="genome_region">genome_region</param> + <param type="dbkey">dbkey</param> + </params> + <template_root>tracks</template_root> + <template>browser.mako</template> + <render_location>_top</render_location> +</visualization> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 config/visualizations/visualization.dtd --- /dev/null +++ b/config/visualizations/visualization.dtd @@ -0,0 +1,132 @@ + + + +<!ELEMENT visualization (data_sources*,params*,template_root*,template,link_text*,render_location*)> + +<!ATTLIST visualization + name CDATA #REQUIRED +> + +<!ELEMENT data_sources (data_source*)> + + <!ELEMENT data_source (model_class,(test|to_param)*)> + <!ELEMENT model_class (#PCDATA)> +  + <!ELEMENT test (#PCDATA)> +  + <!ATTLIST test + type CDATA #IMPLIED + test_attr CDATA #IMPLIED + result_type CDATA #IMPLIED + > + + <!ELEMENT to_param (#PCDATA)> +  + <!ATTLIST to_param + param_attr CDATA #IMPLIED + assign CDATA #IMPLIED + > + +<!ELEMENT params ((param|param_modifier)*)> + + <!ELEMENT param (#PCDATA)> +  + <!ATTLIST param + type CDATA #IMPLIED + default CDATA #IMPLIED + required CDATA #IMPLIED + csv CDATA #IMPLIED + constrain_to CDATA #IMPLIED + var_name_in_template CDATA #IMPLIED + > +  + <!ELEMENT param_modifier (#PCDATA)> + <!ATTLIST param_modifier + modifies CDATA #REQUIRED + type CDATA #IMPLIED + default CDATA #IMPLIED + required CDATA #IMPLIED + csv CDATA #IMPLIED + constrain_to CDATA #IMPLIED + var_name_in_template CDATA #IMPLIED + > + + +<!ELEMENT template_root (#PCDATA)> + +<!ELEMENT template (#PCDATA)> + +<!ELEMENT link_text (#PCDATA)> + + +<!ELEMENT render_location (#PCDATA)> diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -123,8 +123,10 @@ # Load genome indexer tool. load_genome_index_tools( self.toolbox ) # visualizations registry: associates resources with visualizations, controls how to render - self.visualizations_registry = ( VisualizationsRegistry( self.config.root, self.config.visualizations_conf_path ) - if self.config.visualizations_conf_path else None ) + self.visualizations_registry = None + if self.config.visualizations_config_directory: + self.visualizations_registry = VisualizationsRegistry( self.config.root, + self.config.visualizations_config_directory ) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -288,8 +288,8 @@ self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) ) self.fluent_host = kwargs.get( 'fluent_host', 'localhost' ) self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) ) - # visualizations registry config path - self.visualizations_conf_path = kwargs.get( 'visualizations_conf_path', None ) + # visualization registries config directory + self.visualizations_config_directory = kwargs.get( 'visualizations_config_directory', None ) @property def sentry_dsn_public( self ): diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -6,6 +6,7 @@ """ import os import shutil +import glob from galaxy import util import galaxy.model @@ -26,6 +27,7 @@ some confused vocabulary in docs, var names tests: anding, grouping, not + has_dataprovider data_sources: lists of add description element to visualization. @@ -62,10 +64,9 @@ return 'VisualizationsRegistry(%s)' %( listings_keys_str ) def __init__( self, galaxy_root, configuration_filepath ): - # load the registry from the given xml file using the given parser + # load the registry from the xml files located in configuration_filepath using the given parser configuration_filepath = os.path.join( galaxy_root, configuration_filepath ) - configuration_filepath = self.check_conf_filepath( configuration_filepath ) - self.configuration_filepath = configuration_filepath + self.configuration_filepath = self.check_conf_filepath( configuration_filepath ) self.load() # what to use to parse query strings into resources/vars for the template @@ -73,20 +74,13 @@ def check_conf_filepath( self, configuration_filepath ): """ - If given file at filepath exists, return that filepath. If not, - see if filepath + '.sample' exists and, if so, copy that into filepath. - - If neither original or sample exist, throw an IOError (currently, - this is a requireed file). + Checks for the existence of the given filepath. + :param configurarion_filepath: full filepath to the visualization config directory + :raises IOError: if the given directory doesn't exist """ - if os.path.exists( configuration_filepath ): - return configuration_filepath - else: - sample_file = configuration_filepath + '.sample' - if os.path.exists( sample_file ): - shutil.copy2( sample_file, configuration_filepath ) - return configuration_filepath - raise IOError( 'visualization configuration file (%s) not found' %( configuration_filepath ) ) + if not os.path.exists( configuration_filepath ): + raise IOError( 'visualization configuration directory (%s) not found' %( configuration_filepath ) ) + return configuration_filepath def load( self ): """ @@ -274,11 +268,11 @@ VALID_RENDER_LOCATIONS = [ 'galaxy_main', '_top', '_blank' ] @classmethod - def parse( cls, xml_filepath, debug=True ): + def parse( cls, config_dir, debug=True ): """ - Static class interface + Static class interface. """ - return cls( debug ).parse_file( xml_filepath ) + return cls( debug ).parse_files( config_dir ) def __init__( self, debug=False ): self.debug = debug @@ -288,38 +282,47 @@ self.param_parser = ParamParser() self.param_modifier_parser = ParamModifierParser() - def parse_file( self, xml_filepath ): + def parse_files( self, config_dir ): """ - Parse the given XML file for visualizations data. + Parse each XML file in `config_dir` for visualizations config data. - If an error occurs while parsing a visualizations entry it is skipped. + If an error occurs while parsing a visualizations entry, it is skipped. + :returns: registry data in dictionary form """ returned = {} try: - xml_tree = galaxy.util.parse_xml( xml_filepath ) - for visualization_conf in xml_tree.getroot().findall( 'visualization' ): - visualization = None - visualization_name = visualization_conf.get( 'name' ) - + for xml_filepath in glob.glob( os.path.join( config_dir, '*.xml' ) ): try: - visualization = self.parse_visualization( visualization_conf ) + visualization_name, visualization = self.parse_file( xml_filepath ) # skip vis' with parsing errors - don't shutdown the startup except ParsingException, parse_exc: - log.error( 'Skipped visualization configuration "%s" due to parsing errors: %s', - visualization_name, str( parse_exc ), exc_info=self.debug ) + log.error( 'Skipped visualization config "%s" due to parsing errors: %s', + xml_filepath, str( parse_exc ), exc_info=self.debug ) if visualization: returned[ visualization_name ] = visualization + log.debug( 'Visualization config loaded for: %s', visualization_name ) except Exception, exc: - log.error( 'Error parsing visualization configuration file %s: %s', - xml_filepath, str( exc ), exc_info=( not self.debug ) ) - #TODO: change when this is required + log.error( 'Error parsing visualizations configuration directory %s: %s', + config_dir, str( exc ), exc_info=( not self.debug ) ) + #TODO: change when this framework is on by default if self.debug: raise return returned + def parse_file( self, xml_filepath ): + """ + Parse the given XML file for visualizations data. + :returns: tuple of ( `visualization_name`, `visualization` ) + """ + xml_tree = galaxy.util.parse_xml( xml_filepath ) + visualization_conf = xml_tree.getroot() + visualization_name = visualization_conf.get( 'name' ) + visualization = self.parse_visualization( visualization_conf ) + return visualization_name, visualization + def parse_visualization( self, xml_tree ): """ Parse the template, name, and any data_sources and params from the diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -174,9 +174,10 @@ # Galaxy. #datatypes_config_file = datatypes_conf.xml -# Visualizations config file, defines what visualizations apply to particular data and how to pass them -# the necessary parameters -#visualizations_conf_path = visualizations_conf.xml +# Visualizations config directory, where to look for individual visualization +# xml configuration files. Those files define how visualizations apply to +# particular data and how to pass them the necessary parameters +visualizations_config_directory = config/visualizations # Each job is given a unique empty directory as its current working directory. # This option defines in what parent directory those directories will be diff -r 3422736c168d6d864ec3c478d3e725b1184e3778 -r 91de48b4fd3b5628d5a434f68bd6cf2473ad62c3 visualizations_conf.xml.sample --- a/visualizations_conf.xml.sample +++ /dev/null @@ -1,292 +0,0 @@ -<?xml version="1.0"?> - - - - -<!DOCTYPE visualizations [ -  - <!ELEMENT visualizations (visualization*)> -  - <!ELEMENT visualization (data_sources*,params*,template_root*,template,link_text*,render_location*)> -  - <!ATTLIST visualization - name CDATA #REQUIRED - > - - <!ELEMENT data_sources (data_source*)> -  - <!ELEMENT data_source (model_class,(test|to_param)*)> - <!ELEMENT model_class (#PCDATA)> -  - <!ELEMENT test (#PCDATA)> -  - <!ATTLIST test - type CDATA #IMPLIED - test_attr CDATA #IMPLIED - result_type CDATA #IMPLIED - > - - <!ELEMENT to_param (#PCDATA)> -  - <!ATTLIST to_param - param_attr CDATA #IMPLIED - assign CDATA #IMPLIED - > - - <!ELEMENT params ((param|param_modifier)*)> -  - <!ELEMENT param (#PCDATA)> -  - <!ATTLIST param - type CDATA #IMPLIED - default CDATA #IMPLIED - required CDATA #IMPLIED - csv CDATA #IMPLIED - constrain_to CDATA #IMPLIED - var_name_in_template CDATA #IMPLIED - > -  - <!ELEMENT param_modifier (#PCDATA)> - <!ATTLIST param_modifier - modifies CDATA #REQUIRED - type CDATA #IMPLIED - default CDATA #IMPLIED - required CDATA #IMPLIED - csv CDATA #IMPLIED - constrain_to CDATA #IMPLIED - var_name_in_template CDATA #IMPLIED - > - -  - <!ELEMENT template_root (#PCDATA)> -  - <!ELEMENT template (#PCDATA)> -  - <!ELEMENT link_text (#PCDATA)> -  -  - <!ELEMENT render_location (#PCDATA)> -]> - - -<visualizations> - <visualization name="trackster"> -  - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="hda">hda_ldda</to_param> - <to_param param_attr="dbkey">dbkey</to_param> - </data_source> - <data_source> - <model_class>LibraryDatasetDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="ldda">hda_ldda</to_param> - </data_source> - </data_sources> - <params> - <param type="visualization">id</param> - <param type="dataset">dataset_id</param> - <param type="genome_region">genome_region</param> - <param type="dbkey">dbkey</param> - </params> - <template_root>tracks</template_root> - <template>browser.mako</template> - <render_location>_top</render_location> - </visualization> - - <visualization name="circster"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="hda">hda_ldda</to_param> - </data_source> - <data_source> - <model_class>LibraryDatasetDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test> - <to_param param_attr="id">dataset_id</to_param> - <to_param assign="ldda">hda_ldda</to_param> - </data_source> - </data_sources> - <params> - <param type="visualization">id</param> - <param type="hda_or_ldda">dataset_id</param> - <param_modifier type="string" modifies="dataset_id">hda_ldda</param_modifier> - <param type="dbkey">dbkey</param> - </params> - <template>circster.mako</template> - <render_location>_top</render_location> - </visualization> - -  - - <visualization name="phyloviz"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Newick</test> - <test type="isinstance" test_attr="datatype" result_type="datatype">data.Nexus</test> - <to_param param_attr="id">dataset_id</to_param> - </data_source> - </data_sources> - <params> - <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> - <param type="integer" default="0">tree_index</param> - </params> - <template>phyloviz.mako</template> - <render_location>_top</render_location> - </visualization> - - <visualization name="scatterplot"> - <data_sources> - <data_source> - <model_class>HistoryDatasetAssociation</model_class> - <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> - <to_param param_attr="id">dataset_id</to_param> - </data_source> - </data_sources> - <params> - <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> - </params> - <template>scatterplot.mako</template> - </visualization> - -  - -</visualizations> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Dataproviders: change 'map' providers to 'dict' for better consistency w/ python
by commits-noreply＠bitbucket.org 18 Jul '13

18 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3422736c168d/ Changeset: 3422736c168d User: carlfeberhard Date: 2013-07-18 18:46:21 Summary: Dataproviders: change 'map' providers to 'dict' for better consistency w/ python Affected #: 5 files diff -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 -r 3422736c168d6d864ec3c478d3e725b1184e3778 lib/galaxy/datatypes/binary.py --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -285,23 +285,23 @@ settings[ 'comment_char' ] = '@' return dataproviders.column.ColumnarDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) - def map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'dict', dataproviders.column.DictDataProvider.settings ) + def dict_dataprovider( self, dataset, **settings ): samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset ) settings[ 'comment_char' ] = '@' - return dataproviders.column.MapDataProvider( samtools_source, **settings ) + return dataproviders.column.DictDataProvider( samtools_source, **settings ) - # these can't be used directly - may need BamColumn, BamMap (Bam metadata -> column/map) + # these can't be used directly - may need BamColumn, BamDict (Bam metadata -> column/dict) # OR - see genomic_region_dataprovider #(a)dataproviders.decorators.dataprovider_factory( 'dataset-column', dataproviders.column.ColumnarDataProvider.settings ) #def dataset_column_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] = '@' # return super( Sam, self ).dataset_column_dataprovider( dataset, **settings ) - #(a)dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) - #def dataset_map_dataprovider( self, dataset, **settings ): + #(a)dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings ) + #def dataset_dict_dataprovider( self, dataset, **settings ): # settings[ 'comment_char' ] = '@' - # return super( Sam, self ).dataset_map_dataprovider( dataset, **settings ) + # return super( Sam, self ).dataset_dict_dataprovider( dataset, **settings ) @dataproviders.decorators.dataprovider_factory( 'header', dataproviders.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): @@ -309,12 +309,12 @@ samtools_source = dataproviders.dataset.SamtoolsDataProvider( dataset, '-H' ) return dataproviders.line.RegexLineDataProvider( samtools_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', dataproviders.column.MapDataProvider.settings ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', dataproviders.column.DictDataProvider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] = [ 0, 9, 10 ] settings[ 'column_types' ] = [ 'str', 'str', 'str' ] settings[ 'column_names' ] = [ 'id', 'seq', 'qual' ] - return self.map_dataprovider( dataset, **settings ) + return self.dict_dataprovider( dataset, **settings ) @dataproviders.decorators.dataprovider_factory( 'genomic-region', dataproviders.column.ColumnarDataProvider.settings ) def genomic_region_dataprovider( self, dataset, **settings ): @@ -330,12 +330,12 @@ settings[ 'column_types' ] = [ 'str', 'int', 'int' ] return self.column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', dataproviders.column.MapDataProvider.settings ) - def genomic_region_map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'genomic-region-dict', dataproviders.column.DictDataProvider.settings ) + def genomic_region_dict_dataprovider( self, dataset, **settings ): settings[ 'indeces' ] = [ 2, 3, 3 ] settings[ 'column_types' ] = [ 'str', 'int', 'int' ] settings[ 'column_names' ] = [ 'chrom', 'start', 'end' ] - return self.map_dataprovider( dataset, **settings ) + return self.dict_dataprovider( dataset, **settings ) @dataproviders.decorators.dataprovider_factory( 'samtools' ) def samtools_dataprovider( self, dataset, **settings ): diff -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 -r 3422736c168d6d864ec3c478d3e725b1184e3778 lib/galaxy/datatypes/dataproviders/column.py --- a/lib/galaxy/datatypes/dataproviders/column.py +++ b/lib/galaxy/datatypes/dataproviders/column.py @@ -220,9 +220,9 @@ super( FilteredByColumnDataProvider, self ).__init__( source, **kwargs ) -class MapDataProvider( ColumnarDataProvider ): +class DictDataProvider( ColumnarDataProvider ): """ - Data provider that column_names and columns from the source's contents + Data provider that zips column_names and columns from the source's contents into a dictionary. A combination use of both `column_names` and `indeces` allows 'picking' @@ -244,11 +244,11 @@ :type column_names: """ #TODO: allow passing in a map instead of name->index { 'name1': index1, ... } - super( MapDataProvider, self ).__init__( source, **kwargs ) + super( DictDataProvider, self ).__init__( source, **kwargs ) self.column_names = column_names or [] def __iter__( self ): - parent_gen = super( MapDataProvider, self ).__iter__() + parent_gen = super( DictDataProvider, self ).__iter__() for column_values in parent_gen: map = dict( zip( self.column_names, column_values ) ) yield map diff -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 -r 3422736c168d6d864ec3c478d3e725b1184e3778 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -203,16 +203,16 @@ super( DatasetColumnarDataProvider, self ).__init__( dataset_source, **kwargs ) -class DatasetMapDataProvider( column.MapDataProvider ): +class DatasetDictDataProvider( column.DictDataProvider ): """ Data provider that uses a DatasetDataProvider as it's source and the - dataset's metadata to buuild settings for the MapDataProvider it's + dataset's metadata to buuild settings for the DictDataProvider it's inherited from. """ def __init__( self, dataset, **kwargs ): """ - All kwargs are inherited from MapDataProvider. - .. seealso:: column.MapDataProvider + All kwargs are inherited from DictDataProvider. + .. seealso:: column.DictDataProvider If no kwargs are given, this class will attempt to get those kwargs from the dataset source's metadata. @@ -255,7 +255,7 @@ if not kwargs.get( 'column_types', None ): kwargs[ 'column_types' ] = dataset_source.get_metadata_column_types( indeces=indeces ) - super( DatasetMapDataProvider, self ).__init__( dataset_source, **kwargs ) + super( DatasetDictDataProvider, self ).__init__( dataset_source, **kwargs ) # ----------------------------------------------------------------------------- provides a bio-relevant datum diff -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 -r 3422736c168d6d864ec3c478d3e725b1184e3778 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -339,9 +339,9 @@ def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + @dataproviders.decorators.dataprovider_factory( 'genomic-region-dict', dataproviders.dataset.GenomicRegionDataProvider.settings ) - def genomic_region_map_dataprovider( self, dataset, **settings ): + def genomic_region_dict_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) @@ -350,9 +350,9 @@ def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval-map', + @dataproviders.decorators.dataprovider_factory( 'interval-dict', dataproviders.dataset.IntervalDataProvider.settings ) - def interval_map_dataprovider( self, dataset, **settings ): + def interval_dict_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.interval_dataprovider( dataset, **settings ) @@ -818,9 +818,9 @@ def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0, 3, 4, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + @dataproviders.decorators.dataprovider_factory( 'genomic-region-dict', dataproviders.dataset.GenomicRegionDataProvider.settings ) - def genomic_region_map_dataprovider( self, dataset, **settings ): + def genomic_region_dict_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) @@ -829,9 +829,9 @@ def interval_dataprovider( self, dataset, **settings ): return dataproviders.dataset.IntervalDataProvider( dataset, 0, 3, 4, 6, 2, **settings ) - @dataproviders.decorators.dataprovider_factory( 'interval-map', + @dataproviders.decorators.dataprovider_factory( 'interval-dict', dataproviders.dataset.IntervalDataProvider.settings ) - def interval_map_dataprovider( self, dataset, **settings ): + def interval_dict_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.interval_dataprovider( dataset, **settings ) @@ -1206,8 +1206,8 @@ dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) return dataproviders.dataset.WiggleDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'wiggle-map', dataproviders.dataset.WiggleDataProvider.settings ) - def wiggle_map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'wiggle-dict', dataproviders.dataset.WiggleDataProvider.settings ) + def wiggle_dict_dataprovider( self, dataset, **settings ): dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) settings[ 'named_columns' ] = True return dataproviders.dataset.WiggleDataProvider( dataset_source, **settings ) diff -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 -r 3422736c168d6d864ec3c478d3e725b1184e3778 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -357,16 +357,16 @@ """Attempts to get column settings from dataset.metadata""" return dataproviders.dataset.DatasetColumnarDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) - def map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'dict', dataproviders.column.DictDataProvider.settings ) + def dict_dataprovider( self, dataset, **settings ): """Uses column settings that are passed in""" dataset_source = dataproviders.dataset.DatasetDataProvider( dataset ) - return dataproviders.column.MapDataProvider( dataset_source, **settings ) + return dataproviders.column.DictDataProvider( dataset_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) - def dataset_map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings ) + def dataset_dict_dataprovider( self, dataset, **settings ): """Attempts to get column settings from dataset.metadata""" - return dataproviders.dataset.DatasetMapDataProvider( dataset, **settings ) + return dataproviders.dataset.DatasetDictDataProvider( dataset, **settings ) class Taxonomy( Tabular ): @@ -522,15 +522,15 @@ settings[ 'comment_char' ] = '@' return super( Sam, self ).dataset_column_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'map', dataproviders.column.MapDataProvider.settings ) - def map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'dict', dataproviders.column.DictDataProvider.settings ) + def dict_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' - return super( Sam, self ).map_dataprovider( dataset, **settings ) + return super( Sam, self ).dict_dataprovider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'dataset-map', dataproviders.column.MapDataProvider.settings ) - def dataset_map_dataprovider( self, dataset, **settings ): + @dataproviders.decorators.dataprovider_factory( 'dataset-dict', dataproviders.column.DictDataProvider.settings ) + def dataset_dict_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' - return super( Sam, self ).dataset_map_dataprovider( dataset, **settings ) + return super( Sam, self ).dataset_dict_dataprovider( dataset, **settings ) @dataproviders.decorators.dataprovider_factory( 'header', dataproviders.line.RegexLineDataProvider.settings ) def header_dataprovider( self, dataset, **settings ): @@ -538,12 +538,12 @@ headers_source = dataproviders.line.RegexLineDataProvider( dataset_source, regex_list=[ '^@' ] ) return dataproviders.line.RegexLineDataProvider( headers_source, **settings ) - @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', map_dataprovider.settings ) + @dataproviders.decorators.dataprovider_factory( 'id-seq-qual', dict_dataprovider.settings ) def id_seq_qual_dataprovider( self, dataset, **settings ): - # provided as an example of a specified column map (w/o metadata) + # provided as an example of a specified column dict (w/o metadata) settings[ 'indeces' ] = [ 0, 9, 10 ] settings[ 'column_names' ] = [ 'id', 'seq', 'qual' ] - return self.map_dataprovider( dataset, **settings ) + return self.dict_dataprovider( dataset, **settings ) @dataproviders.decorators.dataprovider_factory( 'genomic-region', dataproviders.dataset.GenomicRegionDataProvider.settings ) @@ -551,9 +551,9 @@ settings[ 'comment_char' ] = '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2, 3, 3, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + @dataproviders.decorators.dataprovider_factory( 'genomic-region-dict', dataproviders.dataset.GenomicRegionDataProvider.settings ) - def genomic_region_map_dataprovider( self, dataset, **settings ): + def genomic_region_dict_dataprovider( self, dataset, **settings ): settings[ 'comment_char' ] = '@' return dataproviders.dataset.GenomicRegionDataProvider( dataset, 2, 3, 3, True, **settings ) @@ -628,9 +628,9 @@ def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + @dataproviders.decorators.dataprovider_factory( 'genomic-region-dict', dataproviders.dataset.GenomicRegionDataProvider.settings ) - def genomic_region_map_dataprovider( self, dataset, **settings ): + def genomic_region_dict_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) @@ -677,9 +677,9 @@ def genomic_region_dataprovider( self, dataset, **settings ): return dataproviders.dataset.GenomicRegionDataProvider( dataset, 0, 1, 1, **settings ) - @dataproviders.decorators.dataprovider_factory( 'genomic-region-map', + @dataproviders.decorators.dataprovider_factory( 'genomic-region-dict', dataproviders.dataset.GenomicRegionDataProvider.settings ) - def genomic_region_map_dataprovider( self, dataset, **settings ): + def genomic_region_dict_dataprovider( self, dataset, **settings ): settings[ 'named_columns' ] = True return self.genomic_region_dataprovider( dataset, **settings ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for discovering types to which a repository can be set.
by commits-noreply＠bitbucket.org 18 Jul '13

18 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/416e08c46ed6/ Changeset: 416e08c46ed6 User: greg Date: 2013-07-18 16:57:29 Summary: Fix for discovering types to which a repository can be set. Affected #: 2 files diff -r d95be6981cc9a862a458bebb218a5180319ecbd7 -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -164,7 +164,7 @@ return True if self.times_downloaded == 0: return True - if self.type == rt_util.DEFAULT: + if self.type == rt_util.UNRESTRICTED: return True return False diff -r d95be6981cc9a862a458bebb218a5180319ecbd7 -r 416e08c46ed6b03598581c5d6c6b44587aa9f170 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -155,7 +155,7 @@ message += "This repository currently contains a single file named <b>%s</b>. If additional files will " % suc.TOOL_DEPENDENCY_DEFINITION_FILENAME message += "not be added to this repository, then it's type should be set to <b>%s</b>.<br/>" % tool_dependency_definition_type_class.label else: - message += "This repository contains no tools, so these tool dependencies are considered orphans within this repository.<br/>" + message += "This repository contains no tools, so it's defined tool dependencies are considered orphans within this repository.<br/>" return message def get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ): 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: greg: Enhance messaging in the tool shed as a result of the introduction of support for repository types.
by commits-noreply＠bitbucket.org 18 Jul '13

18 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d95be6981cc9/ Changeset: d95be6981cc9 User: greg Date: 2013-07-18 16:51:23 Summary: Enhance messaging in the tool shed as a result of the introduction of support for repository types. Affected #: 7 files diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 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 @@ -2174,11 +2174,12 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) - # Handle messaging for orphan tool dependencies. - orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( metadata ) - if orphan_message: - message += orphan_message - status = 'warning' + if str( repository.type ) != rt_util.TOOL_DEPENDENCY_DEFINITION: + # Handle messaging for orphan tool dependencies. + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata ) + if orphan_message: + message += orphan_message + status = 'warning' if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -2976,11 +2977,6 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) - # Handle messaging for orphan tool dependencies. - orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( metadata ) - if orphan_message: - message += orphan_message - status = 'warning' else: metadata = None is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -206,15 +206,16 @@ metadata_dict = repository.metadata_revisions[0].metadata else: metadata_dict = {} - # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch - # or some other problem. Tool dependency definitions can define orphan tool dependencies (no relationship to any tools contained in the repository), - # so warning messages are important because orphans are always valid. The repository owner must be warned in case they did not intend to define an - # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition. - # Handle messaging for orphan tool dependencies. - orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( metadata_dict ) - if orphan_message: - message += orphan_message - status = 'warning' + if str( repository.type ) != rt_util.TOOL_DEPENDENCY_DEFINITION: + # Provide a warning message if a tool_dependencies.xml file is provided, but tool dependencies weren't loaded due to a requirement tag mismatch + # or some other problem. Tool dependency definitions can define orphan tool dependencies (no relationship to any tools contained in the repository), + # so warning messages are important because orphans are always valid. The repository owner must be warned in case they did not intend to define an + # orphan dependency, but simply provided incorrect information (tool shed, name owner, changeset_revision) for the definition. + # Handle messaging for orphan tool dependencies. + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata_dict ) + if orphan_message: + message += orphan_message + status = 'warning' # Handle messaging for invalid tool dependencies. invalid_tool_dependencies_message = tool_dependency_util.generate_message_for_invalid_tool_dependencies( metadata_dict ) if invalid_tool_dependencies_message: diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -171,7 +171,7 @@ def can_change_type_to( self, app, new_type_label ): if self.can_change_type( app ): new_type = app.repository_types_registry.get_class_by_label( new_type_label ) - if new_type.is_valid_for_type( self ): + if new_type.is_valid_for_type( app, self ): return True return False diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 lib/tool_shed/repository_types/metadata.py --- a/lib/tool_shed/repository_types/metadata.py +++ b/lib/tool_shed/repository_types/metadata.py @@ -18,7 +18,7 @@ repo = hg.repository( ui.ui(), repository.repo_path( app ) ) return repo.changelog - def is_valid_for_type( self, repository, revisions_to_check=None ): + def is_valid_for_type( self, app, repository, revisions_to_check=None ): raise "Unimplemented Method" diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -5,6 +5,7 @@ from galaxy import util from galaxy.model.orm import and_ import tool_shed.util.shed_util_common as suc +import tool_shed.repository_types.util as rt_util from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -115,7 +116,7 @@ message = '%s ' % str( error ) return message -def generate_message_for_orphan_tool_dependencies( metadata_dict ): +def generate_message_for_orphan_tool_dependencies( trans, repository, metadata_dict ): """ The introduction of the support for orphan tool dependency definitions in tool shed repositories has resulted in the inability to define an improperly configured tool dependency definition / tool config requirements tag combination as an invalid tool @@ -127,28 +128,34 @@ if metadata_dict: orphan_tool_dependencies = metadata_dict.get( 'orphan_tool_dependencies', None ) if orphan_tool_dependencies: - if 'tools' not in metadata_dict and 'invalid_tools' not in metadata_dict: + if 'tools' in metadata_dict or 'invalid_tools' in metadata_dict: + for td_key, requirements_dict in orphan_tool_dependencies.items(): + if td_key == 'set_environment': + # "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}] + message += "The settings for <b>name</b> and <b>type</b> from a contained tool configuration file's <b>requirement</b> tag " + message += "does not match the information for the following tool dependency definitions in the <b>tool_dependencies.xml</b> " + message += "file, so these tool dependencies have no relationship with any tools within this repository.<br/>" + for env_requirements_dict in requirements_dict: + name = env_requirements_dict[ 'name' ] + type = env_requirements_dict[ 'type' ] + message += "<b>* name:</b> %s, <b>type:</b> %s<br/>" % ( str( name ), str( type ) ) + else: + # "R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1"} + message += "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration file's " + message += "<b>requirement</b> tag does not match the information for the following tool dependency definitions in the " + message += "<b>tool_dependencies.xml</b> file, so these tool dependencies have no relationship with any tools within " + message += "this repository.<br/>" + name = requirements_dict[ 'name' ] + type = requirements_dict[ 'type' ] + version = requirements_dict[ 'version' ] + message += "<b>* name:</b> %s, <b>type:</b> %s, <b>version:</b> %s<br/>" % ( str( name ), str( type ), str( version ) ) + message += "<br/>" + elif repository.can_change_type_to( trans.app, rt_util.TOOL_DEPENDENCY_DEFINITION ): + tool_dependency_definition_type_class = trans.app.repository_types_registry.get_class_by_label( rt_util.TOOL_DEPENDENCY_DEFINITION ) + message += "This repository currently contains a single file named <b>%s</b>. If additional files will " % suc.TOOL_DEPENDENCY_DEFINITION_FILENAME + message += "not be added to this repository, then it's type should be set to <b>%s</b>.<br/>" % tool_dependency_definition_type_class.label + else: message += "This repository contains no tools, so these tool dependencies are considered orphans within this repository.<br/>" - for td_key, requirements_dict in orphan_tool_dependencies.items(): - if td_key == 'set_environment': - # "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}] - message += "The settings for <b>name</b> and <b>type</b> from a contained tool configuration file's <b>requirement</b> tag " - message += "does not match the information for the following tool dependency definitions in the <b>tool_dependencies.xml</b> " - message += "file, so these tool dependencies are considered orphans within this repository.<br/>" - for env_requirements_dict in requirements_dict: - name = env_requirements_dict[ 'name' ] - type = env_requirements_dict[ 'type' ] - message += "<b>* name:</b> %s, <b>type:</b> %s<br/>" % ( str( name ), str( type ) ) - else: - # "R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1"} - message += "The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool configuration file's " - message += "<b>requirement</b> tag does not match the information for the following tool dependency definitions in the " - message += "<b>tool_dependencies.xml</b> file, so these tool dependencies are considered orphans within this repository.<br/>" - name = requirements_dict[ 'name' ] - type = requirements_dict[ 'type' ] - version = requirements_dict[ 'version' ] - message += "<b>* name:</b> %s, <b>type:</b> %s, <b>version:</b> %s<br/>" % ( str( name ), str( type ), str( version ) ) - message += "<br/>" return message def get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ): diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 test/tool_shed/functional/test_0100_complex_repository_dependencies.py --- a/test/tool_shed/functional/test_0100_complex_repository_dependencies.py +++ b/test/tool_shed/functional/test_0100_complex_repository_dependencies.py @@ -51,7 +51,7 @@ uncompress_file=False, remove_repo_files_not_in_tar=False, commit_message='Uploaded tool_dependencies.xml.', - strings_displayed=[ 'The settings for <b>name</b>, <b>version</b> and <b>type</b> from a contained tool' ], + strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], strings_not_displayed=[] ) # Visit the manage repository page for package_bwa_0_5_9_0100. self.display_manage_repository_page( repository, strings_displayed=[ 'Tool dependencies', 'may not be', 'in this repository' ] ) diff -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 -r d95be6981cc9a862a458bebb218a5180319ecbd7 test/tool_shed/functional/test_0170_complex_prior_installation_required.py --- a/test/tool_shed/functional/test_0170_complex_prior_installation_required.py +++ b/test/tool_shed/functional/test_0170_complex_prior_installation_required.py @@ -56,7 +56,7 @@ uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded matplotlib tool dependency tarball.', - strings_displayed=['orphan'], + strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], strings_not_displayed=[] ) def test_0010_create_numpy_repository( self ): @@ -80,7 +80,7 @@ uncompress_file=True, remove_repo_files_not_in_tar=False, commit_message='Uploaded numpy tool dependency tarball.', - strings_displayed=['orphan'], + strings_displayed=[ 'This repository currently contains a single file named <b>tool_dependencies.xml</b>' ], strings_not_displayed=[] ) def test_0015_create_complex_repository_dependency( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True
by commits-noreply＠bitbucket.org 17 Jul '13

17 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3985ecec291f/ Changeset: 3985ecec291f User: carlfeberhard Date: 2013-07-18 00:46:42 Summary: Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True Affected #: 1 file diff -r e008f7f78892ceb35bd1198d9e56528616ddfddb -r 3985ecec291f3b1a52997f0ad4fb6579045f16c2 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -225,7 +225,13 @@ params = cur_filter_dict.copy() params['sort'] = sort_key params['async'] = ( 'async' in kwargs ) - trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + + #TODO:?? + # commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn + # is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True ) + # in mapping.py. If you change that to False, the log_action doesn't affect the query + # Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page + #trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) # Render grid. def url( *args, **kwargs ): @@ -260,7 +266,7 @@ # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid # results via a controller method, which is require substantial changes. Hence, for now, return grid # as str. - return trans.fill_template( iff( async_request, self.async_template, self.template ), + page = trans.fill_template( iff( async_request, self.async_template, self.template ), grid=self, query=query, cur_page_num = page_num, @@ -280,6 +286,9 @@ # Pass back kwargs so that grid template can set and use args without # grid explicitly having to pass them. kwargs=kwargs ) + trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + return page + def get_ids( self, **kwargs ): id = [] if 'id' in kwargs: 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: Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True
by commits-noreply＠bitbucket.org 17 Jul '13

17 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9ebd7732e616/ Changeset: 9ebd7732e616 Branch: stable User: carlfeberhard Date: 2013-07-18 00:42:46 Summary: Saved histories (and grids in gen.): fix busted query in grids when using log_actions=True Affected #: 1 file diff -r fd4113962c32b67ea0623b6cfd37be63e26ef7c6 -r 9ebd7732e616492f4570587496f1b9074cb2eac7 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -225,7 +225,13 @@ params = cur_filter_dict.copy() params['sort'] = sort_key params['async'] = ( 'async' in kwargs ) - trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + + #TODO:?? + # commenting this out; when this fn calls session.add( action ) and session.flush the query from this fn + # is effectively 'wiped' out. Nate believes it has something to do with our use of session( autocommit=True ) + # in mapping.py. If you change that to False, the log_action doesn't affect the query + # Below, I'm rendering the template first (that uses query), then calling log_action, then returning the page + #trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) # Render grid. def url( *args, **kwargs ): @@ -260,7 +266,7 @@ # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid # results via a controller method, which is require substantial changes. Hence, for now, return grid # as str. - return trans.fill_template( iff( async_request, self.async_template, self.template ), + page = trans.fill_template( iff( async_request, self.async_template, self.template ), grid=self, query=query, cur_page_num = page_num, @@ -280,6 +286,9 @@ # Pass back kwargs so that grid template can set and use args without # grid explicitly having to pass them. kwargs=kwargs ) + trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + return page + def get_ids( self, **kwargs ): id = [] if 'id' in kwargs: 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: Dataset display eye-icon, fix context menu
by commits-noreply＠bitbucket.org 17 Jul '13

17 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e008f7f78892/ Changeset: e008f7f78892 User: guerler Date: 2013-07-17 22:58:56 Summary: Dataset display eye-icon, fix context menu Affected #: 1 file diff -r ff21a344b9e14e0deb896bbe89a45c70ad608331 -r e008f7f78892ceb35bd1198d9e56528616ddfddb static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -237,7 +237,13 @@ } else { displayBtnData.title = _l( 'View data' ); - displayBtnData.href = "javascript:parent.frame_manager.frame_new({title: 'Data Viewer', type: 'url', location: 'center', content: '" + this.urls.display + "'});"; + + // default link for dataset + displayBtnData.href = this.urls.display; + + // add frame manager option onclick event + var self = this; + displayBtnData.on_click = function() { parent.frame_manager.frame_new({title: "Data Viewer", type: "url", location: "center", content: self.urls.display }); }; } this.displayButton = new IconButtonView({ model : new IconButton( displayBtnData ) }); 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: greg: Fixes when pushing changes to a repository in the tool shed from the command line: (a) only allow changes to a single file named tool_dependencies.xml to be pushed to a repository whose type is "Tool dependency definition" and (b) for any changes that are made to dependency definition files, validate the attributes of any <repository> tags, making sure that all required attributes (toolshed, name, owner, changeset_revision) are defined since automatically popula
by commits-noreply＠bitbucket.org 17 Jul '13

17 Jul '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff21a344b9e1/ Changeset: ff21a344b9e1 User: greg Date: 2013-07-17 21:34:54 Summary: Fixes when pushing changes to a repository in the tool shed from the command line: (a) only allow changes to a single file named tool_dependencies.xml to be pushed to a repository whose type is "Tool dependency definition" and (b) for any changes that are made to dependency definition files, validate the attributes of any <repository> tags, making sure that all required attributes (toolshed, name, owner, changeset_revision) are defined since automatically populating these attributes is supported only when using the tool shed's upload utility. Affected #: 2 files diff -r ef5cc1d272d2805d1c6597b200f9df58a291d863 -r ff21a344b9e14e0deb896bbe89a45c70ad608331 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -1,19 +1,28 @@ -""" -Middleware for handling hg authentication for users pushing change sets to local repositories. -""" -import os, logging +"""Middle-ware for handling hg authentication for users pushing change sets to local repositories.""" +import os +import logging import sqlalchemy +import sys +import tempfile from paste.auth.basic import AuthBasicAuthenticator from paste.httpheaders import AUTH_TYPE from paste.httpheaders import REMOTE_USER from galaxy.util import asbool +from galaxy.util import json from galaxy.webapps.tool_shed import model from galaxy.util.hash_util import new_secure_hash +import tool_shed.util.shed_util_common as suc +from tool_shed.util import commit_util +import tool_shed.repository_types.util as rt_util + +from galaxy import eggs +eggs.require( 'mercurial' ) import mercurial.__version__ log = logging.getLogger(__name__) +CHUNK_SIZE = 65536 class Hg( object ): @@ -23,10 +32,6 @@ self.config = config # Authenticate this mercurial request using basic authentication self.authentication = AuthBasicAuthenticator( 'hgweb in the tool shed', self.__basic_authentication ) - self.remote_address = None - self.repository = None - self.username = None - self.action = None # Determine the database url if 'database_connection' in self.config: self.db_url = self.config[ 'database_connection' ] @@ -42,26 +47,21 @@ # # Increment the value of the times_downloaded column in the repository table for the cloned repository. if 'PATH_INFO' in environ: - path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) - # An example of path_info is: '/repos/test/column1' - path_info_components = path_info.split( '/' ) - username = path_info_components[1] - name = path_info_components[2] # Instantiate a database connection engine = sqlalchemy.create_engine( self.db_url ) connection = engine.connect() - result_set = connection.execute( "select id from galaxy_user where username = '%s'" % username.lower() ) - for row in result_set: - # Should only be 1 row... - user_id = row[ 'id' ] - result_set = connection.execute( "select times_downloaded from repository where user_id = %d and name = '%s'" % ( user_id, name.lower() ) ) + path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) + user_id, repository_name = self.__get_user_id_repository_name_from_path_info( connection, path_info ) + sql_cmd = "SELECT times_downloaded FROM repository WHERE user_id = %d AND name = '%s'" % ( user_id, repository_name.lower() ) + result_set = connection.execute( sql_cmd ) for row in result_set: # Should only be 1 row... times_downloaded = row[ 'times_downloaded' ] times_downloaded += 1 - connection.execute( "update repository set times_downloaded = %d where user_id = %d and name = '%s'" % ( times_downloaded, user_id, name.lower() ) ) + sql_cmd = "UPDATE repository SET times_downloaded = %d WHERE user_id = %d AND name = '%s'" % ( times_downloaded, user_id, repository_name.lower() ) + connection.execute( sql_cmd ) connection.close() - if cmd in [ 'unbundle', 'pushkey' ]: + elif cmd in [ 'unbundle', 'pushkey' ]: # This is an hg push from the command line. When doing this, the following commands, in order, # will be retrieved from environ (see the docs at http://mercurial.selenic.com/wiki/WireProtocol): # # If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey -> listkeys @@ -87,6 +87,71 @@ # If all of these mechanisms fail, Mercurial will fail, printing an error message. In this case, it # will not let you commit until you set up a username. result = self.authentication( environ ) + if not isinstance( result, str ) and cmd == 'unbundle' and 'wsgi.input' in environ: + bundle_data_stream = environ[ 'wsgi.input' ] + # Convert the incoming mercurial bundle into a json object and persit it to a temporary file for inspection. + fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-hg-bundle" ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + while 1: + chunk = bundle_data_stream.read( CHUNK_SIZE ) + if not chunk: + break + fh.write( chunk ) + fh.close() + fh = open( tmp_filename, 'rb' ) + changeset_groups = json.from_json_string( commit_util.bundle_to_json( fh ) ) + fh.close() + try: + os.unlink( tmp_filename ) + except: + pass + if changeset_groups: + # Check the repository type to make sure inappropriate files are not being pushed. + if 'PATH_INFO' in environ: + # Instantiate a database connection + engine = sqlalchemy.create_engine( self.db_url ) + connection = engine.connect() + path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) + user_id, repository_name = self.__get_user_id_repository_name_from_path_info( connection, path_info ) + sql_cmd = "SELECT type FROM repository WHERE user_id = %d AND name = '%s'" % ( user_id, repository_name.lower() ) + result_set = connection.execute( sql_cmd ) + for row in result_set: + # Should only be 1 row... + repository_type = str( row[ 'type' ] ) + if repository_type == rt_util.TOOL_DEPENDENCY_DEFINITION: + # Handle repositories of type tool_dependency_definition, which can only contain a single file named tool_dependencies.xml. + for entry in changeset_groups: + if len( entry ) == 2: + # We possibly found an altered file entry. + filename, change_list = entry + if filename and isinstance( filename, str ): + if filename == suc.TOOL_DEPENDENCY_DEFINITION_FILENAME: + # Make sure the any complex repository dependency definitions contain valid <repository> tags. + is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + if not is_valid: + log.debug( error_msg ) + return self.__display_exception_remotely( start_response, error_msg ) + else: + msg = "Only a single file named tool_dependencies.xml can be pushed to a repository of type 'Tool dependency definition'." + log.debug( msg ) + return self.__display_exception_remotely( start_response, msg ) + else: + # If the changeset includes changes to dependency definition files, make sure tag sets are not missing "toolshed" or + # "changeset_revision" attributes since automatically populating them is not supported when pushing from the command line. + # These attributes are automatically populated only when using the tool shed upload utility. + for entry in changeset_groups: + if len( entry ) == 2: + # We possibly found an altered file entry. + filename, change_list = entry + if filename and isinstance( filename, str ): + if filename in [ suc.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, suc.TOOL_DEPENDENCY_DEFINITION_FILENAME ]: + # We check both files since tool dependency definitions files can contain complex repository dependency definitions. + is_valid, error_msg = commit_util.repository_tags_are_valid( filename, change_list ) + if not is_valid: + log.debug( error_msg ) + return self.__display_exception_remotely( start_response, error_msg ) if isinstance( result, str ): # Authentication was successful AUTH_TYPE.update( environ, 'basic' ) @@ -95,6 +160,13 @@ return result.wsgi_application( environ, start_response ) return self.app( environ, start_response ) + def __display_exception_remotely( self, start_response, msg ): + # Display the exception to the remote user's command line. + status = "500 %s" % msg + response_headers = [ ("content-type", "text/plain") ] + start_response( status, response_headers, sys.exc_info() ) + return [ msg ] + def __get_hg_command( self, **kwd ): """Pulls mercurial commands from environ[ 'QUERY_STRING" ] and returns them.""" if 'QUERY_STRING' in kwd: @@ -103,6 +175,18 @@ return qry.split( '=' )[ -1 ] return None + def __get_user_id_repository_name_from_path_info( self, db_connection, path_info ): + # An example of path_info is: '/repos/test/column1' + path_info_components = path_info.split( '/' ) + username = path_info_components[ 1 ] + repository_name = path_info_components[ 2 ] + # Get the id of the current user using hg from the command line. + result_set = db_connection.execute( "select id from galaxy_user where username = '%s'" % username.lower() ) + for row in result_set: + # Should only be 1 row... + user_id = row[ 'id' ] + return user_id, repository_name + def __basic_authentication( self, environ, username, password ): """The environ parameter is needed in basic authentication. We also check it if use_remote_user is true.""" if asbool( self.config.get( 'use_remote_user', False ) ): @@ -140,7 +224,7 @@ result_set = connection.execute( "select email, username, password from galaxy_user where email = '%s'" % ru_email ) for row in result_set: # Should only be 1 row... - db_email = row[ 'email' ] + db_email = row[ 'email' ] db_password = row[ 'password' ] db_username = row[ 'username' ] connection.close() diff -r ef5cc1d272d2805d1c6597b200f9df58a291d863 -r ff21a344b9e14e0deb896bbe89a45c70ad608331 lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -1,7 +1,9 @@ +import cStringIO import logging import os import pkg_resources import shutil +import struct import tempfile from galaxy import util from galaxy.datatypes import checkers @@ -10,19 +12,29 @@ import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_util from tool_shed.util import xml_util -from galaxy import eggs import tool_shed.repository_types.util as rt_util +from galaxy import eggs eggs.require( 'mercurial' ) from mercurial import commands from mercurial import hg from mercurial import ui +from mercurial.changegroup import readbundle +from mercurial.changegroup import readexactly +from mercurial.changegroup import writebundle log = logging.getLogger( __name__ ) UNDESIRABLE_DIRS = [ '.hg', '.svn', '.git', '.cvs' ] UNDESIRABLE_FILES = [ '.hg_archival.txt', 'hgrc', '.DS_Store' ] +def bundle_to_json( fh ): + """Convert the received HG10xx data stream (a mercurial 1.0 bundle created using hg push from the command line) to a json object.""" + # See http://www.wstein.org/home/wstein/www/home/was/patches/hg_json + hg_unbundle10_obj = readbundle( fh, None ) + groups = [ group for group in unpack_groups( hg_unbundle10_obj ) ] + return json.to_json_string( groups, indent=4 ) + def check_archive( repository, archive ): for member in archive.getmembers(): # Allow regular files and directories only @@ -63,6 +75,23 @@ message = 'The file "%s" contains image content.\n' % str( file_path ) return message +def get_change_lines_in_file_for_tag( tag, change_dict ): + """ + The received change_dict is the jsonified version of the changes to a file in a changeset being pushed to the tool shed from the command line. + This method cleans and returns appropriate lines for inspection. + """ + cleaned_lines = [] + data_list = change_dict.get( 'data', [] ) + for data_dict in data_list: + block = data_dict.get( 'block', '' ) + lines = block.split( '\\n' ) + for line in lines: + index = line.find( tag ) + if index > -1: + line = line[ index: ] + cleaned_lines.append( line ) + return cleaned_lines + def get_upload_point( repository, **kwd ): upload_point = kwd.get( 'upload_point', None ) if upload_point is not None: @@ -149,8 +178,8 @@ except OSError, e: # The directory is not empty. pass - # See if any admin users have chosen to receive email alerts when a repository is - # updated. If so, check every uploaded file to ensure content is appropriate. + # See if any admin users have chosen to receive email alerts when a repository is updated. If so, check every uploaded file to ensure + # content is appropriate. check_contents = check_file_contents_for_email_alerts( trans ) for filename_in_archive in filenames_in_archive: # Check file content to ensure it is appropriate. @@ -307,6 +336,39 @@ return altered, root return False, None +def repository_tag_is_valid( filename, line ): + """ + Checks changes made to <repository> tags in a dependency definition file being pushed to the tool shed from the command line to ensure that + all required attributes exist. + """ + required_attributes = [ 'toolshed', 'name', 'owner', 'changeset_revision' ] + defined_attributes = line.split() + for required_attribute in required_attributes: + defined = False + for defined_attribute in defined_attributes: + if defined_attribute.startswith( required_attribute ): + defined = True + break + if not defined: + error_msg = 'The %s file contains a <repository> tag that is missing the required attribute %s. ' % ( filename, required_attribute ) + error_msg += 'Automatically populating dependency definition attributes occurs only when using the tool shed upload utility. ' + return False, error_msg + return True, '' + +def repository_tags_are_valid( filename, change_list ): + """ + Make sure the any complex repository dependency definitions contain valid <repository> tags when pushing changes to the tool shed on the command + line. + """ + tag = '<repository' + for change_dict in change_list: + lines = get_change_lines_in_file_for_tag( tag, change_dict ) + for line in lines: + is_valid, error_msg = repository_tag_is_valid( filename, line ) + if not is_valid: + return False, error_msg + return True, '' + def uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: handle_gzip( repository, uploaded_file_name ) @@ -314,3 +376,60 @@ if isbz2: handle_bz2( repository, uploaded_file_name ) return uploaded_file_filename.rstrip( '.bz2' ) + +def unpack_chunks( hg_unbundle10_obj ): + """ + This method provides a generator of parsed chunks of a "group" in a mercurial unbundle10 object which is created when a changeset that is pushed + to a tool shed repository using hg push from the command line is read using readbundle. + """ + while True: + length, = struct.unpack( '>l', readexactly( hg_unbundle10_obj, 4 ) ) + if length <= 4: + # We found a "null chunk", which ends the group. + break + if length < 84: + raise Exception( "negative data length" ) + node, p1, p2, cs = struct.unpack( '20s20s20s20s', readexactly( hg_unbundle10_obj, 80 ) ) + yield { 'node': node.encode( 'hex' ), + 'p1': p1.encode( 'hex' ), + 'p2': p2.encode( 'hex' ), + 'cs': cs.encode( 'hex' ), + 'data': [ patch for patch in unpack_patches( hg_unbundle10_obj, length - 84 ) ] } + +def unpack_groups( hg_unbundle10_obj ): + """ + This method provides a generator of parsed groups from a mercurial unbundle10 object which is created when a changeset that is pushed + to a tool shed repository using hg push from the command line is read using readbundle. + """ + # Process the changelog group. + yield [ chunk for chunk in unpack_chunks( hg_unbundle10_obj ) ] + # Process the manifest group. + yield [ chunk for chunk in unpack_chunks( hg_unbundle10_obj ) ] + while True: + length, = struct.unpack( '>l', readexactly( hg_unbundle10_obj, 4 ) ) + if length <= 4: + # We found a "null meta chunk", which ends the changegroup. + break + filename = readexactly( hg_unbundle10_obj, length-4 ).encode( 'string_escape' ) + # Process the file group. + yield ( filename, [ chunk for chunk in unpack_chunks( hg_unbundle10_obj ) ] ) + +def unpack_patches( hg_unbundle10_obj, remaining ): + """ + This method provides a generator of patches from the data field in a chunk. As there is no delimiter for this data field, a length argument is + required. + """ + while remaining >= 12: + start, end, blocklen = struct.unpack( '>lll', readexactly( hg_unbundle10_obj, 12 ) ) + remaining -= 12 + if blocklen > remaining: + raise Exception( "unexpected end of patch stream" ) + block = readexactly( hg_unbundle10_obj, blocklen ) + remaining -= blocklen + yield { 'start': start, + 'end': end, + 'blocklen': blocklen, + 'block': block.encode( 'string_escape' ) } + if remaining > 0: + print remaining + raise Exception( "unexpected end of patch stream" ) 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 July 2013