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commit/galaxy-central: inithello: Added tool_sheds_conf.xml.sample to buildbot_setup.sh.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81527d3d8962/ changeset: 81527d3d8962 user: inithello date: 2013-02-27 21:45:43 summary: Added tool_sheds_conf.xml.sample to buildbot_setup.sh. affected #: 1 file diff -r 22aaf90bc420bb93862c08c8f24549e76d701b7d -r 81527d3d8962f3d5f5804fa1457f4e7a782c7136 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -68,6 +68,7 @@ datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample +tool_sheds_conf.xml.sample shed_tool_data_table_conf.xml.sample migrated_tools_conf.xml.sample data_manager_conf.xml.sample 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: 5 new changesets
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f46c9a707af8/ changeset: f46c9a707af8 user: jmchilton date: 2013-02-23 21:09:53 summary: Implement macro mechanism for tool config XML. This should allow for a drastic reduction in 'code' duplication across XML files in a tool repository or inside of an XML file (repeated blocks in different when statements for instance). affected #: 1 file diff -r fa34924860aaa282fe3c3021a257f2523848a6e6 -r f46c9a707af8ae9256b762cf7ef26c38da69c3a2 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -17,6 +17,7 @@ from galaxy.util.template import fill_template from galaxy import util, jobs, model from galaxy.jobs import ParallelismInfo +from copy import deepcopy from elementtree import ElementTree from parameters import * from parameters.grouping import * @@ -520,7 +521,7 @@ def load_tool( self, config_file, guid=None, **kwds ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element - tree = util.parse_xml( config_file ) + tree = self._load_and_preprocess_tool_xml( config_file ) root = tree.getroot() # Allow specifying a different tool subclass to instantiate if root.find( "type" ) is not None: @@ -704,7 +705,86 @@ rval = tools return rval - + + def _load_and_preprocess_tool_xml(self, config_file): + tree = util.parse_xml(config_file) + root = tree.getroot() + macros_el = root.find('macros') + if not macros_el: + return tree + tool_dir = os.path.dirname(config_file) + macros = self._load_macros(macros_el, tool_dir) + # HACK for elementtree, newer implementations (etree/lxml) won't + # require this parent_map data structure but elementtree does not + # track parents or recongnize .find('..'). + parent_map = dict((c, p) for p in tree.getiterator() for c in p) + for expand_el in root.findall('.//expand'): + macro_name = expand_el.get('macro') + macro_def = macros[macro_name] + self._xml_replace(expand_el, macro_def, parent_map) + return tree + + def _load_macros(self, macros_el, tool_dir): + macros = {} + # Import macros from external files. + macros.update(self._load_imported_macros(macros_el, tool_dir)) + # Load all directly defined macros. + macros.update(self._load_embedded_macros(macros_el, tool_dir)) + return macros + + def _load_embedded_macros(self, macros_el, tool_dir): + macros = {} + + macro_els = [] + if macros_el: + macro_els = macros_el.findall("macro") + for macro in macro_els: + macro_name = macro.get("name") + macros[macro_name] = self._load_macro_def(macro) + + return macros + + def _load_imported_macros(self, macros_el, tool_dir): + macros = {} + + macro_import_els = [] + if macros_el: + macro_import_els = macros_el.findall("import") + for macro_import_el in macro_import_els: + raw_import_path = macro_import_el.text + tool_relative_import_path = \ + os.path.basename(raw_import_path) # Sanitize this + import_path = \ + os.path.join(tool_dir, tool_relative_import_path) + file_macros = self._load_macro_file(import_path, tool_dir) + macros.update(file_macros) + + return macros + + def _load_macro_file(self, path, tool_dir): + tree = util.parse_xml(path) + root = tree.getroot() + return self._load_macros(root, tool_dir) + + def _load_macro_def(self, macro): + return list(macro.getchildren()) + + def _xml_replace(self, query, targets, parent_map): + #parent_el = query.find('..') ## Something like this would be better with newer xml library + parent_el = parent_map[query] + matching_index = -1 + #for index, el in enumerate(parent_el.iter('.')): ## Something like this for newer implementation + for index, el in enumerate(parent_el.getchildren()): + if el == query: + matching_index = index + break + assert matching_index >= 0 + current_index = matching_index + for target in targets: + current_index += 1 + parent_el.insert(current_index, deepcopy(target)) + parent_el.remove(query) + class ToolSection( object ): """ A group of tools with similar type/purpose that will be displayed as a https://bitbucket.org/galaxy/galaxy-central/commits/7ae831ebb4aa/ changeset: 7ae831ebb4aa user: jmchilton date: 2013-02-23 21:09:53 summary: Extend tool config macro engine so that macros may be rendered inside other macros. affected #: 1 file diff -r f46c9a707af8ae9256b762cf7ef26c38da69c3a2 -r 7ae831ebb4aad4989cbf6ecba0e8128413a28403 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -714,16 +714,24 @@ return tree tool_dir = os.path.dirname(config_file) macros = self._load_macros(macros_el, tool_dir) - # HACK for elementtree, newer implementations (etree/lxml) won't - # require this parent_map data structure but elementtree does not - # track parents or recongnize .find('..'). - parent_map = dict((c, p) for p in tree.getiterator() for c in p) - for expand_el in root.findall('.//expand'): - macro_name = expand_el.get('macro') - macro_def = macros[macro_name] - self._xml_replace(expand_el, macro_def, parent_map) + + self._expand_macros([root], macros) return tree + def _expand_macros(self, elements, macros): + for element in elements: + # HACK for elementtree, newer implementations (etree/lxml) won't + # require this parent_map data structure but elementtree does not + # track parents or recongnize .find('..'). + parent_map = dict((c, p) for p in element.getiterator() for c in p) + for expand_el in element.findall('.//expand'): + macro_name = expand_el.get('macro') + macro_def = macros[macro_name] + + # Recursively expand contained macros. + self._expand_macros(macro_def, macros) + self._xml_replace(expand_el, macro_def, parent_map) + def _load_macros(self, macros_el, tool_dir): macros = {} # Import macros from external files. @@ -785,6 +793,7 @@ parent_el.insert(current_index, deepcopy(target)) parent_el.remove(query) + class ToolSection( object ): """ A group of tools with similar type/purpose that will be displayed as a https://bitbucket.org/galaxy/galaxy-central/commits/0d78c9da2cc8/ changeset: 0d78c9da2cc8 user: jmchilton date: 2013-02-23 21:09:53 summary: Add ability to pass sub-blocks of XML to macros and corresponding ability to render those (via the new <yield /> tag) from macros. affected #: 1 file diff -r 7ae831ebb4aad4989cbf6ecba0e8128413a28403 -r 0d78c9da2cc82c25f919f1850be39774b46fbb57 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -726,7 +726,16 @@ parent_map = dict((c, p) for p in element.getiterator() for c in p) for expand_el in element.findall('.//expand'): macro_name = expand_el.get('macro') - macro_def = macros[macro_name] + macro_def = deepcopy(macros[macro_name]) # deepcopy needed? + + yield_els = [yield_el for macro_def_el in macro_def for yield_el in macro_def_el.findall('.//yield')] + + expand_el_children = expand_el.getchildren() + macro_def_parent_map = \ + dict((c, p) for macro_def_el in macro_def for p in macro_def_el.getiterator() for c in p) + + for yield_el in yield_els: + self._xml_replace(yield_el, expand_el_children, macro_def_parent_map) # Recursively expand contained macros. self._expand_macros(macro_def, macros) https://bitbucket.org/galaxy/galaxy-central/commits/f522eea2d4c1/ changeset: f522eea2d4c1 user: jmchilton date: 2013-02-23 21:09:53 summary: Rework some duplication out tophat wrappers using macros. This dmeonstrates how macros can reduce duplication inside a file (e.g. the dbKeyActions macro) and between files (e.g. the own_junctionsConditional macro). affected #: 4 files diff -r 0d78c9da2cc82c25f919f1850be39774b46fbb57 -r f522eea2d4c19d7c7c24209afc1a4dee5bd71aa3 tools/ngs_rna/tophat2_wrapper.xml --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -143,23 +143,12 @@ </param></when></conditional> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-in genomes were created using default options"> - <option value="indexed" selected="True">Use a built-in genome</option> - <option value="history">Use a genome from history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="tophat2_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No genomes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> - </when> - </conditional> + <expand macro="refGenomeSourceConditional"> + <options from_data_table="tophat2_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No genomes are available for the selected input dataset"/> + </options> + </expand><conditional name="params"><param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."><option value="preSet">Use Defaults</option> @@ -182,17 +171,7 @@ <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> - <conditional name="indel_search"> - <param name="allow_indel_search" type="select" label="Allow indel search"> - <option value="Yes">Yes</option> - <option value="No">No</option> - </param> - <when value="No"/> - <when value="Yes"> - <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> - <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> - </when> - </conditional> + <expand macro="indel_searchConditional" /> alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -201,40 +180,7 @@ <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> - <conditional name="own_junctions"> - <param name="use_junctions" type="select" label="Use Own Junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="Yes"> - <conditional name="gene_model_ann"> - <param name="use_annotations" type="select" label="Use Gene Annotation Model"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No" /> - <when value="Yes"> - <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> - </when> - </conditional> - <conditional name="raw_juncs"> - <param name="use_juncs" type="select" label="Use Raw Junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No" /> - <when value="Yes"> - <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> - </when> - </conditional> - <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - </when> - <when value="No" /> - </conditional> - + <expand macro="own_junctionsConditional" /><conditional name="coverage_search"><param name="use_search" type="select" label="Use Coverage Search" help="Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity."> @@ -319,83 +265,40 @@ <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data><data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data></outputs> - + <macros> + <import>tophat_macros.xml</import> + <macro name="dbKeyActions"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat2_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </macro> + </macros><tests><test> diff -r 0d78c9da2cc82c25f919f1850be39774b46fbb57 -r f522eea2d4c19d7c7c24209afc1a4dee5bd71aa3 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -154,23 +154,12 @@ </command><inputs><param format="fastqcssanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Color-space: Must have Sanger-scaled quality values with ASCII offset 33" /> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="tophat_indexes_color"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> - </when> - </conditional> + <expand macro="refGenomeSourceConditional"> + <options from_data_table="tophat_indexes_color"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available for the selected input dataset"/> + </options> + </expand><conditional name="singlePaired"><param name="sPaired" type="select" label="Is this library mate-paired?"><option value="single">Single-end</option> @@ -194,17 +183,7 @@ <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> - <conditional name="indel_search"> - <param name="allow_indel_search" type="select" label="Allow indel search"> - <option value="Yes">Yes</option> - <option value="No">No</option> - </param> - <when value="No"/> - <when value="Yes"> - <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> - <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> - </when> - </conditional> + <expand macro="indel_searchConditional" /><param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -230,20 +209,8 @@ <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/></when></conditional> - <conditional name="raw_juncs"> - <param name="use_juncs" type="select" label="Use Raw Junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No" /> - <when value="Yes"> - <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> - </when> - </conditional> - <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> + <expand macro="raw_juncsConditional" /> + <expand macro="no_novel_juncsParam" /></when><when value="No" /></conditional> @@ -301,17 +268,7 @@ <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> - <conditional name="indel_search"> - <param name="allow_indel_search" type="select" label="Allow indel search"> - <option value="Yes">Yes</option> - <option value="No">No</option> - </param> - <when value="No"/> - <when value="Yes"> - <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> - <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> - </when> - </conditional> + <expand macro="indel_searchConditional" /><param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /><param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> @@ -399,90 +356,50 @@ ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) ) </filter> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> - <filter> + <expand macro="dbKeyActions" /> + </data> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"> + <expand macro="dbKeyActions" /> + </data> + <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"> + <expand macro="dbKeyActions" /> + </data> + </outputs> + <macros> + <import>tophat_macros.xml</import> + <macro name="bedFilter"> + <filter> ( ( ( 'sParams' in singlePaired ) and ( 'indel_search' in singlePaired['sParams'] ) and ( singlePaired['sParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) or ( ( 'pParams' in singlePaired ) and ( 'indel_search' in singlePaired['pParams'] ) and ( singlePaired['pParams']['indel_search']['allow_indel_search'] == 'Yes' ) ) ) - </filter> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> - </data> - </outputs> + </filter> + </macro> + <macro name="dbKeyActions"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat_indexes_color" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </macro> + </macros><tests><test> diff -r 0d78c9da2cc82c25f919f1850be39774b46fbb57 -r f522eea2d4c19d7c7c24209afc1a4dee5bd71aa3 tools/ngs_rna/tophat_macros.xml --- /dev/null +++ b/tools/ngs_rna/tophat_macros.xml @@ -0,0 +1,72 @@ +<macros> + <macro name="refGenomeSourceConditional"> + <conditional name="refGenomeSource"> + <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options"> + <option value="indexed" selected="True">Use a built-in genome</option> + <option value="history">Use a genome from history</option> + </param> + <when value="indexed"> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <yield /> + </param> + </when> + <when value="history"> + <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> + </when> + </conditional> + </macro> + <macro name="indel_searchConditional"> + <conditional name="indel_search"> + <param name="allow_indel_search" type="select" label="Allow indel search"> + <option value="Yes">Yes</option> + <option value="No">No</option> + </param> + <when value="No"/> + <when value="Yes"> + <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> + <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> + </when> + </conditional> + </macro> + <macro name="own_junctionsConditional"> + <conditional name="own_junctions"> + <param name="use_junctions" type="select" label="Use Own Junctions"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <conditional name="gene_model_ann"> + <param name="use_annotations" type="select" label="Use Gene Annotation Model"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No" /> + <when value="Yes"> + <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> + </when> + </conditional> + <expand macro="raw_juncsConditional" /> + <expand macro="no_novel_juncsParam" /> + </when> + <when value="No" /> + </conditional> + </macro> + <macro name="raw_juncsConditional"> + <conditional name="raw_juncs"> + <param name="use_juncs" type="select" label="Use Raw Junctions"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No" /> + <when value="Yes"> + <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> + </when> + </conditional> + </macro> + <macro name="no_novel_juncsParam"> + <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </macro> +</macros> diff -r 0d78c9da2cc82c25f919f1850be39774b46fbb57 -r f522eea2d4c19d7c7c24209afc1a4dee5bd71aa3 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -151,23 +151,12 @@ </command><inputs><param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" /> - <conditional name="refGenomeSource"> - <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options"> - <option value="indexed" selected="True">Use a built-in genome</option> - <option value="history">Use a genome from history</option> - </param> - <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_data_table="tophat_indexes"> - <filter type="sort_by" column="2"/> - <validator type="no_options" message="No genomes are available for the selected input dataset"/> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> - </when> - </conditional> + <expand macro="refGenomeSourceConditional"> + <options from_data_table="tophat_indexes"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No genomes are available for the selected input dataset"/> + </options> + </expand><conditional name="singlePaired"><param name="sPaired" type="select" label="Is this library mate-paired?"><option value="single">Single-end</option> @@ -298,17 +287,7 @@ <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /><param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /><param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> - <conditional name="indel_search"> - <param name="allow_indel_search" type="select" label="Allow indel search"> - <option value="Yes">Yes</option> - <option value="No">No</option> - </param> - <when value="No"/> - <when value="Yes"> - <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." /> - <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." /> - </when> - </conditional> + <expand macro="indel_searchConditional" /><param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" /><param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /><param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> @@ -316,40 +295,7 @@ <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /><param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> - <conditional name="own_junctions"> - <param name="use_junctions" type="select" label="Use Own Junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="Yes"> - <conditional name="gene_model_ann"> - <param name="use_annotations" type="select" label="Use Gene Annotation Model"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No" /> - <when value="Yes"> - <param format="gtf" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/> - </when> - </conditional> - <conditional name="raw_juncs"> - <param name="use_juncs" type="select" label="Use Raw Junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - <when value="No" /> - <when value="Yes"> - <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/> - </when> - </conditional> - <param name="no_novel_juncs" type="select" label="Only look for supplied junctions"> - <option value="No">No</option> - <option value="Yes">Yes</option> - </param> - </when> - <when value="No" /> - </conditional> - + <expand macro="own_junctionsConditional" /><conditional name="closure_search"><param name="use_search" type="select" label="Use Closure Search"> @@ -387,83 +333,40 @@ <outputs><data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data><data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam"> - <actions> - <conditional name="refGenomeSource.genomeSource"> - <when value="indexed"> - <action type="metadata" name="dbkey"> - <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> - <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> - <filter type="param_value" ref="refGenomeSource.index" column="0"/> - </option> - </action> - </when> - <when value="history"> - <action type="metadata" name="dbkey"> - <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> - </action> - </when> - </conditional> - </actions> + <expand macro="dbKeyActions" /></data></outputs> - + <macros> + <import>tophat_macros.xml</import> + <macro name="dbKeyActions"> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="tophat_indexes" column="1" offset="0"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="refGenomeSource.index" column="0"/> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </macro> + </macros><tests><test> https://bitbucket.org/galaxy/galaxy-central/commits/22aaf90bc420/ changeset: 22aaf90bc420 user: jgoecks date: 2013-02-27 21:21:30 summary: Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #129) Implement Macro Engine to Reduce Tool Config XML Duplication affected #: 5 files Diff not available. 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: inithello: Enhance twill automated repository installation framework to get a list of repositories from the tool shed API, install, run functional tests defined in the tools' XML, and report success or failure back to the tool shed.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d87d7c61912/ changeset: 9d87d7c61912 user: inithello date: 2013-02-27 20:28:12 summary: Enhance twill automated repository installation framework to get a list of repositories from the tool shed API, install, run functional tests defined in the tools' XML, and report success or failure back to the tool shed. affected #: 3 files diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -55,7 +55,7 @@ name = repository_info_dict[ 'name' ] owner = repository_info_dict[ 'owner' ] changeset_revision = repository_info_dict[ 'changeset_revision' ] - encoded_repository_id = repository_info_dict[ 'encoded_repository_id' ] + encoded_repository_id = repository_info_dict[ 'repository_id' ] tool_shed_url = repository_info_dict[ 'tool_shed_url' ] preview_params = urllib.urlencode( dict( repository_id=encoded_repository_id, changeset_revision=changeset_revision ) ) self.visit_url( '%s/repository/preview_tools_in_changeset?%s' % ( tool_shed_url, preview_params ) ) diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -3,7 +3,7 @@ from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository log = logging.getLogger(__name__) -class TestInstallRepositories( InstallTestRepository ): +class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" def do_installation( self, repository_info_dict ): self.logout() @@ -35,11 +35,11 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestInstallRepository_" + repository_dict[ 'name' ] - baseclasses = ( TestInstallRepositories, ) + baseclasses = ( InstallTestRepositories, ) namespace = dict() def make_install_method( repository_dict ): def test_install_repository( self ): @@ -61,11 +61,11 @@ G = globals() # Eliminate all previous tests from G. for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ): + if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestUninstallRepository_' ) or key.startswith( 'TestForTool_' ): del G[ key ] # Create a new subclass with a method named install_repository_XXX that installs the repository specified by the provided dict. name = "TestUninstallRepository_" + repository_dict[ 'name' ] - baseclasses = ( TestInstallRepositories, ) + baseclasses = ( InstallTestRepositories, ) namespace = dict() def make_uninstall_method( repository_dict ): def test_install_repository( self ): diff -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 -r 9d87d7c6191284aaf48ade4462256131c0345c8d test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -4,7 +4,7 @@ # order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh # will execute this script with the appropriate parameters. -import os, sys, shutil, tempfile, re, string +import os, sys, shutil, tempfile, re, string, urllib # Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() @@ -19,7 +19,7 @@ default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ) ] +new_path = [ os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ), os.path.join( cwd, 'scripts', 'api' ) ] new_path.extend( sys.path ) sys.path = new_path @@ -48,6 +48,7 @@ from galaxy.app import UniverseApplication from galaxy.web import buildapp from galaxy.util import parse_xml +from galaxy.util.json import from_json_string, to_json_string import nose.core import nose.config @@ -56,6 +57,8 @@ from base.util import parse_tool_panel_config +from common import update + log = logging.getLogger( 'install_and_test_repositories' ) default_galaxy_test_port_min = 10000 @@ -95,7 +98,10 @@ ''' # Define a default location to find the list of repositories to check. -galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_FILE', 'repository_list.json' ) +galaxy_repository_list = os.environ.get( 'GALAXY_INSTALL_TEST_REPOSITORY_LIST_LOCATIOM', 'repository_list.json' ) +galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', 'http://toolshed.local:10001' ) +tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) +assert tool_shed_api_key is not None, 'Unable to proceed without API key.' if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: galaxy_encode_secret = 'changethisinproductiontoo' @@ -103,7 +109,28 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] -def get_repositories_to_install( format='json' ): +def get_api_url( base, parts=[], params=None, key=None ): + if 'api' in parts and parts.index( 'api' ) != 0: + parts.pop( parts.index( 'api' ) ) + parts.insert( 0, 'api' ) + elif 'api' not in parts: + parts.insert( 0, 'api' ) + url = '%s/%s' % ( base, '/'.join( parts ) ) + if key: + url += '?%s' % urllib.urlencode( dict( key=key ) ) + else: + url += '?%s' % urllib.urlencode( dict( key=tool_shed_api_key ) ) + if params: + url += '&%s' % params + return url + +def get_repository_info_from_api( url, repository_info_dict ): + parts = [ 'api', 'repositories', repository_info_dict[ 'repository_id' ] ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict = json_from_url( api_url ) + return extended_dict + +def get_repositories_to_install( location, source='file', format='json' ): ''' Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: [ @@ -118,11 +145,34 @@ ] NOTE: If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. ''' + if source == 'file': + listing = file( location, 'r' ).read() + elif source == 'url': + assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.' + params = urllib.urlencode( dict( downloadable='true' ) ) + api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params ) + if format == 'json': + return json_from_url( api_url ) + else: + raise AssertionError( 'Do not know how to handle source type %s.' % source ) if format == 'json': - return simplejson.loads( file( galaxy_repository_list, 'r' ).read() ) + return from_json_string( listing ) else: raise AssertonError( 'Unknown format %s.' % format ) +def json_from_url( url ): + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + return from_json_string( url_contents ) + +def register_test_failure( url, metadata_id, test_errors ): + params = dict( tools_functionally_correct='false', do_not_test='true', tool_test_errors=test_errors ) + return update( tool_shed_api_key, '%s/api/%s' % ( galaxy_tool_shed_url, '/'.join( [ 'repository_revisions', metadata_id ] ) ), params ) + +def register_test_success( url, metadata_id ): + params = dict( tools_functionally_correct='true', do_not_test='false' ) + return update( tool_shed_api_key, '%s/api/%s' % ( galaxy_tool_shed_url, '/'.join( [ 'repository_revisions', metadata_id ] ) ), params ) + def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config ) plug_loader = test_config.plugins.prepareTestLoader( loader ) @@ -162,6 +212,7 @@ galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) else: @@ -302,8 +353,13 @@ log.info( "Tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) success = False try: + repository_status = [] # Iterate through a list of repository info dicts. - for repository_dict in get_repositories_to_install(): + for repository_dict in get_repositories_to_install( galaxy_tool_shed_url, source='url' ): + metadata_revision_id = repository_dict[ 'id' ] + repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + repository_info = get_repository_info_from_api( galaxy_tool_shed_url, repository_dict ) + repository_dict = dict( repository_info.items() + repository_dict.items() ) # Generate the method that will install this repository into the running Galaxy instance. test_install_repositories.generate_install_method( repository_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host @@ -319,9 +375,12 @@ if success: log.debug( 'Installation of %s succeeded, running any defined functional tests.' % repository_dict[ 'name' ] ) # Parse the tool panel config to get the test-data path for this repository. - shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, {} ) + if not os.path.exists( galaxy_shed_tools_dict ): + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) + shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + log.debug( shed_tools_dict ) # Write this to a file, so the functional test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( simplejson.dumps( shed_tools_dict ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) # Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework. os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host @@ -337,10 +396,52 @@ # Run the configured tests. result = run_tests( test_config ) success = result.wasSuccessful() + repository_dict[ 'functional_tests_passed' ] = success if success: + register_test_success( galaxy_tool_shed_url, metadata_revision_id ) log.debug( 'Repository %s installed and passed functional tests.' % repository_dict[ 'name' ] ) else: + # If the functional tests fail, log the output and submit it to the tool shed whence the repository was installed. + repository_dict[ 'tool_test_errors' ] = [] + for failure in result.failures: + label = str( failure[0] ) + log_output = failure[1].replace( '\\n', '\n' ) + log_output = re.sub( r'control \d+:.+', r'', log_output ) + log_output = re.sub( r'\n+', r'\n', log_output ) + appending_to = 'output' + tmp_output = {} + output = {} + for line in log_output.split( '\n' ): + if line.startswith( 'Traceback' ): + appending_to = 'traceback' + elif 'request returned None from get_history' in line: + continue + elif '>> begin captured logging <<' in line: + appending_to = 'logging' + continue + elif '>> begin captured stdout <<' in line: + appending_to = 'stdout' + continue + elif '>> begin captured stderr <<' in line: + appending_to = 'stderr' + continue + if appending_to not in tmp_output: + tmp_output[ appending_to ] = [] + tmp_output[ appending_to ].append( line ) + for output_type in tmp_output: + output[ output_type ] = '\n'.join( tmp_output[ output_type ] ) + repository_dict[ 'tool_test_errors' ].append( dict( test=label, output=output ) ) + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_dict[ 'tool_test_errors' ] ) log.debug( 'Repository %s installed, but did not pass functional tests.' % repository_dict[ 'name' ] ) + repository_status.append( repository_dict ) + # Delete the completed tool functional tests from the test_toolbox.__dict__, otherwise nose will find them and try to re-run the + # tests after uninstalling the repository. + tests_to_delete = [] + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + tests_to_delete.append( key ) + for key in tests_to_delete: + del test_toolbox.__dict__[ key ] # Generate an uninstall method for this repository, so that the next repository has a clean environment for testing. test_install_repositories.generate_uninstall_method( repository_dict ) # Set up nose to run the generated uninstall method as a functional test. 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.

1 0

commit/galaxy-central: inithello: Remove some unneeded data from the repository metadata API collection view.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fabb0ae1edab/ changeset: fabb0ae1edab user: inithello date: 2013-02-27 20:23:07 summary: Remove some unneeded data from the repository metadata API collection view. affected #: 1 file diff -r b9c7813848e989d1a228a53745bb57f958b05467 -r fabb0ae1edabf77f9aceb018fa5a988ce05500f9 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -191,8 +191,7 @@ fp.close() class RepositoryMetadata( object, APIItem ): - api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', - 'do_not_test', 'time_last_tested', 'tool_test_errors' ) + api_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable' ) api_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', 'do_not_test', 'time_last_tested', 'tool_test_errors' ) def __init__( self, id=None, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, 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.

1 0

commit/galaxy-central: inithello: Attempt to resolve issue with tool shed registry when running buildbot functional tests.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9c7813848e9/ changeset: b9c7813848e9 user: inithello date: 2013-02-27 20:12:07 summary: Attempt to resolve issue with tool shed registry when running buildbot functional tests. affected #: 1 file diff -r 8bad40b5b8ab0aee26c09ef8d59ca15227e1fec3 -r b9c7813848e989d1a228a53745bb57f958b05467 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -314,6 +314,7 @@ log.info( "Functional tests will be run against %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) success = False try: + tool_configs = app.config.tool_configs # What requires these? Handy for (eg) functional tests to save outputs? if galaxy_test_save: os.environ[ 'GALAXY_TEST_SAVE' ] = galaxy_test_save @@ -337,7 +338,6 @@ # Eliminate the migrated_tool_panel_config from the app's tool_configs, append the list of installed_tool_panel_configs, # and reload the app's toolbox. relative_migrated_tool_panel_config = os.path.join( app.config.root, migrated_tool_panel_config ) - tool_configs = app.config.tool_configs if relative_migrated_tool_panel_config in tool_configs: tool_configs.remove( relative_migrated_tool_panel_config ) for installed_tool_panel_config in installed_tool_panel_configs: 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.

1 0

commit/galaxy-central: inithello: Clean up remaining references to galaxy.util.shed_util_common.
by commits-noreply＠bitbucket.org 27 Feb '13

27 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8bad40b5b8ab/ changeset: 8bad40b5b8ab user: inithello date: 2013-02-27 17:16:10 summary: Clean up remaining references to galaxy.util.shed_util_common. affected #: 2 files diff -r b985587c33926d8d38fa4456b51eecbc68953bb9 -r 8bad40b5b8ab0aee26c09ef8d59ca15227e1fec3 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -920,7 +920,7 @@ def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. if self.tool_shed: - return galaxy.util.shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, + return tool_shed.util.shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, self.tool_shed, self.repository_name, self.repository_owner, diff -r b985587c33926d8d38fa4456b51eecbc68953bb9 -r 8bad40b5b8ab0aee26c09ef8d59ca15227e1fec3 lib/tool_shed/galaxy_install/__init__.py --- a/lib/tool_shed/galaxy_install/__init__.py +++ b/lib/tool_shed/galaxy_install/__init__.py @@ -28,7 +28,7 @@ ElementInclude.include( root ) tool_path = root.get( 'tool_path', None ) if tool_path: - tool_shed = galaxy.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) + tool_shed = tool_shed.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) relative_path = os.path.join( tool_path, tool_shed, 'repos', 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.

1 0

commit/galaxy-central: greg: Rename community template path to tool_shed.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b985587c3392/ changeset: b985587c3392 user: greg date: 2013-02-26 23:12:52 summary: Rename community template path to tool_shed. affected #: 101 files diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -36,7 +36,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/admin/index.mako', + return trans.fill_template( '/webapps/tool_shed/admin/index.mako', message=message, status=status ) @web.expose @@ -49,7 +49,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/admin/center.mako', + return trans.fill_template( '/webapps/tool_shed/admin/center.mako', message=message, status=status ) @web.expose diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -454,7 +454,7 @@ """ Column that displays community ratings for an item. """ def get_value( self, trans, grid, item ): ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, item, webapp_model=trans.model ) - return trans.fill_template( "community_rating.mako", + return trans.fill_template( "tool_shed_rating.mako", ave_item_rating=ave_item_rating, num_ratings=num_ratings, item_id=trans.security.encode_id( item.id ) ) diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -403,7 +403,7 @@ # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" columns = [ IdColumn( "Id", @@ -567,7 +567,7 @@ action='manage_categories', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/category/create_category.mako', + return trans.fill_template( '/webapps/tool_shed/category/create_category.mako', name=name, description=description, message=message, @@ -667,7 +667,7 @@ action='manage_categories', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/category/edit_category.mako', + return trans.fill_template( '/webapps/tool_shed/category/edit_category.mako', category=category, message=message, status=status ) @@ -677,7 +677,7 @@ if 'f-free-text-search' in kwd: # Trick to enable searching repository name, description from the CategoryGrid. # What we've done is rendered the search box for the RepositoryGrid on the grid.mako - # template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. + # template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. # Since we are searching repositories and not categories, redirect to browse_repositories(). return trans.response.send_redirect( web.url_for( controller='admin', action='browse_repositories', @@ -714,7 +714,7 @@ if 'regenerate_statistics_button' in kwd: trans.app.shed_counter.generate_statistics() message = "Successfully regenerated statistics" - return trans.fill_template( '/webapps/community/admin/statistics.mako', + return trans.fill_template( '/webapps/tool_shed/admin/statistics.mako', message=message, status=status ) @web.expose @@ -726,7 +726,7 @@ message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repositories_select_field = suc.build_repository_ids_select_field( trans ) - return trans.fill_template( '/webapps/community/admin/reset_metadata_on_selected_repositories.mako', + return trans.fill_template( '/webapps/tool_shed/admin/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, status=status ) diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -46,7 +46,7 @@ return 0 title = "Categories" model_class = model.Category - template='/webapps/community/category/grid.mako' + template='/webapps/tool_shed/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -82,7 +82,7 @@ return 0 title = "Categories of valid repositories" model_class = model.Category - template='/webapps/community/category/valid_grid.mako' + template='/webapps/tool_shed/category/valid_grid.mako' default_sort_key = "name" columns = [ CategoryGrid.NameColumn( "Name", @@ -172,7 +172,7 @@ # Grid definition title = "Repositories" model_class = model.Repository - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -503,7 +503,7 @@ # Grid definition title = "Matching repositories" model_class = model.RepositoryMetadata - template='/webapps/community/repository/grid.mako' + template='/webapps/tool_shed/repository/grid.mako' default_sort_key = "Repository.name" columns = [ NameColumn( "Repository name", @@ -571,7 +571,7 @@ # The request came from the tool shed. if 'f-free-text-search' in kwd: # Trick to enable searching repository name, description from the CategoryGrid. What we've done is rendered the search box for the - # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/community/category/grid.mako. Since we + # RepositoryGrid on the grid.mako template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako. Since we # are searching repositories and not categories, redirect to browse_repositories(). if 'id' in kwd and 'f-free-text-search' in kwd and kwd[ 'id' ] == kwd[ 'f-free-text-search' ]: # The value of 'id' has been set to the search string, which is a repository name. We'll try to get the desired encoded repository @@ -629,7 +629,7 @@ repository.name, repository.user.username, downloadable_revision.changeset_revision ) - return trans.fill_template( '/webapps/community/repository/browse_invalid_tools.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_invalid_tools.mako', cntrller=cntrller, invalid_tools_dict=invalid_tools_dict, message=message, @@ -747,7 +747,7 @@ suc.update_repository( repo ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repository=repository, metadata=metadata, commit_message=commit_message, @@ -937,7 +937,7 @@ repository = suc.get_repository_in_tool_shed( trans, id ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) if trans.user and trans.user.email: - return trans.fill_template( "/webapps/community/repository/contact_owner.mako", + return trans.fill_template( "/webapps/tool_shed/repository/contact_owner.mako", repository=repository, metadata=metadata, message=message, @@ -1032,7 +1032,7 @@ action='view_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) - return trans.fill_template( '/webapps/community/repository/create_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/create_repository.mako', name=name, description=description, long_description=long_description, @@ -1073,7 +1073,7 @@ is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, repository_id, changeset_revision ) try: - return trans.fill_template( "/webapps/community/repository/tool_form.mako", + return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, metadata=metadata, changeset_revision=changeset_revision, @@ -1197,7 +1197,7 @@ message = "No search performed - each field must contain the same number of comma-separated items." status = "error" exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_tools.mako', + return trans.fill_template( '/webapps/tool_shed/repository/find_tools.mako', tool_id=self.__stringify( tool_ids ), tool_name=self.__stringify( tool_names ), tool_version=self.__stringify( tool_versions ), @@ -1286,7 +1286,7 @@ exact_matches_checked = False workflow_names = [] exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) - return trans.fill_template( '/webapps/community/repository/find_workflows.mako', + return trans.fill_template( '/webapps/tool_shed/repository/find_workflows.mako', workflow_name=self.__stringify( workflow_names ), exact_matches_check_box=exact_matches_check_box, message=message, @@ -1690,7 +1690,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) + return trans.fill_template( '/webapps/tool_shed/repository/help.mako', message=message, status=status, **kwd ) def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): found = False if tool_id and not tool_name and not tool_version: @@ -1762,7 +1762,7 @@ user_id = params.get( 'user_id', None ) repository_id = params.get( 'repository_id', None ) changeset_revision = params.get( 'changeset_revision', None ) - return trans.fill_template( '/webapps/community/index.mako', + return trans.fill_template( '/webapps/tool_shed/index.mako', repository_metadata=repository_metadata, has_reviewed_repositories=has_reviewed_repositories, has_deprecated_repositories=has_deprecated_repositories, @@ -1813,7 +1813,7 @@ elif error_message: message = error_message try: - return trans.fill_template( "/webapps/community/repository/tool_form.mako", + return trans.fill_template( "/webapps/tool_shed/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, tool=tool, @@ -1872,7 +1872,7 @@ .order_by( trans.model.Repository.table.c.name ): if user.email in repository.email_alerts: email_alert_repositories.append( repository ) - return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", + return trans.fill_template( "/webapps/tool_shed/user/manage_email_alerts.mako", new_repo_alert_check_box=new_repo_alert_check_box, email_alert_repositories=email_alert_repositories, message=message, @@ -2056,7 +2056,7 @@ review_id = None can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - return trans.fill_template( '/webapps/community/repository/manage_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, long_description=long_description, @@ -2163,7 +2163,7 @@ add_id_to_name=False, downloadable=False ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) - return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', + return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, containers_dict=containers_dict, repository_metadata_id=repository_metadata_id, @@ -2230,7 +2230,7 @@ rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/rate_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, avg_rating=avg_rating, @@ -2242,7 +2242,7 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - # This method is called only from the ~/templates/webapps/community/repository/manage_repository.mako template. + # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. # It resets all metadata on the complete changelog for a single repository in the tool shed. invalid_file_tups, metadata_dict = suc.reset_all_metadata_on_repository_in_tool_shed( trans, id, **kwd ) if invalid_file_tups: @@ -2405,7 +2405,7 @@ message = "Select at least 1 file to delete from the repository before clicking <b>Delete selected files</b>." status = "error" is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/browse_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/browse_repository.mako', repo=repo, repository=repository, commit_message=commit_message, @@ -2672,7 +2672,7 @@ changesets.insert( 0, change_dict ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, repository.tip( trans.app ) ) - return trans.fill_template( '/webapps/community/repository/view_changelog.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_changelog.mako', repository=repository, metadata=metadata, changesets=changesets, @@ -2703,7 +2703,7 @@ diffs.append( suc.to_safe_string( diff, to_html=True ) ) is_malicious = suc.changeset_is_malicious( trans, id, repository.tip( trans.app ) ) metadata = self.get_metadata( trans, id, ctx_str ) - return trans.fill_template( '/webapps/community/repository/view_changeset.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_changeset.mako', repository=repository, metadata=metadata, ctx=ctx, @@ -2810,7 +2810,7 @@ review_id = None containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) can_browse_repository_reviews = suc.can_browse_repository_reviews( trans, repository ) - return trans.fill_template( '/webapps/community/repository/view_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', repo=repo, repository=repository, repository_metadata_id=repository_metadata_id, @@ -2893,7 +2893,7 @@ review_id = trans.security.encode_id( review.id ) else: review_id = None - return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", + return trans.fill_template( "/webapps/tool_shed/repository/view_tool_metadata.mako", repository=repository, metadata=metadata, tool=tool, @@ -2919,7 +2919,7 @@ repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) changeset_revision = repository_metadata.changeset_revision metadata = repository_metadata.metadata - return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + return trans.fill_template( "/webapps/tool_shed/repository/view_workflow.mako", repository=repository, changeset_revision=changeset_revision, repository_metadata_id=repository_metadata_id, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/repository_review.py --- a/lib/galaxy/webapps/community/controllers/repository_review.py +++ b/lib/galaxy/webapps/community/controllers/repository_review.py @@ -27,7 +27,7 @@ return component.description title = "Repository review components" model_class = model.Component - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -89,7 +89,7 @@ return rval title = "All reviewed repositories" model_class = model.Repository - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = "Repository.name" columns = [ RepositoryGrid.NameColumn( "Repository name", @@ -196,7 +196,7 @@ return '' title = "Reviews by user" model_class = model.RepositoryReview - template='/webapps/community/repository_review/grid.mako' + template='/webapps/tool_shed/repository_review/grid.mako' default_sort_key = 'repository_id' columns = [ RepositoryNameColumn( "Repository Name", @@ -316,7 +316,7 @@ repository = review.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/browse_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/browse_review.mako', repository=repository, changeset_revision_label=changeset_revision_label, review=review, @@ -361,7 +361,7 @@ action='manage_components', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/repository_review/create_component.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/create_component.mako', name=name, description=description, message=message, @@ -456,7 +456,7 @@ action='manage_components', message=message, status=status ) ) - return trans.fill_template( '/webapps/community/repository_review/edit_component.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/edit_component.mako', component=component, message=message, status=status ) @@ -576,7 +576,7 @@ selected_value=selected_value, for_component=False ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/edit_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, review=review, changeset_revision_label=changeset_revision_label, @@ -688,7 +688,7 @@ installable=installable, can_add_review=can_add_review ) reviews_dict[ changeset_revision ] = revision_dict - return trans.fill_template( '/webapps/community/repository_review/reviews_of_repository.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_repository.mako', repository=repository, reviews_dict=reviews_dict, mine=mine, @@ -709,7 +709,7 @@ installable = changeset_revision in [ metadata_revision.changeset_revision for metadata_revision in repository.metadata_revisions ] rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) reviews = suc.get_reviews_by_repository_id_changeset_revision( trans, repository_id, changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/reviews_of_changeset_revision.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako', repository=repository, changeset_revision=changeset_revision, changeset_revision_label=changeset_revision_label, @@ -773,7 +773,7 @@ repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) previous_reviews_dict = suc.get_previous_repository_reviews( trans, repository, changeset_revision ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) - return trans.fill_template( '/webapps/community/repository_review/select_previous_review.mako', + return trans.fill_template( '/webapps/tool_shed/repository_review/select_previous_review.mako', repository=repository, changeset_revision=changeset_revision, changeset_revision_label=changeset_revision_label, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -204,7 +204,7 @@ # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] - return trans.fill_template( '/webapps/community/repository/upload.mako', + return trans.fill_template( '/webapps/tool_shed/repository/upload.mako', repository=repository, url=url, commit_message=commit_message, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/galaxy/controllers/admin.py --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -733,7 +733,7 @@ status = util.restore_text( kwd.get( 'status', 'done' ) ) migration_stages_dict = odict() migration_modules = [] - migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'galaxy', 'tool_shed', 'migrate', 'versions' ) ) + migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions' ) ) migration_scripts_dir_contents = os.listdir( migration_scripts_dir ) for item in migration_scripts_dir_contents: if os.path.isfile( os.path.join( migration_scripts_dir, item ) ) and item.endswith( '.py' ): diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -735,7 +735,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/user/manage_info.mako', + return trans.fill_template( '/webapps/tool_shed/user/manage_info.mako', cntrller=cntrller, user=user, email=email, diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -1,4 +1,4 @@ -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="browse_files(title_text, directory_path)"><script type="text/javascript"> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%namespace file="/admin/tool_shed_repository/common.mako" import="*" /><%def name="stylesheets()"> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako --- a/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako +++ b/templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="common_misc_javascripts" /><%def name="javascripts()"> ${parent.javascripts()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" /><%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><%def name="stylesheets()"> ${parent.stylesheets()} diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/admin/tool_shed_repository/view_workflow.mako --- a/templates/admin/tool_shed_repository/view_workflow.mako +++ b/templates/admin/tool_shed_repository/view_workflow.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="*" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><% from galaxy.web.framework.helpers import time_ago @@ -11,7 +11,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/webapps/community/base_panels.mako' + return '/webapps/tool_shed/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/community_rating.mako --- a/templates/community_rating.mako +++ /dev/null @@ -1,33 +0,0 @@ -<% - label = "ratings" - if num_ratings == 1: - label = "rating" -%> -<div> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="1" - %if ave_item_rating > 0 and ave_item_rating <= 1.5: - checked="checked" - %endif - - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="2" - %if ave_item_rating > 1.5 and ave_item_rating <= 2.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="3" - %if ave_item_rating > 2.5 and ave_item_rating <= 3.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="4" - %if ave_item_rating > 3.5 and ave_item_rating <= 4.5: - checked="checked" - %endif - /> - <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="5" - %if ave_item_rating > 4.5: - checked="checked" - %endif - /> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/tool_shed_rating.mako --- /dev/null +++ b/templates/tool_shed_rating.mako @@ -0,0 +1,33 @@ +<% + label = "ratings" + if num_ratings == 1: + label = "rating" +%> +<div> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="1" + %if ave_item_rating > 0 and ave_item_rating <= 1.5: + checked="checked" + %endif + + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="2" + %if ave_item_rating > 1.5 and ave_item_rating <= 2.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="3" + %if ave_item_rating > 2.5 and ave_item_rating <= 3.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="4" + %if ave_item_rating > 3.5 and ave_item_rating <= 4.5: + checked="checked" + %endif + /> + <input name="star1-${item_id}" type="radio" class="community_rating_star star" disabled="disabled" value="5" + %if ave_item_rating > 4.5: + checked="checked" + %endif + /> +</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako +++ b/templates/user/dbkeys.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/logout.mako --- a/templates/user/logout.mako +++ b/templates/user/logout.mako @@ -1,4 +1,4 @@ -<%inherit file="/base_panels.mako"/> +<%inherit file="/webapps/galaxy/base_panels.mako"/><%namespace file="/message.mako" import="render_msg" /> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/user/openid_associate.mako --- a/templates/user/openid_associate.mako +++ b/templates/user/openid_associate.mako @@ -1,7 +1,7 @@ <%! def inherit(context): if context.get('use_panels'): - return '/base_panels.mako' + return '/webapps/galaxy/base_panels.mako' else: return '/base.mako' %> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/center.mako --- a/templates/webapps/community/admin/center.mako +++ /dev/null @@ -1,50 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - - -<%def name="title()">Galaxy Administration</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<h2>Administration</h2> - -<p>The menu on the left provides the following features</p> -<ul> - <li> - <strong>Categories</strong> - <p/> - <ul> - <li> - <strong>Manage categories</strong> - </li> - <p/> - </ul> - </li> - <li> - <strong>Security</strong> - <p/> - <ul> - <li> - <strong>Manage users</strong> - provides a view of the registered users and all groups and non-private roles associated - with each user. - </li> - <p/> - <li> - <strong>Manage groups</strong> - provides a view of all groups along with the members of the group and the roles associated with - each group (both private and non-private roles). The group names include a link to a page that allows you to manage the users and - roles that are associated with the group. - </li> - <p/> - <li> - <strong>Manage roles</strong> - provides a view of all non-private roles along with the role type, and the users and groups that - are associated with the role. The role names include a link to a page that allows you to manage the users and groups that are associated - with the role. The page also includes a view of the data library datasets that are associated with the role and the permissions applied - to each dataset. - </li> - </ul> - </li> - <p/> -</ul> -<br/> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako +++ /dev/null @@ -1,139 +0,0 @@ -<%inherit file="/webapps/community/base_panels.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="stylesheets()"> - ## Include "base.css" for styling tool menu and forms (details) - ${h.css( "base", "autocomplete_tagging", "tool_menu" )} - - ## But make sure styles for the layout take precedence - ${parent.stylesheets()} - - <style type="text/css"> - body { margin: 0; padding: 0; overflow: hidden; } - #left { - background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> - <% - self.has_left_panel=True - self.has_right_panel=False - self.active_view="tools" - %> - %if trans.app.config.require_login and not trans.user: - <script type="text/javascript"> - if ( window != top ) { - top.location.href = location.href; - } - </script> - %endif -</%def> - -<%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %> - <div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>Administration</div> - </div> - <div class="page-container" style="padding: 10px;"> - <div class="toolMenu"> - <div class="toolSectionList"> - <div class="toolSectionTitle"> - Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repositories' )}">Browse all repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}">Reset selected metadata</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_repository_metadata' )}">Browse metadata</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='admin' )}">Browse invalid tools</a> - </div> - </div> - </div> - %if can_review_repositories: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Reviewing Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - %if trans.user.repository_reviews: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a> - </div> - </div> - </div> - %endif - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Categories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories' )}">Manage categories</a> - </div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Security - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='users' )}">Manage users</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='groups' )}">Manage groups</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='roles' )}">Manage roles</a> - </div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Statistics - </div> - <div class="toolSectionBody"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='admin', action='regenerate_statistics' )}">View shed statistics</a> - </div> - </div> - </div> - </div> - </div> -</%def> - -<%def name="center_panel()"> - <% - center_url = h.url_for(controller='admin', action='center' ) - %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako +++ /dev/null @@ -1,40 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="common_misc_javascripts" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${common_misc_javascripts()} -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="warningmessage"> - Resetting metadata may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. - Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not be helpful. Watch - the tool shed paster log to pass the time if necessary. -</div> - -<div class="toolForm"> - <div class="toolFormTitle">Reset all metadata on each selected repository</div> - <form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories_in_tool_shed' )}" method="post" > - <div class="form-row"> - Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="checkbox" id="checkAll" name="select_all_repositories_checkbox" value="true" onclick="checkAllFields('repository_ids');"/><input type="hidden" name="select_all_repositories_checkbox" value="true"/><b>Select/unselect all repositories</b> - </div> - <div style="clear: both"></div> - <div class="form-row"> - ${repositories_select_field.get_html()} - </div> - <div style="clear: both"></div> - <div class="form-row"> - <input type="submit" name="reset_metadata_on_selected_repositories_button" value="Reset metadata on selected repositories"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/admin/statistics.mako --- a/templates/webapps/community/admin/statistics.mako +++ /dev/null @@ -1,56 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Tool shed statistics generated on ${trans.app.shed_counter.generation_time}</div> - <form name="regenerate_statistics" id="regenerate_statistics" action="${h.url_for( controller='admin', action='regenerate_statistics' )}" method="post" > - <div class="form-row"> - <table class="grid"> - <tr> - <th>Item</th> - <th>Count</th> - </tr> - <tr> - <td>Total repositories</td> - <td>${trans.app.shed_counter.repositories | h}</td> - </tr> - ##<tr> - ## <td>Empty repositories</td> - ## <td>${trans.app.shed_counter.new_repositories | h}</td> - ##</tr> - <tr> - <td>Deleted repositories</td> - <td>${trans.app.shed_counter.deleted_repositories | h}</td> - </tr> - <tr> - <td>Valid tools</td> - <td>${trans.app.shed_counter.valid_tools | h}</td> - </tr> - <tr> - <td>Invalid tools</td> - <td>${trans.app.shed_counter.invalid_tools | h}</td> - </tr> - <tr> - <td>Workflows</td> - <td>${trans.app.shed_counter.workflows | h}</td> - </tr> - <tr> - <td>Proprietary datatypes</td> - <td>${trans.app.shed_counter.proprietary_datatypes | h}</td> - </tr> - <tr> - <td>Total clones</td> - <td>${trans.app.shed_counter.total_clones | h}</td> - </tr> - </table> - </div> - <div class="form-row"> - <input type="submit" name="regenerate_statistics_button" value="Regenerate statistics"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako +++ /dev/null @@ -1,133 +0,0 @@ -<%inherit file="/base/base_panels.mako"/> - -## Default title -<%def name="title()">Galaxy Tool Shed</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -## Masthead -<%def name="masthead()"> - - ## Tab area, fills entire width - <div style="position: relative; right: -50%; float: left;"> - <div style="display: block; position: relative; right: 50%;"> - - <ul class="nav" border="0" cellspacing="0"> - - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> - <% - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "<b class='caret'></b>" - style = "" - if not visible: - style = "display: none;" - %> - <li class="${cls}" style="${style}"> - %if href: - <a class="${a_cls}" data-toggle="dropdown" target="${target}" href="${href}">${display}${extra}</a> - %else: - <a class="${a_cls}" data-toggle="dropdown">${display}${extra}</a> - %endif - %if menu_options: - <ul class="dropdown-menu"> - %for menu_item in menu_options: - %if not menu_item: - <li class="divider"></li> - %else: - <li> - %if len ( menu_item ) == 1: - ${menu_item[0]} - %elif len ( menu_item ) == 2: - <% name, link = menu_item %> - <a href="${link}">${name | h}</a> - %else: - <% name, link, target = menu_item %> - <a target="${target}" href="${link}">${name | h}</a> - %endif - </li> - %endif - %endfor - </ul> - %endif - </li> - </%def> - - ## Repositories tab. - ${tab( "repositories", "Repositories", h.url_for( controller='/repository', action='index' ) )} - - ## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - ## Help tab. - <% - menu_options = [] - qa_url = app.config.get( "qa_url", None ) - if qa_url: - menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ] - menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.g2.bx.psu.edu/Support" ), "_blank" ], - [_('Tool shed wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/Tool%20Shed" ), "_blank" ], - [_('Galaxy wiki'), app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ], - [_('Video tutorials (screencasts)'), app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" ), "_blank" ] - ] ) - tab( "help", _("Help"), None, menu_options=menu_options ) - %> - - ## User tabs. - <% - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ '<a>Logged in as <span id="user-email">%s</span></a>' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - %> - </ul> - </div> - </div> - - ## Logo, layered over tabs to be clickable - <div class="title"> - <a href="${h.url_for( app.config.get( 'logo_url', '/' ) )}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}"> - Galaxy Tool Shed - %if app.config.brand: - <span>/ ${app.config.brand}</span> - %endif - </a> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/create_category.mako --- a/templates/webapps/community/category/create_category.mako +++ /dev/null @@ -1,34 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Create Category</div> - <div class="toolFormBody"> - <form name="create_category_form" id="create_category_form" action="${h.url_for(controller='admin', action='create_category' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <input name="name" type="textfield" value="${name | h}" size=40"/> - </div> - <div class="form-row"> - <label>Description:</label> - <input name="description" type="textfield" value="${description | h}" size=40"/> - </div> - <div class="form-row"> - <input type="submit" name="create_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/edit_category.mako --- a/templates/webapps/community/category/edit_category.mako +++ /dev/null @@ -1,43 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="edit_category" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > - <div class="form-row"> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name | h}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description | h}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="edit_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/grid.mako --- a/templates/webapps/community/category/grid.mako +++ /dev/null @@ -1,64 +0,0 @@ -<%namespace file="/display_common.mako" import="render_message" /> -<%namespace file="/grid_base.mako" import="*" /> -<%namespace file="/grid_common.mako" import="*" /> -<%inherit file="/grid_base.mako" /> - -## Render grid header. -## TODO: This is very similar to this directory's valid_grid.mako, so see if we can re-use this code in a better way. -<%def name="render_grid_header( grid, repo_grid, render_title=True)"> - <div class="grid-header"> - %if render_title: - ${grid_title()} - %endif - %if grid.global_actions: - <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: - %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a> - %endfor - </div> - %endif - </ul> - %endif - ${render_grid_filters( repo_grid, render_advanced_search=False )} - </div> -</%def> - -<%def name="make_grid( grid, repo_grid )"> - <div class="loading-elt-overlay"></div> - <table> - <tr> - <td width="75%">${self.render_grid_header( grid, repo_grid )}</td> - <td></td> - <td></td> - </tr> - <tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> - <td></td> - <td></td> - </tr> - </table> - ${render_grid_table( grid, show_item_checkboxes )} -</%def> - -<%def name="grid_body( grid )"> - <% - from galaxy.webapps.community.controllers.repository import RepositoryGrid - repo_grid = RepositoryGrid() - %> - ${self.make_grid( grid, repo_grid )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${self.grid_body( grid )} - </div> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/category/valid_grid.mako --- a/templates/webapps/community/category/valid_grid.mako +++ /dev/null @@ -1,63 +0,0 @@ -<%namespace file="/display_common.mako" import="render_message" /> -<%namespace file="/grid_base.mako" import="*" /> -<%namespace file="/grid_common.mako" import="*" /> -<%inherit file="/grid_base.mako" /> - -## Render grid header. -<%def name="render_grid_header( grid, repo_grid, render_title=True)"> - <div class="grid-header"> - %if render_title: - ${grid_title()} - %endif - %if grid.global_actions: - <ul class="manage-table-actions"> - %if len( grid.global_actions ) < 4: - %for action in grid.global_actions: - <li><a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a></li> - %endfor - %else: - <li><a class="action-button" id="action-8675309-popup" class="menubutton">Actions</a></li> - <div popupmenu="action-8675309-popup"> - %for action in grid.global_actions: - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label | h}</a> - %endfor - </div> - %endif - </ul> - %endif - ${render_grid_filters( repo_grid, render_advanced_search=False )} - </div> -</%def> - -<%def name="make_grid( grid, repo_grid )"> - <div class="loading-elt-overlay"></div> - <table> - <tr> - <td width="75%">${self.render_grid_header( grid, repo_grid )}</td> - <td></td> - <td></td> - </tr> - <tr> - <td width="100%" id="grid-message" valign="top">${render_message( message, status )}</td> - <td></td> - <td></td> - </tr> - </table> - ${render_grid_table( grid, show_item_checkboxes )} -</%def> - -<%def name="grid_body( grid )"> - <% - from galaxy.webapps.community.controllers.repository import ValidRepositoryGrid - repo_grid = ValidRepositoryGrid() - %> - ${self.make_grid( grid, repo_grid )} -</%def> - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%"> - <div class="page-container" style="padding: 10px;"> - ${self.grid_body( grid )} - </div> - </div> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/common/common.mako --- a/templates/webapps/community/common/common.mako +++ /dev/null @@ -1,84 +0,0 @@ -<%def name="common_misc_javascripts()"> - <script type="text/javascript"> - function checkAllFields( name ) - { - var chkAll = document.getElementById( 'checkAll' ); - var checks = document.getElementsByTagName( 'input' ); - var boxLength = checks.length; - var allChecked = false; - var totalChecked = 0; - if ( chkAll.checked == true ) - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( name ) != -1 ) - { - checks[i].checked = true; - } - } - } - else - { - for ( i=0; i < boxLength; i++ ) - { - if ( checks[i].name.indexOf( name ) != -1 ) - { - checks[i].checked = false - } - } - } - } - </script> -</%def> - -<%def name="render_star_rating( name, rating, disabled=False )"> - <% - if disabled: - disabled_str = ' disabled="disabled"' - else: - disabled_str = '' - html = '' - for index in range( 1, 6 ): - html += '<input name="%s" type="radio" class="star" value="%s" %s' % ( str( name ), str( index ), disabled_str ) - if rating > ( index - 0.5 ) and rating < ( index + 0.5 ): - html += ' checked="checked"' - html += '/>' - %> - ${html} -</%def> - -<%def name="render_long_description( description_text )"> - <style type="text/css"> - #description_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style> - <div class="form-row"> - <label>Detailed description:</label> - <table id="description_table"> - <tr><td>${description_text}</td></tr> - </table> - <div style="clear: both"></div> - </div> -</%def> - -<%def name="render_review_comment( comment_text )"> - <style type="text/css"> - #reviews_table{ table-layout:fixed; - width:100%; - overflow-wrap:normal; - overflow:hidden; - border:0px; - word-break:keep-all; - word-wrap:break-word; - line-break:strict; } - </style> - <table id="reviews_table"> - <tr><td>${comment_text}</td></tr> - </table> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako +++ /dev/null @@ -1,165 +0,0 @@ -<%inherit file="/webapps/community/base_panels.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ## Include "base.css" for styling tool menu and forms (details) - ${h.css( "base", "autocomplete_tagging", "tool_menu" )} - - ## But make sure styles for the layout take precedence - ${parent.stylesheets()} - - <style type="text/css"> - body { margin: 0; padding: 0; overflow: hidden; } - #left { - background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} -</%def> - -<%def name="init()"> - <% - self.has_left_panel=True - self.has_right_panel=False - self.active_view="tools" - %> - %if trans.app.config.require_login and not trans.user: - <script type="text/javascript"> - if ( window != top ) { - top.location.href = location.href; - } - </script> - %endif -</%def> - -<%def name="left_panel()"> - <% can_review_repositories = trans.app.security_agent.user_can_review_repositories( trans.user ) %> - <div class="unified-panel-header" unselectable="on"> - <div class='unified-panel-header-inner'>${trans.app.shed_counter.valid_tools | h} valid tools on ${trans.app.shed_counter.generation_time | h}</div> - </div> - <div class="page-container" style="padding: 10px;"> - <div class="toolMenu"> - <div class="toolSectionList"> - %if user_id or repository_id: - ## The route in was a sharable url, and may have included a changeset_revision, although we don't check for it. - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - All Repositories - </div> - <div class="toolTitle"> - <a href="${h.url_for( controller='repository', action='index' )}">Browse by category</a> - </div> - %else: - %if repository_metadata: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Search - </div> - <div class="toolSectionBody"> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a> - </div> - </div> - %endif - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - All Repositories - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_categories' )}">Browse by category</a> - </div> - %if trans.user: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - My Repositories and Tools - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='repositories_i_own' )}">Repositories I own</a> - </div> - %if has_reviewed_repositories: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='reviewed_repositories_i_own' )}">Reviewed repositories I own</a> - </div> - %endif - %if has_deprecated_repositories: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='deprecated_repositories_i_own' )}">Deprecated repositories I own</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repositories', operation='my_writable_repositories' )}">My writable repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_invalid_tools', cntrller='repository' )}">My invalid tools</a> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository', action='create_repository' )}">Create new repository</a> - </div> - %if can_review_repositories: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Reviewing Repositories - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - %if trans.user.repository_reviews: - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_reviewed_by_me' )}">Repositories reviewed by me</a> - </div> - %endif - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_with_reviews' )}">All reviewed repositories</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_repositories_without_reviews' )}">Repositories with no reviews</a> - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='repository_review', action='manage_components' )}">Manage review components</a> - </div> - </div> - </div> - %endif - %else: - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - Available Actions - </div> - <div class="toolTitle"> - <a target="galaxy_main" href="${h.url_for( controller='/user', action='login' )}">Login to create a repository</a> - </div> - %endif - %endif - </div> - </div> - </div> -</%def> - -<%def name="center_panel()"> - <% - if trans.app.config.require_login and not trans.user: - center_url = h.url_for( controller='user', action='login', message=message, status=status ) - elif repository_id and changeset_revision: - # Route in was a sharable url: /view/{owner}/{name}/{changeset_revision}. - center_url = h.url_for( controller='repository', action='view_repository', id=repository_id, changeset_revision=changeset_revision, message=message, status=status ) - elif repository_id: - # Route in was a sharable url: /view/{owner}/{name}. - center_url = h.url_for( controller='repository', action='view_repository', id=repository_id, message=message, status=status ) - elif user_id: - # Route in was a sharable url: /view/{owner}. - center_url = h.url_for( controller='repository', action='browse_repositories', operation="repositories_by_user", user_id=user_id, message=message, status=status ) - else: - center_url = h.url_for( controller='repository', action='browse_categories', message=message, status=status ) - %> - <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> -</%def> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/message.mako --- a/templates/webapps/community/message.mako +++ /dev/null @@ -1,1 +0,0 @@ -<%inherit file="../../message.mako"/> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/repository/browse_invalid_tools.mako --- a/templates/webapps/community/repository/browse_invalid_tools.mako +++ /dev/null @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - %if invalid_tools_dict: - <div class="toolFormTitle">Invalid tools<i> - click the tool config file name to see why the tool is invalid</i></div> - <div class="form-row"> - <table class="grid"> - <tr> - <th>Tool config</th> - <th>Repository name</th> - <th>Repository owner</th> - <th>Changeset revision</th> - </tr> - %for invalid_tool_config, repository_tup in invalid_tools_dict.items(): - <% repository_id, repository_name, repository_owner, changeset_revision = repository_tup %> - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='repository', action='load_invalid_tool', repository_id=trans.security.encode_id( repository_id ), tool_config=invalid_tool_config, changeset_revision=changeset_revision )}"> - ${invalid_tool_config} - </a> - </td> - <td>${repository_name | h}</td> - <td>${repository_owner | h}</td> - <td>${changeset_revision | h}</td> - </tr> - %endfor - </table> - </div> - </div> - %else: - <div class="form-row"> - %if cntrller == 'admin' and trans.user_is_admin(): - No repositories in this tool shed contain invalid tools. - %else: - None of your repositories contain invalid tools. - %endif - </div> - %endif -</div> diff -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 -r b985587c33926d8d38fa4456b51eecbc68953bb9 templates/webapps/community/repository/browse_repository.mako --- a/templates/webapps/community/repository/browse_repository.mako +++ /dev/null @@ -1,156 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/webapps/community/common/common.mako" import="*" /> -<%namespace file="/webapps/community/repository/common.mako" import="*" /> - -<% - from galaxy.web.framework.helpers import time_ago - is_admin = trans.user_is_admin() - is_new = repository.is_new( trans.app ) - can_contact_owner = trans.user and trans.user != repository.user - can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) - can_upload = can_push and ( not repository.deprecated ) - can_download = not is_new and ( not is_malicious or can_push ) - can_browse_contents = not is_new - can_rate = trans.user and repository.user != trans.user - can_manage = is_admin or repository.user == trans.user - can_view_change_log = not is_new - has_readme = metadata and 'readme' in metadata -%> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "jquery.rating", "dynatree_skin/ui.dynatree" )} - <style type="text/css"> - ul.fileBrowser, - ul.toolFile { - margin-left: 0; - padding-left: 0; - list-style: none; - } - ul.fileBrowser { - margin-left: 20px; - } - .fileBrowser li, - .toolFile li { - padding-left: 20px; - background-repeat: no-repeat; - background-position: 0; - min-height: 20px; - } - .toolFile li { - background-image: url( ${h.url_for( '/static/images/silk/page_white_compressed.png' )} ); - } - .fileBrowser li { - background-image: url( ${h.url_for( '/static/images/silk/page_white.png' )} ); - } - </style> -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.rating", "libs/jquery/jquery-ui", "libs/jquery/jquery.cookie", "libs/jquery/jquery.dynatree" )} - ${common_javascripts(repository)} -</%def> - -<br/><br/> -<ul class="manage-table-actions"> - %if is_new: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %else: - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> - <div popupmenu="repository-${repository.id}-popup"> - %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> - %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> - %endif - %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %endif - %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> - %endif - %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> - %endif - %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ), file_type='zip' )}">Download as a zip file</a> - %endif - </div> - %endif -</ul> - -%if message: - ${render_msg( message, status )} -%endif - -%if can_browse_contents: - <div class="toolForm"> - <div class="toolFormTitle">Browse ${repository.name | h} revision ${repository.tip( trans.app ) | h} (repository tip)</div> - %if can_download: - <div class="form-row"> - <label>Clone this repository:</label> - ${render_clone_str( repository )} - </div> - %endif - %if can_push: - <form name="select_files_to_delete" id="select_files_to_delete" action="${h.url_for( controller='repository', action='select_files_to_delete', id=trans.security.encode_id( repository.id ))}" method="post" > - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... - </div> - <div class="toolParamHelp" style="clear: both;"> - Click on a file to display it's contents below. You may delete files from the repository by clicking the check box next to each file and clicking the <b>Delete selected files</b> button. - </div> - <input id="selected_files_to_delete" name="selected_files_to_delete" type="hidden" value=""/> - </div> - <div class="form-row"> - <label>Message:</label> - <div class="form-row-input"> - %if commit_message: - <textarea name="commit_message" rows="3" cols="35">${commit_message | h}</textarea> - %else: - <textarea name="commit_message" rows="3" cols="35"></textarea> - %endif - </div> - <div class="toolParamHelp" style="clear: both;"> - This is the commit message for the mercurial change set that will be created if you delete selected files. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="select_files_to_delete_button" value="Delete selected files"/> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </form> - %else: - <div class="toolFormBody"> - <div class="form-row" > - <label>Contents:</label> - <div id="tree" > - Loading... - </div> - </div> - <div class="form-row"> - <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> - </div> - </div> - %endif - </div> - <p/> -%endif This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: inithello: Added name attribute to MigrateToolsApplication to generate a correct metadata dict for migrated tools.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddfdfd2fce3e/ changeset: ddfdfd2fce3e user: inithello date: 2013-02-26 22:59:17 summary: Added name attribute to MigrateToolsApplication to generate a correct metadata dict for migrated tools. affected #: 1 file diff -r b9a7f2ae70a830e7ad5ef2a4c7e24f43d4575fa1 -r ddfdfd2fce3ef42d50f4b7b5a02db1cad03c5663 lib/tool_shed/galaxy_install/migrate/common.py --- a/lib/tool_shed/galaxy_install/migrate/common.py +++ b/lib/tool_shed/galaxy_install/migrate/common.py @@ -14,6 +14,7 @@ def __init__( self, tools_migration_config ): install_dependencies = 'install_dependencies' in sys.argv galaxy_config_file = 'universe_wsgi.ini' + self.name = 'galaxy' if '-c' in sys.argv: pos = sys.argv.index( '-c' ) sys.argv.pop( pos ) 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.

1 0

commit/galaxy-central: jgoecks: Add missing import.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9a7f2ae70a8/ changeset: b9a7f2ae70a8 user: jgoecks date: 2013-02-26 22:42:11 summary: Add missing import. affected #: 1 file diff -r 5d71d6193bbaf758ae901de19a601bce6c34aeca -r b9a7f2ae70a830e7ad5ef2a4c7e24f43d4575fa1 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -6,6 +6,7 @@ from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesVisualizationMixin from galaxy.web.framework.helpers import time_ago, grids from galaxy import util +from galaxy.datatypes.interval import Bed from galaxy.util.json import from_json_string from galaxy.util.sanitize_html import sanitize_html from galaxy.visualization.genomes import decode_dbkey 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: Force absolute imprts in Galaxy's app.
by commits-noreply＠bitbucket.org 26 Feb '13

26 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d71d6193bba/ changeset: 5d71d6193bba user: greg date: 2013-02-26 22:33:57 summary: Force absolute imprts in Galaxy's app. affected #: 1 file diff -r 6f0050c4e06ef6f5fdce3f7326280c07c63ef62e -r 5d71d6193bbaf758ae901de19a601bce6c34aeca lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -1,3 +1,4 @@ +from __future__ import absolute_import import sys, os, atexit from galaxy import config, jobs, util, tools, web @@ -151,10 +152,10 @@ self.memdump = memdump.Memdump() # Transfer manager client if self.config.get_bool( 'enable_beta_job_managers', False ): - from jobs import transfer_manager + from galaxy.jobs import transfer_manager self.transfer_manager = transfer_manager.TransferManager( self ) # Start the job manager - from jobs import manager + from galaxy.jobs import manager self.job_manager = manager.JobManager( self ) # FIXME: These are exposed directly for backward compatibility self.job_queue = self.job_manager.job_queue 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.

1 0