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[hg] galaxy 3134: Improved loading state for AJAXed grids: when ...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6e742ffb16a5 changeset: 3134:6e742ffb16a5 user: jeremy goecks <jeremy.goecks at emory.edu> date: Tue Dec 01 11:07:20 2009 -0500 description: Improved loading state for AJAXed grids: when grid is loading, gray out table and prevent further user actions. diffstat: templates/grid_base.mako | 16 +++++++++++++++- 1 files changed, 15 insertions(+), 1 deletions(-) diffs (47 lines): diff -r e75b55cc9e08 -r 6e742ffb16a5 templates/grid_base.mako --- a/templates/grid_base.mako Tue Dec 01 09:53:36 2009 -0500 +++ b/templates/grid_base.mako Tue Dec 01 11:07:20 2009 -0500 @@ -601,6 +601,7 @@ // If there's an operation in the args, do POST; otherwise, do GET. var operation = url_args['operation']; var method = (operation != null && operation != undefined ? "POST" : "GET" ); + $('.loading-elt-overlay').show(); // Show overlay to indicate loading and prevent user actions. $.ajax({ type: method, url: "${h.url_for()}", @@ -660,6 +661,9 @@ } } + // Hide loading overlay. + $('.loading-elt-overlay').hide(); + // Show message if there is one. var message = $.trim( parsed_response_text[2] ); if (message != "") @@ -711,6 +715,15 @@ .gray-background { background-color: #DDDDDD; } + .loading-elt-overlay { + background-color : white; + opacity : 0.5; + width : 100%; + height : 85%; + z-index : 14000; + position : absolute; + display: none; + } </style> </%def> @@ -750,7 +763,8 @@ ## Render grid. <%def name="render_grid_table()"> <form action="${url()}" method="post" onsubmit="return false;"> - <table class="grid"> + <div class='loading-elt-overlay'></div> + <table id='grid-table' class="grid"> <thead id="grid-table-header"> <tr> <th></th>

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[hg] galaxy 3135: Adding back 'wiggle to interval' converter
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/eb317734e391 changeset: 3135:eb317734e391 user: guru date: Tue Dec 01 11:49:07 2009 -0500 description: Adding back 'wiggle to interval' converter diffstat: datatypes_conf.xml.sample | 1 + lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py | 44 +++++++ lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml | 11 + test-data/3.wig | 37 ++++++ test-data/3_wig.bed | 26 ++++ tool_conf.xml.main | 1 + tool_conf.xml.sample | 1 + tools/filters/wiggle_to_simple.py | 43 +++++++ tools/filters/wiggle_to_simple.xml | 88 ++++++++++++++ 9 files changed, 252 insertions(+), 0 deletions(-) diffs (306 lines): diff -r 6e742ffb16a5 -r eb317734e391 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Tue Dec 01 11:07:20 2009 -0500 +++ b/datatypes_conf.xml.sample Tue Dec 01 11:49:07 2009 -0500 @@ -58,6 +58,7 @@ <datatype extension="txtseq.zip" type="galaxy.datatypes.data:Txtseq" mimetype="application/zip" display_in_upload="true"/> <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> <converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/> + <converter file="wiggle_to_simple_converter.xml" target_datatype="interval"/> </datatype> <datatype extension="array_tree" type="galaxy.datatypes.data:Data" /> <datatype extension="interval_index" type="galaxy.datatypes.data:Data" /> diff -r 6e742ffb16a5 -r eb317734e391 lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.py Tue Dec 01 11:49:07 2009 -0500 @@ -0,0 +1,44 @@ +#!/usr/bin/env python +#code is same as ~/tools/stats/wiggle_to_simple.py + +""" +Read a wiggle track and print out a series of lines containing +"chrom position score". Ignores track lines, handles bed, variableStep +and fixedStep wiggle lines. +""" +import sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +import bx.wiggle +from galaxy.tools.exception_handling import * + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def main(): + if len( sys.argv ) > 1: + in_file = open( sys.argv[1] ) + else: + in_file = open( sys.stdin ) + + if len( sys.argv ) > 2: + out_file = open( sys.argv[2], "w" ) + else: + out_file = sys.stdout + + try: + for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ): + out_file.write( "%s\n" % "\t".join( map( str, fields ) ) ) + except UCSCLimitException: + # Wiggle data was truncated, at the very least need to warn the user. + print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.' + except ValueError, e: + in_file.close() + out_file.close() + stop_err( str( e ) ) + + in_file.close() + out_file.close() + +if __name__ == "__main__": main() diff -r 6e742ffb16a5 -r eb317734e391 lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/wiggle_to_simple_converter.xml Tue Dec 01 11:49:07 2009 -0500 @@ -0,0 +1,11 @@ +<tool id="CONVERTER_wiggle_to_interval_0" name="Wiggle to Interval"> +  +  + <command interpreter="python">wiggle_to_simple_converter.py $input $out_file1 </command> + <inputs> + <param format="wig" name="input" type="data" label="Convert"/> + </inputs> + <outputs> + <data format="interval" name="out_file1" /> + </outputs> +</tool> diff -r 6e742ffb16a5 -r eb317734e391 test-data/3.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3.wig Tue Dec 01 11:49:07 2009 -0500 @@ -0,0 +1,37 @@ +track type=wiggle_0 name="LaminB1 (Tig3)" description="NKI LaminB1 DamID Map (log2-ratio scores, Tig3 cells)" +# output date: 2009-07-22 15:55:44 UTC +# chrom specified: chr20 +# position specified: 1-62435964 +# data values >= 4 +# This data has been compressed with a minor loss in resolution. +# (Worst case: 0.0448672) The original source data +# (before querying and compression) is available at +# http://hgdownload.cse.ucsc.edu/downloads.html +variableStep chrom=chr20 span=60 +1953668 4.029 +9749454 4.033 +12219969 4.053 +12571904 4.548 +12663417 4.207 +15198014 4.041 +16613945 4.526 +16994767 4.08 +19456653 4.014 +37706076 4.293 +38010695 4.14 +38418792 4.133 +38595669 4.032 +40038834 4.144 +50693133 4.206 +51294426 4 +52890600 4.12 +57414708 4.026 +57623989 4.031 +58977191 5.678 +59059925 4.325 +variableStep chrom=chr12 span=60 +1953668 -4.029 +9749454 -4.033 +12219969 -4.053 +12571904 -4.548 +12663417 -4.207 diff -r 6e742ffb16a5 -r eb317734e391 test-data/3_wig.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/3_wig.bed Tue Dec 01 11:49:07 2009 -0500 @@ -0,0 +1,26 @@ +chr20 1953667 1953727 + 4.029 +chr20 9749453 9749513 + 4.033 +chr20 12219968 12220028 + 4.053 +chr20 12571903 12571963 + 4.548 +chr20 12663416 12663476 + 4.207 +chr20 15198013 15198073 + 4.041 +chr20 16613944 16614004 + 4.526 +chr20 16994766 16994826 + 4.08 +chr20 19456652 19456712 + 4.014 +chr20 37706075 37706135 + 4.293 +chr20 38010694 38010754 + 4.14 +chr20 38418791 38418851 + 4.133 +chr20 38595668 38595728 + 4.032 +chr20 40038833 40038893 + 4.144 +chr20 50693132 50693192 + 4.206 +chr20 51294425 51294485 + 4.0 +chr20 52890599 52890659 + 4.12 +chr20 57414707 57414767 + 4.026 +chr20 57623988 57624048 + 4.031 +chr20 58977190 58977250 + 5.678 +chr20 59059924 59059984 + 4.325 +chr12 1953667 1953727 + -4.029 +chr12 9749453 9749513 + -4.033 +chr12 12219968 12220028 + -4.053 +chr12 12571903 12571963 + -4.548 +chr12 12663416 12663476 + -4.207 diff -r 6e742ffb16a5 -r eb317734e391 tool_conf.xml.main --- a/tool_conf.xml.main Tue Dec 01 11:07:20 2009 -0500 +++ b/tool_conf.xml.main Tue Dec 01 11:49:07 2009 -0500 @@ -47,6 +47,7 @@ <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="filters/wiggle_to_simple.xml" /> </section> <section name="FASTA manipulation" id="fasta_manipulation"> <tool file="fasta_tools/fasta_compute_length.xml" /> diff -r 6e742ffb16a5 -r eb317734e391 tool_conf.xml.sample --- a/tool_conf.xml.sample Tue Dec 01 11:07:20 2009 -0500 +++ b/tool_conf.xml.sample Tue Dec 01 11:49:07 2009 -0500 @@ -71,6 +71,7 @@ <tool file="maf/maf_to_fasta.xml" /> <tool file="fasta_tools/tabular_to_fasta.xml" /> <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="filters/wiggle_to_simple.xml" /> </section> <section name="Extract Features" id="features"> <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> diff -r 6e742ffb16a5 -r eb317734e391 tools/filters/wiggle_to_simple.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/wiggle_to_simple.py Tue Dec 01 11:49:07 2009 -0500 @@ -0,0 +1,43 @@ +#!/usr/bin/env python + +""" +Read a wiggle track and print out a series of lines containing +"chrom position score". Ignores track lines, handles bed, variableStep +and fixedStep wiggle lines. +""" +import sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +import bx.wiggle +from galaxy.tools.exception_handling import * + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def main(): + if len( sys.argv ) > 1: + in_file = open( sys.argv[1] ) + else: + in_file = open( sys.stdin ) + + if len( sys.argv ) > 2: + out_file = open( sys.argv[2], "w" ) + else: + out_file = sys.stdout + + try: + for fields in bx.wiggle.IntervalReader( UCSCOutWrapper( in_file ) ): + out_file.write( "%s\n" % "\t".join( map( str, fields ) ) ) + except UCSCLimitException: + # Wiggle data was truncated, at the very least need to warn the user. + print 'Encountered message from UCSC: "Reached output limit of 100000 data values", so be aware your data was truncated.' + except ValueError, e: + in_file.close() + out_file.close() + stop_err( str( e ) ) + + in_file.close() + out_file.close() + +if __name__ == "__main__": main() diff -r 6e742ffb16a5 -r eb317734e391 tools/filters/wiggle_to_simple.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/filters/wiggle_to_simple.xml Tue Dec 01 11:49:07 2009 -0500 @@ -0,0 +1,88 @@ +<tool id="wiggle2simple1" name="Wiggle-to-Interval"> + <description>converter</description> + <command interpreter="python">wiggle_to_simple.py $input $out_file1 </command> + <inputs> + <param format="wig" name="input" type="data" label="Convert"/> + </inputs> + <outputs> + <data format="interval" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input" value="2.wig" /> + <output name="out_file1" file="2.interval"/> + </test> + <test> + <param name="input" value="3.wig" /> + <output name="out_file1" file="3_wig.bed"/> + </test> + </tests> + <help> +**Syntax** + +This tool converts wiggle data into interval type. + +- **Wiggle format**: The .wig format is line-oriented. Wiggle data is preceded by a UCSC track definition line. Following the track definition line is the track data, which can be entered in three different formats described below. + + - **BED format** with no declaration line and four columns of data:: + + chromA chromStartA chromEndA dataValueA + chromB chromStartB chromEndB dataValueB + + - **variableStep** two column data; started by a declaration line and followed with chromosome positions and data values:: + + variableStep chrom=chrN [span=windowSize] + chromStartA dataValueA + chromStartB dataValueB + + - **fixedStep** single column data; started by a declaration line and followed with data values:: + + fixedStep chrom=chrN start=position step=stepInterval [span=windowSize] + dataValue1 + dataValue2 + +----- + +**Example** + +- input wiggle format file:: + + #track type=wiggle_0 name="Bed Format" description="BED format" + chr19 59302000 59302300 -1.0 + chr19 59302300 59302600 -0.75 + chr19 59302600 59302900 -0.50 + chr19 59302900 59303200 -0.25 + chr19 59303200 59303500 0.0 + #track type=wiggle_0 name="variableStep" description="variableStep format" + variableStep chrom=chr19 span=150 + 59304701 10.0 + 59304901 12.5 + 59305401 15.0 + 59305601 17.5 + #track type=wiggle_0 name="fixedStep" description="fixed step" visibility=full + fixedStep chrom=chr19 start=59307401 step=300 span=200 + 1000 + 900 + 800 + 700 + 600 + +- convert the above file to interval file:: + + chr19 59302000 59302300 + -1.0 + chr19 59302300 59302600 + -0.75 + chr19 59302600 59302900 + -0.5 + chr19 59302900 59303200 + -0.25 + chr19 59303200 59303500 + 0.0 + chr19 59304701 59304851 + 10.0 + chr19 59304901 59305051 + 12.5 + chr19 59305401 59305551 + 15.0 + chr19 59305601 59305751 + 17.5 + chr19 59307701 59307901 + 1000.0 + chr19 59308001 59308201 + 900.0 + chr19 59308301 59308501 + 800.0 + chr19 59308601 59308801 + 700.0 + chr19 59308901 59309101 + 600.0 + +</help> +</tool>

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[hg] galaxy 3130: Framework for recording user actions for repor...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f98643c26eb7 changeset: 3130:f98643c26eb7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 30 17:53:25 2009 -0500 description: Framework for recording user actions for reports; framework is modelled after event recording. Currently two types of actions are recorded: (a) tagging/untagging and (b) filtering/searching in grids. diffstat: lib/galaxy/config.py | 1 + lib/galaxy/model/__init__.py | 10 +++++ lib/galaxy/model/mapping.py | 13 ++++++ lib/galaxy/model/migrate/versions/0029_user_actions.py | 47 +++++++++++++++++++++++ lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/tag.py | 24 ++++++++--- lib/galaxy/web/framework/__init__.py | 17 ++++++++ lib/galaxy/web/framework/helpers/grids.py | 13 +++++- templates/dataset/edit_attributes.mako | 2 +- templates/history/view.mako | 2 +- templates/root/history.mako | 2 +- templates/tagging_common.mako | 8 ++-- universe_wsgi.ini.sample | 3 + 14 files changed, 128 insertions(+), 18 deletions(-) diffs (335 lines): diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/config.py Mon Nov 30 17:53:25 2009 -0500 @@ -79,6 +79,7 @@ self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) ) self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) ) self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) ) + self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",") diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/model/__init__.py Mon Nov 30 17:53:25 2009 -0500 @@ -1441,6 +1441,16 @@ def __init__( self, name=None, value=None ): self.name = name self.value = value + +class UserAction( object ): + def __init__( self, id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None): + self.id = id + self.create_time = create_time + self.user_id = user_id + self.session_id = session_id + self.action = action + self.params = params + self.context = context ## ---- Utility methods ------------------------------------------------------- diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/model/mapping.py Mon Nov 30 17:53:25 2009 -0500 @@ -743,6 +743,15 @@ Column( "name", Unicode( 255 ), index=True), Column( "value", Unicode( 1024 ) ) ) +UserAction.table = Table( "user_action", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "action", Unicode( 255 ) ), + Column( "context", Unicode( 512 ) ), + Column( "params", Unicode( 1024 ) ) ) + # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -1237,6 +1246,10 @@ assign_mapper( context, UserPreference, UserPreference.table, properties = {} ) + +assign_mapper( context, UserAction, UserAction.table, + properties = dict( user=relation( User.mapper ) ) + ) def db_next_hid( self ): """ diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/model/migrate/versions/0029_user_actions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0029_user_actions.py Mon Nov 30 17:53:25 2009 -0500 @@ -0,0 +1,47 @@ +""" +This migration script adds a user actions table to Galaxy. +""" + +from sqlalchemy import * +from migrate import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def display_migration_details(): + print "" + print "This migration script adds a user actions table to Galaxy." + print "" + + +# New table to store user actions. +UserAction_table = Table( "user_action", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "action", Unicode( 255 ) ), + Column( "context", Unicode( 512 ) ), + Column( "params", Unicode( 1024 ) ) ) + +def upgrade(): + display_migration_details() + metadata.reflect() + try: + UserAction_table.create() + except Exception, e: + print str(e) + log.debug( "Creating user_action table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + UserAction_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping user_action table failed: %s" % str( e ) ) \ No newline at end of file diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Mon Nov 30 17:53:25 2009 -0500 @@ -87,7 +87,7 @@ link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced" ), + grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Nov 30 17:53:25 2009 -0500 @@ -94,7 +94,7 @@ link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/web/controllers/tag.py Mon Nov 30 17:53:25 2009 -0500 @@ -28,28 +28,38 @@ @web.expose @web.require_login( "Add tag to an item." ) - def add_tag_async( self, trans, id=None, item_class=None, new_tag=None ): + def add_tag_async( self, trans, id=None, item_class=None, new_tag=None, context=None ): """ Add tag to an item. """ - item = self._get_item(trans, item_class, trans.security.decode_id(id)) - self._do_security_check(trans, item) + # Check that user owns item. + item = self._get_item(trans, item_class, trans.security.decode_id( id ) ) + self._do_security_check( trans, item ) + # Apply tag. self.tag_handler.apply_item_tags( trans.sa_session, item, new_tag.encode('utf-8') ) trans.sa_session.flush() + # Log. + params = dict( item_id=item.id, item_class=item_class, tag=new_tag) + trans.log_action( unicode( "tag"), context, params ) + @web.expose @web.require_login( "Remove tag from an item." ) - def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None ): + def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None, context=None ): """ Remove tag from an item. """ + + # Check that user owns item. item = self._get_item(trans, item_class, trans.security.decode_id(id)) - self._do_security_check(trans, item) + # Remove tag. self.tag_handler.remove_item_tag( trans, item, tag_name.encode('utf-8') ) - #print tag_name - #print unicode(tag_name) trans.sa_session.flush() + # Log. + params = dict( item_id=item.id, item_class=item_class, tag=tag_name) + trans.log_action( unicode( "untag"), context, params ) + # Retag an item. All previous tags are deleted and new tags are applied. @web.expose @web.require_login( "Apply a new set of tags to an item; previous tags are deleted." ) diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Mon Nov 30 17:53:25 2009 -0500 @@ -10,6 +10,7 @@ import base import pickle from galaxy import util +from galaxy.util.json import to_json_string pkg_resources.require( "simplejson" ) import simplejson @@ -170,6 +171,22 @@ to allow migration toward a more SQLAlchemy 0.4 style of use. """ return self.app.model.context.current + def log_action( self, action, context, params): + """ + Application-level logging of user actions. + """ + if self.app.config.log_actions: + action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) + try: + action.user = self.user + except: + action.user = None + try: + action.session_id = self.galaxy_session.id + except: + action.session_id = None + self.sa_session.add( action ) + self.sa_session.flush() def log_event( self, message, tool_id=None, **kwargs ): """ Application level logging. Still needs fleshing out (log levels and such) diff -r 9d4945bbdcf5 -r f98643c26eb7 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 30 15:33:45 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Nov 30 17:53:25 2009 -0500 @@ -200,6 +200,13 @@ trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) ) trans.sa_session.flush() + # Log grid view. + context = unicode( self.__class__.__name__ ) + params = cur_filter_dict.copy() + params['sort'] = sort_key + params['async'] = ( 'async' in kwargs ) + trans.log_action( unicode( "grid.view"), context, params ) + # Render grid. def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another @@ -340,17 +347,19 @@ # Generic column that supports tagging. class TagsColumn( TextColumn ): - def __init__( self, col_name, key, model_class, model_tag_association_class, filterable ): + def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) self.model_tag_association_class = model_tag_association_class # Tags cannot be sorted. self.sortable = False + # Column-specific attributes. self.tag_elt_id_gen = 0 + self.grid_name = grid_name def get_value( self, trans, grid, item ): self.tag_elt_id_gen += 1 elt_id="tagging-elt" + str( self.tag_elt_id_gen ) div_elt = "<div id=%s></div>" % elt_id - return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, + return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, elt_context=self.grid_name, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Mon Nov 30 15:33:45 2009 -0500 +++ b/templates/dataset/edit_attributes.mako Mon Nov 30 17:53:25 2009 -0500 @@ -59,7 +59,7 @@ </div> <div style="clear: both"></div> </div> - ${render_tagging_element(data, "dataset-tag-area", use_toggle_link="false", in_form="true", input_size="30")} + ${render_tagging_element(data, "dataset-tag-area", "edit_attributes.mako", use_toggle_link="false", in_form="true", input_size="30")} %endif %for name, spec in data.metadata.spec.items(): %if spec.visible: diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/history/view.mako --- a/templates/history/view.mako Mon Nov 30 15:33:45 2009 -0500 +++ b/templates/history/view.mako Mon Nov 30 17:53:25 2009 -0500 @@ -327,7 +327,7 @@ %if trans.get_user() is not None: <div id='history-tag-area' class="tag-element"></div> - ${render_tagging_element(history, "history-tag-area", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} + ${render_tagging_element(history, "history-tag-area", "history/view.mako", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} %endif %if not datasets: diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/root/history.mako --- a/templates/root/history.mako Mon Nov 30 15:33:45 2009 -0500 +++ b/templates/root/history.mako Mon Nov 30 17:53:25 2009 -0500 @@ -325,7 +325,7 @@ %if trans.get_user() is not None: <div id='history-tag-area' class="tag-element"></div> - ${render_tagging_element(history, "history-tag-area", get_toggle_link_text_fn='get_toggle_link_text')} + ${render_tagging_element( tagged_item=history, elt_id="history-tag-area", elt_context="history.mako", get_toggle_link_text_fn='get_toggle_link_text' )} %endif %if not datasets: diff -r 9d4945bbdcf5 -r f98643c26eb7 templates/tagging_common.mako --- a/templates/tagging_common.mako Mon Nov 30 15:33:45 2009 -0500 +++ b/templates/tagging_common.mako Mon Nov 30 17:53:25 2009 -0500 @@ -1,10 +1,10 @@ ## Render a tagging element if there is a tagged_item. %if tagged_item is not None and elt_id is not None: - ${render_tagging_element(tagged_item, elt_id=elt_id, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)} + ${render_tagging_element(tagged_item=tagged_item, elt_id=elt_id, elt_context=elt_context, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)} %endif ## Render the tags 'tags' as an autocomplete element. -<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')"> +<%def name="render_tagging_element(tagged_item, elt_id, elt_context, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')"> <script type="text/javascript"> // // Set up autocomplete tagger. @@ -75,8 +75,8 @@ tag_click_fn: ${tag_click_fn}, <% tagged_item_id = trans.security.encode_id(tagged_item.id) %> ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", + ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", add_tag_img: "${h.url_for('/static/images/add_icon.png')}", diff -r 9d4945bbdcf5 -r f98643c26eb7 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Mon Nov 30 15:33:45 2009 -0500 +++ b/universe_wsgi.ini.sample Mon Nov 30 17:53:25 2009 -0500 @@ -144,6 +144,9 @@ # Log events log_events = True +# Log user actions +log_actions = True + # Configuration for debugging middleware debug = True use_lint = False

1 0

[hg] galaxy 3136: Added some error checking to pileup_parser too...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fe853d8e062d changeset: 3136:fe853d8e062d user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Tue Dec 01 16:18:25 2009 -0500 description: Added some error checking to pileup_parser tool so that it exits with a meaningful message if the user tries to do some 6-column work on a 10-column file, or vice versa. diffstat: tools/samtools/pileup_interval.py | 16 ++++++++++++++-- 1 files changed, 14 insertions(+), 2 deletions(-) diffs (40 lines): diff -r eb317734e391 -r fe853d8e062d tools/samtools/pileup_interval.py --- a/tools/samtools/pileup_interval.py Tue Dec 01 11:49:07 2009 -0500 +++ b/tools/samtools/pileup_interval.py Tue Dec 01 16:18:25 2009 -0500 @@ -1,7 +1,7 @@ #! /usr/bin/python """ -Creates a pileup file from a bam file and a reference. +Condenses pileup format into ranges of bases. usage: %prog [options] -i, --input=i: Input pileup file @@ -18,6 +18,7 @@ from galaxy import eggs import pkg_resources; pkg_resources.require( "bx-python" ) from bx.cookbook import doc_optparse +import sys def stop_err( msg ): sys.stderr.write( msg ) @@ -56,7 +57,18 @@ bases = [] while inLine.strip() != '': lineParts = inLine.split('\t') - seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex]) + try: + seq, loc, base, cov = lineParts[seqIndex], int(lineParts[locIndex]), lineParts[baseIndex], int(lineParts[covIndex]) + except IndexError, ei: + if options.format == 'ten': + stop_err( 'It appears that you have selected 10 columns while your file has 6. Make sure that the number of columns you specify matches the number in your file.\n' + str( ei ) ) + else: + stop_err( 'There appears to be something wrong with your column index values.\n' + str( ei ) ) + except ValueError, ev: + if options.format == 'six': + stop_err( 'It appears that you have selected 6 columns while your file has 10. Make sure that the number of columns you specify matches the number in your file.\n' + str( ev ) ) + else: + stop_err( 'There appears to be something wrong with your column index values.\n' + str( ev ) ) # strout += str(startLoc) + '\n' # strout += str(bases) + '\n' # strout += '%s\t%s\t%s\t%s\n' % (seq, loc, base, cov)

1 0

[hg] galaxy 3133: Merge
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e75b55cc9e08 changeset: 3133:e75b55cc9e08 user: Enis Afgan <afgane(a)gmail.com> date: Tue Dec 01 09:53:36 2009 -0500 description: Merge diffstat: lib/galaxy/config.py | 1 + lib/galaxy/model/__init__.py | 10 +++++ lib/galaxy/model/mapping.py | 13 ++++++ lib/galaxy/model/migrate/versions/0029_user_actions.py | 47 +++++++++++++++++++++++ lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/controllers/history.py | 2 +- lib/galaxy/web/controllers/tag.py | 24 ++++++++--- lib/galaxy/web/framework/__init__.py | 17 ++++++++ lib/galaxy/web/framework/helpers/grids.py | 13 +++++- templates/dataset/edit_attributes.mako | 2 +- templates/history/view.mako | 2 +- templates/root/history.mako | 2 +- templates/tagging_common.mako | 8 ++-- universe_wsgi.ini.sample | 3 + 14 files changed, 128 insertions(+), 18 deletions(-) diffs (335 lines): diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/config.py --- a/lib/galaxy/config.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/config.py Tue Dec 01 09:53:36 2009 -0500 @@ -79,6 +79,7 @@ self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) ) self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) ) self.log_memory_usage = string_as_bool( kwargs.get( 'log_memory_usage', 'False' ) ) + self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) ) self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",") self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "main,test,tair" ).lower().split(",") diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/model/__init__.py Tue Dec 01 09:53:36 2009 -0500 @@ -1441,6 +1441,16 @@ def __init__( self, name=None, value=None ): self.name = name self.value = value + +class UserAction( object ): + def __init__( self, id=None, create_time=None, user_id=None, session_id=None, action=None, params=None, context=None): + self.id = id + self.create_time = create_time + self.user_id = user_id + self.session_id = session_id + self.action = action + self.params = params + self.context = context ## ---- Utility methods ------------------------------------------------------- diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Dec 01 09:53:36 2009 -0500 @@ -743,6 +743,15 @@ Column( "name", Unicode( 255 ), index=True), Column( "value", Unicode( 1024 ) ) ) +UserAction.table = Table( "user_action", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "action", Unicode( 255 ) ), + Column( "context", Unicode( 512 ) ), + Column( "params", Unicode( 1024 ) ) ) + # With the tables defined we can define the mappers and setup the # relationships between the model objects. @@ -1237,6 +1246,10 @@ assign_mapper( context, UserPreference, UserPreference.table, properties = {} ) + +assign_mapper( context, UserAction, UserAction.table, + properties = dict( user=relation( User.mapper ) ) + ) def db_next_hid( self ): """ diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/model/migrate/versions/0029_user_actions.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0029_user_actions.py Tue Dec 01 09:53:36 2009 -0500 @@ -0,0 +1,47 @@ +""" +This migration script adds a user actions table to Galaxy. +""" + +from sqlalchemy import * +from migrate import * + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def display_migration_details(): + print "" + print "This migration script adds a user actions table to Galaxy." + print "" + + +# New table to store user actions. +UserAction_table = Table( "user_action", metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), + Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True ), + Column( "action", Unicode( 255 ) ), + Column( "context", Unicode( 512 ) ), + Column( "params", Unicode( 1024 ) ) ) + +def upgrade(): + display_migration_details() + metadata.reflect() + try: + UserAction_table.create() + except Exception, e: + print str(e) + log.debug( "Creating user_action table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + UserAction_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping user_action table failed: %s" % str( e ) ) \ No newline at end of file diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Dec 01 09:53:36 2009 -0500 @@ -87,7 +87,7 @@ link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced" ), + grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Dec 01 09:53:36 2009 -0500 @@ -94,7 +94,7 @@ link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/web/controllers/tag.py Tue Dec 01 09:53:36 2009 -0500 @@ -28,28 +28,38 @@ @web.expose @web.require_login( "Add tag to an item." ) - def add_tag_async( self, trans, id=None, item_class=None, new_tag=None ): + def add_tag_async( self, trans, id=None, item_class=None, new_tag=None, context=None ): """ Add tag to an item. """ - item = self._get_item(trans, item_class, trans.security.decode_id(id)) - self._do_security_check(trans, item) + # Check that user owns item. + item = self._get_item(trans, item_class, trans.security.decode_id( id ) ) + self._do_security_check( trans, item ) + # Apply tag. self.tag_handler.apply_item_tags( trans.sa_session, item, new_tag.encode('utf-8') ) trans.sa_session.flush() + # Log. + params = dict( item_id=item.id, item_class=item_class, tag=new_tag) + trans.log_action( unicode( "tag"), context, params ) + @web.expose @web.require_login( "Remove tag from an item." ) - def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None ): + def remove_tag_async( self, trans, id=None, item_class=None, tag_name=None, context=None ): """ Remove tag from an item. """ + + # Check that user owns item. item = self._get_item(trans, item_class, trans.security.decode_id(id)) - self._do_security_check(trans, item) + # Remove tag. self.tag_handler.remove_item_tag( trans, item, tag_name.encode('utf-8') ) - #print tag_name - #print unicode(tag_name) trans.sa_session.flush() + # Log. + params = dict( item_id=item.id, item_class=item_class, tag=tag_name) + trans.log_action( unicode( "untag"), context, params ) + # Retag an item. All previous tags are deleted and new tags are applied. @web.expose @web.require_login( "Apply a new set of tags to an item; previous tags are deleted." ) diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Tue Dec 01 09:53:36 2009 -0500 @@ -10,6 +10,7 @@ import base import pickle from galaxy import util +from galaxy.util.json import to_json_string pkg_resources.require( "simplejson" ) import simplejson @@ -170,6 +171,22 @@ to allow migration toward a more SQLAlchemy 0.4 style of use. """ return self.app.model.context.current + def log_action( self, action, context, params): + """ + Application-level logging of user actions. + """ + if self.app.config.log_actions: + action = self.app.model.UserAction(action=action, context=context, params=unicode( to_json_string( params ) ) ) + try: + action.user = self.user + except: + action.user = None + try: + action.session_id = self.galaxy_session.id + except: + action.session_id = None + self.sa_session.add( action ) + self.sa_session.flush() def log_event( self, message, tool_id=None, **kwargs ): """ Application level logging. Still needs fleshing out (log levels and such) diff -r efed28fa6a5e -r e75b55cc9e08 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 30 16:47:18 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Dec 01 09:53:36 2009 -0500 @@ -200,6 +200,13 @@ trans.get_user().preferences[pref_name] = unicode( to_json_string( sort_key ) ) trans.sa_session.flush() + # Log grid view. + context = unicode( self.__class__.__name__ ) + params = cur_filter_dict.copy() + params['sort'] = sort_key + params['async'] = ( 'async' in kwargs ) + trans.log_action( unicode( "grid.view"), context, params ) + # Render grid. def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another @@ -340,17 +347,19 @@ # Generic column that supports tagging. class TagsColumn( TextColumn ): - def __init__( self, col_name, key, model_class, model_tag_association_class, filterable ): + def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) self.model_tag_association_class = model_tag_association_class # Tags cannot be sorted. self.sortable = False + # Column-specific attributes. self.tag_elt_id_gen = 0 + self.grid_name = grid_name def get_value( self, trans, grid, item ): self.tag_elt_id_gen += 1 elt_id="tagging-elt" + str( self.tag_elt_id_gen ) div_elt = "<div id=%s></div>" % elt_id - return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, + return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, elt_context=self.grid_name, elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) def filter( self, db_session, query, column_filter ): """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ diff -r efed28fa6a5e -r e75b55cc9e08 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Mon Nov 30 16:47:18 2009 -0500 +++ b/templates/dataset/edit_attributes.mako Tue Dec 01 09:53:36 2009 -0500 @@ -59,7 +59,7 @@ </div> <div style="clear: both"></div> </div> - ${render_tagging_element(data, "dataset-tag-area", use_toggle_link="false", in_form="true", input_size="30")} + ${render_tagging_element(data, "dataset-tag-area", "edit_attributes.mako", use_toggle_link="false", in_form="true", input_size="30")} %endif %for name, spec in data.metadata.spec.items(): %if spec.visible: diff -r efed28fa6a5e -r e75b55cc9e08 templates/history/view.mako --- a/templates/history/view.mako Mon Nov 30 16:47:18 2009 -0500 +++ b/templates/history/view.mako Tue Dec 01 09:53:36 2009 -0500 @@ -327,7 +327,7 @@ %if trans.get_user() is not None: <div id='history-tag-area' class="tag-element"></div> - ${render_tagging_element(history, "history-tag-area", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} + ${render_tagging_element(history, "history-tag-area", "history/view.mako", use_toggle_link='false', get_toggle_link_text_fn='get_toggle_link_text', editable=user_owns_history)} %endif %if not datasets: diff -r efed28fa6a5e -r e75b55cc9e08 templates/root/history.mako --- a/templates/root/history.mako Mon Nov 30 16:47:18 2009 -0500 +++ b/templates/root/history.mako Tue Dec 01 09:53:36 2009 -0500 @@ -325,7 +325,7 @@ %if trans.get_user() is not None: <div id='history-tag-area' class="tag-element"></div> - ${render_tagging_element(history, "history-tag-area", get_toggle_link_text_fn='get_toggle_link_text')} + ${render_tagging_element( tagged_item=history, elt_id="history-tag-area", elt_context="history.mako", get_toggle_link_text_fn='get_toggle_link_text' )} %endif %if not datasets: diff -r efed28fa6a5e -r e75b55cc9e08 templates/tagging_common.mako --- a/templates/tagging_common.mako Mon Nov 30 16:47:18 2009 -0500 +++ b/templates/tagging_common.mako Tue Dec 01 09:53:36 2009 -0500 @@ -1,10 +1,10 @@ ## Render a tagging element if there is a tagged_item. %if tagged_item is not None and elt_id is not None: - ${render_tagging_element(tagged_item, elt_id=elt_id, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)} + ${render_tagging_element(tagged_item=tagged_item, elt_id=elt_id, elt_context=elt_context, in_form=in_form, input_size=input_size, tag_click_fn=tag_click_fn)} %endif ## Render the tags 'tags' as an autocomplete element. -<%def name="render_tagging_element(tagged_item, elt_id, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')"> +<%def name="render_tagging_element(tagged_item, elt_id, elt_context, use_toggle_link='true', in_form='false', input_size='15', tag_click_fn='default_tag_click_fn', get_toggle_link_text_fn='default_get_toggle_link_text_fn', editable='true')"> <script type="text/javascript"> // // Set up autocomplete tagger. @@ -75,8 +75,8 @@ tag_click_fn: ${tag_click_fn}, <% tagged_item_id = trans.security.encode_id(tagged_item.id) %> ajax_autocomplete_tag_url: "${h.url_for( controller='tag', action='tag_autocomplete_data', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", - ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__ )}", + ajax_add_tag_url: "${h.url_for( controller='tag', action='add_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", + ajax_delete_tag_url: "${h.url_for( controller='tag', action='remove_tag_async', id=tagged_item_id, item_class=tagged_item.__class__.__name__, context=elt_context )}", delete_tag_img: "${h.url_for('/static/images/delete_tag_icon_gray.png')}", delete_tag_img_rollover: "${h.url_for('/static/images/delete_tag_icon_white.png')}", add_tag_img: "${h.url_for('/static/images/add_icon.png')}", diff -r efed28fa6a5e -r e75b55cc9e08 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Mon Nov 30 16:47:18 2009 -0500 +++ b/universe_wsgi.ini.sample Tue Dec 01 09:53:36 2009 -0500 @@ -144,6 +144,9 @@ # Log events log_events = True +# Log user actions +log_actions = True + # Configuration for debugging middleware debug = True use_lint = False

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[hg] galaxy 3129: Fix MAF to BED tool. This tool should be rewri...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9d4945bbdcf5 changeset: 3129:9d4945bbdcf5 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Nov 30 15:33:45 2009 -0500 description: Fix MAF to BED tool. This tool should be rewritten to not use a code file, but instead use one of the standard ways to create additional outputs, similar to how maf_to_interval functions. diffstat: tools/maf/maf_to_bed.py | 3 +-- tools/maf/maf_to_bed.xml | 4 ++-- tools/maf/maf_to_bed_code.py | 1 + 3 files changed, 4 insertions(+), 4 deletions(-) diffs (36 lines): diff -r 92d6a9796b24 -r 9d4945bbdcf5 tools/maf/maf_to_bed.py --- a/tools/maf/maf_to_bed.py Mon Nov 30 14:55:30 2009 -0500 +++ b/tools/maf/maf_to_bed.py Mon Nov 30 15:33:45 2009 -0500 @@ -15,8 +15,7 @@ input_filename = sys.argv[1] output_filename = sys.argv[2] #where to store files that become additional output - database_tmp_dir = './database/tmp' #os.path.join(os.path.split(os.path.split(os.path.realpath(output_filename))[0])[0],'tmp') #database/tmp - + database_tmp_dir = sys.argv[5] species = sys.argv[3].split(',') partial = sys.argv[4] diff -r 92d6a9796b24 -r 9d4945bbdcf5 tools/maf/maf_to_bed.xml --- a/tools/maf/maf_to_bed.xml Mon Nov 30 14:55:30 2009 -0500 +++ b/tools/maf/maf_to_bed.xml Mon Nov 30 15:33:45 2009 -0500 @@ -1,6 +1,6 @@ -<tool id="MAF_To_BED1" name="Maf to BED"> +<tool id="MAF_To_BED1" name="Maf to BED" force_history_refresh="True"> <description>Converts a MAF formated file to the BED format</description> - <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks</command> + <command interpreter="python">maf_to_bed.py $input1 $out_file1 $species $complete_blocks $__new_file_path__</command> <inputs> <param format="maf" name="input1" type="data" label="MAF file to convert"/> <param name="species" type="select" label="Select species" display="checkboxes" multiple="true" help="a separate history item will be created for each checked species"> diff -r 92d6a9796b24 -r 9d4945bbdcf5 tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py Mon Nov 30 14:55:30 2009 -0500 +++ b/tools/maf/maf_to_bed_code.py Mon Nov 30 15:33:45 2009 -0500 @@ -46,6 +46,7 @@ newdata.state = newdata.states.ERROR newdata.dbkey = dbkey newdata.init_meta() + newdata.set_meta() newdata.set_peek() app.model.context.flush() output_data_list.append(newdata)

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[hg] galaxy 3128: When setting metadata externally, substitute a...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/92d6a9796b24 changeset: 3128:92d6a9796b24 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Nov 30 14:55:30 2009 -0500 description: When setting metadata externally, substitute a MetadataTempFile object for all populated metadata FileParameters. Fixes the problem with writting to metadata FileParameter files on cluster nodes with read-only database/files directory. diffstat: lib/galaxy/datatypes/metadata.py | 21 +++- lib/galaxy/model/mapping.py | 1 + lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py | 47 +++++++++ scripts/set_metadata.py | 23 ++++- tools/regVariation/quality_filter.xml | 2 +- 5 files changed, 87 insertions(+), 7 deletions(-) diffs (172 lines): diff -r 9f7a2a3be0e7 -r 92d6a9796b24 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Mon Nov 30 11:59:54 2009 -0500 +++ b/lib/galaxy/datatypes/metadata.py Mon Nov 30 14:55:30 2009 -0500 @@ -429,7 +429,9 @@ if MetadataTempFile.is_JSONified_value( value ): value = MetadataTempFile.from_JSON( value ) if isinstance( value, MetadataTempFile ): - mf = self.new_file( dataset = parent, **value.kwds ) + mf = parent.metadata.get( self.spec.name, None) + if mf is None: + mf = self.new_file( dataset = parent, **value.kwds ) shutil.move( value.file_name, mf.file_name ) value = mf.id return value @@ -521,7 +523,7 @@ if dataset_path.false_path and dataset_path.real_path == metadata_files.dataset.file_name: return dataset_path.false_path return "" - return "%s,%s,%s,%s,%s" % ( metadata_files.filename_in, metadata_files.filename_kwds, metadata_files.filename_out, metadata_files.filename_results_code, __get_filename_override() ) + return "%s,%s,%s,%s,%s,%s" % ( metadata_files.filename_in, metadata_files.filename_kwds, metadata_files.filename_out, metadata_files.filename_results_code, __get_filename_override(), metadata_files.filename_override_metadata ) if not isinstance( datasets, list ): datasets = [ datasets ] if exec_dir is None: @@ -558,11 +560,22 @@ open( metadata_files.filename_out, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) #file to store a 'return code' indicating the results of the set_meta() call #results code is like (True/False - if setting metadata was successful/failed , exception or string of reason of success/failure ) - metadata_files.filename_results_code = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_out_%s_" % key ).name ) + metadata_files.filename_results_code = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_results_%s_" % key ).name ) simplejson.dump( ( False, 'External set_meta() not called' ), open( metadata_files.filename_results_code, 'wb+' ) ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) #file to store kwds passed to set_meta() metadata_files.filename_kwds = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_kwds_%s_" % key ).name ) simplejson.dump( kwds, open( metadata_files.filename_kwds, 'wb+' ), ensure_ascii=True ) + #existing metadata file parameters need to be overridden with cluster-writable file locations + metadata_files.filename_override_metadata = relpath( tempfile.NamedTemporaryFile( dir = tmp_dir, prefix = "metadata_override_%s_" % key ).name ) + open( metadata_files.filename_override_metadata, 'wb+' ) # create the file on disk, so it cannot be reused by tempfile (unlikely, but possible) + override_metadata = [] + for meta_key, spec_value in dataset.metadata.spec.iteritems(): + if isinstance( spec_value.param, FileParameter ) and dataset.metadata.get( meta_key, None ) is not None: + metadata_temp = MetadataTempFile() + shutil.copy( dataset.metadata.get( meta_key, None ).file_name, metadata_temp.file_name ) + override_metadata.append( ( meta_key, metadata_temp.to_JSON() ) ) + simplejson.dump( override_metadata, open( metadata_files.filename_override_metadata, 'wb+' ) ) + #add to session and flush sa_session.add( metadata_files ) sa_session.flush() metadata_files_list.append( metadata_files ) @@ -585,7 +598,7 @@ #can occur if the job was stopped before completion, but a MetadataTempFile is used in the set_meta MetadataTempFile.cleanup_from_JSON_dict_filename( metadata_files.filename_out ) dataset_key = self.get_dataset_metadata_key( metadata_files.dataset ) - for key, fname in [ ( 'filename_in', metadata_files.filename_in ), ( 'filename_out', metadata_files.filename_out ), ( 'filename_results_code', metadata_files.filename_results_code ), ( 'filename_kwds', metadata_files.filename_kwds ) ]: + for key, fname in [ ( 'filename_in', metadata_files.filename_in ), ( 'filename_out', metadata_files.filename_out ), ( 'filename_results_code', metadata_files.filename_results_code ), ( 'filename_kwds', metadata_files.filename_kwds ), ( 'filename_override_metadata', metadata_files.filename_override_metadata ) ]: try: os.remove( fname ) except Exception, e: diff -r 9f7a2a3be0e7 -r 92d6a9796b24 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Mon Nov 30 11:59:54 2009 -0500 +++ b/lib/galaxy/model/mapping.py Mon Nov 30 14:55:30 2009 -0500 @@ -358,6 +358,7 @@ Column( "filename_out", String( 255 ) ), Column( "filename_results_code", String( 255 ) ), Column( "filename_kwds", String( 255 ) ), + Column( "filename_override_metadata", String( 255 ) ), Column( "job_runner_external_pid", String( 255 ) ) ) Event.table = Table( "event", metadata, diff -r 9f7a2a3be0e7 -r 92d6a9796b24 lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0028_external_metadata_file_override.py Mon Nov 30 14:55:30 2009 -0500 @@ -0,0 +1,47 @@ +""" +This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, +allowing existing metadata files to be written when using external metadata and a cluster +set up with read-only access to database/files +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +from migrate.changeset import * +import datetime +now = datetime.datetime.utcnow +import sys, logging +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def display_migration_details(): + print "========================================" + print "This script adds the filename_override_metadata column to the JobExternalOutputMetadata table," + print" allowing existing metadata files to be written when using external metadata and a cluster" + print "set up with read-only access to database/files" + print "========================================" +def upgrade(): + display_migration_details() + # Load existing tables + metadata.reflect() + try: + job_external_output_metadata = Table( "job_external_output_metadata", metadata, autoload=True ) + col = Column( "filename_override_metadata", String( 255 ) ) + col.create( job_external_output_metadata ) + assert col is job_external_output_metadata.c.filename_override_metadata + except Exception, e: + log.debug( "Adding column 'filename_override_metadata' to job_external_output_metadata table failed: %s" % ( str( e ) ) ) + +def downgrade(): + pass diff -r 9f7a2a3be0e7 -r 92d6a9796b24 scripts/set_metadata.py --- a/scripts/set_metadata.py Mon Nov 30 11:59:54 2009 -0500 +++ b/scripts/set_metadata.py Mon Nov 30 14:55:30 2009 -0500 @@ -50,17 +50,36 @@ except: continue for filenames in sys.argv[1:]: - filename_in, filename_kwds, filename_out, filename_results_code, dataset_filename_override = filenames.split( ',' ) + fields = filenames.split( ',' ) + filename_in = fields.pop( 0 ) + filename_kwds = fields.pop( 0 ) + filename_out = fields.pop( 0 ) + filename_results_code = fields.pop( 0 ) + dataset_filename_override = fields.pop( 0 ) + #Need to be careful with the way that these parameters are populated from the filename splitting, + #because if a job is running when the server is updated, any existing external metadata command-lines + #will not have info about the newly added override_metadata file + if fields: + override_metadata = fields.pop( 0 ) + else: + override_metadata = None try: dataset = cPickle.load( open( filename_in ) ) #load DatasetInstance if dataset_filename_override: dataset.dataset.external_filename = dataset_filename_override if ext_override.get( dataset.dataset.id, None ): dataset.extension = ext_override[ dataset.dataset.id ] + #Metadata FileParameter types may not be writable on a cluster node, and are therefore temporarily substituted with MetadataTempFiles + if override_metadata: + override_metadata = simplejson.load( open( override_metadata ) ) + for metadata_name, metadata_file_override in override_metadata: + if galaxy.datatypes.metadata.MetadataTempFile.is_JSONified_value( metadata_file_override ): + metadata_file_override = galaxy.datatypes.metadata.MetadataTempFile.from_JSON( metadata_file_override ) + setattr( dataset.metadata, metadata_name, metadata_file_override ) kwds = stringify_dictionary_keys( simplejson.load( open( filename_kwds ) ) )#load kwds; need to ensure our keywords are not unicode dataset.datatype.set_meta( dataset, **kwds ) dataset.metadata.to_JSON_dict( filename_out ) # write out results of set_meta - simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded + simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has succeeded except Exception, e: simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow clear_mappers() diff -r 9f7a2a3be0e7 -r 92d6a9796b24 tools/regVariation/quality_filter.xml --- a/tools/regVariation/quality_filter.xml Mon Nov 30 11:59:54 2009 -0500 +++ b/tools/regVariation/quality_filter.xml Mon Nov 30 14:55:30 2009 -0500 @@ -61,7 +61,7 @@ </conditional> </inputs> <outputs> - <data format="maf" name="out_file1"/> + <data format="maf" name="out_file1" metadata_source="input"/> </outputs> <requirements> <requirement type="python-module">numpy</requirement>

1 0

[hg] galaxy 3127: Fixed a bug in 'fetch closest features' tool.
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9f7a2a3be0e7 changeset: 3127:9f7a2a3be0e7 user: guru date: Mon Nov 30 11:59:54 2009 -0500 description: Fixed a bug in 'fetch closest features' tool. diffstat: tools/new_operations/flanking_features.py | 5 ++--- 1 files changed, 2 insertions(+), 3 deletions(-) diffs (22 lines): diff -r 71b779fde315 -r 9f7a2a3be0e7 tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Mon Nov 30 11:56:58 2009 -0500 +++ b/tools/new_operations/flanking_features.py Mon Nov 30 11:59:54 2009 -0500 @@ -121,7 +121,7 @@ map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields - if either: + if either and (result_up or result_down): if result_up and result_down: if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)): map(outfields.append, result_up[res_ind].other) @@ -131,8 +131,7 @@ map(outfields.append, result_up[res_ind].other) elif result_down: map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval - yield outfields - + yield outfields def main(): options, args = doc_optparse.parse( __doc__ )

1 0

[hg] galaxy 3125: Fix for request_events table migration script ...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a8234f4d7012 changeset: 3125:a8234f4d7012 user: rc date: Mon Nov 30 09:35:21 2009 -0500 description: Fix for request_events table migration script for MySQL & sqlite diffstat: lib/galaxy/model/migrate/versions/0027_request_events.py | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (16 lines): diff -r 341d7c1c5c9a -r a8234f4d7012 lib/galaxy/model/migrate/versions/0027_request_events.py --- a/lib/galaxy/model/migrate/versions/0027_request_events.py Mon Nov 30 09:05:28 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0027_request_events.py Mon Nov 30 09:35:21 2009 -0500 @@ -73,9 +73,10 @@ "%s AS create_time," + \ "%s AS update_time," + \ "request.id AS request_id," + \ - "request.state AS state " + \ + "request.state AS state," + \ + "'%s' AS comment " + \ "FROM request;" - cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp() ) + cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp(), 'Imported from request table') db_session.execute( cmd ) # Delete the state column

1 0

[hg] galaxy 3122: Request events & request rejection (resolves i...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8d149264b777 changeset: 3122:8d149264b777 user: rc date: Wed Nov 25 14:06:28 2009 -0500 description: Request events & request rejection (resolves issue #221) - added request_events table - removed 'state' field in the request table - added 'new' & 'rejected' request states - color coded request states in the request grid Grids framework - added a confirm flag in grid operations which require confirmation before going through with operation diffstat: lib/galaxy/model/__init__.py | 35 +- lib/galaxy/model/mapping.py | 16 +- lib/galaxy/model/migrate/versions/0027_request_events.py | 94 ++++++ lib/galaxy/web/controllers/requests.py | 157 +++++++-- lib/galaxy/web/controllers/requests_admin.py | 299 +++++++++++++------ lib/galaxy/web/framework/helpers/grids.py | 4 +- templates/admin/requests/events.mako | 36 ++ templates/admin/requests/reject.mako | 42 ++ templates/admin/requests/show_request.mako | 13 +- templates/grid_base.mako | 6 +- templates/requests/events.mako | 39 ++ templates/requests/show_request.mako | 17 +- templates/sample/sample_events.mako | 43 +- test/base/twilltestcase.py | 9 +- test/functional/test_forms_and_requests.py | 30 +- 15 files changed, 651 insertions(+), 189 deletions(-) diffs (1296 lines): diff -r 5761948422a8 -r 8d149264b777 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Tue Nov 24 14:53:19 2009 -0500 +++ b/lib/galaxy/model/__init__.py Wed Nov 25 14:06:28 2009 -0500 @@ -1260,11 +1260,12 @@ self.content = content class Request( object ): - states = Bunch( UNSUBMITTED = 'Unsubmitted', + states = Bunch( NEW = 'New', SUBMITTED = 'Submitted', + REJECTED = 'Rejected', COMPLETE = 'Complete') def __init__(self, name=None, desc=None, request_type=None, user=None, - form_values=None, library=None, folder=None, state=False): + form_values=None, library=None, folder=None): self.name = name self.desc = desc self.type = request_type @@ -1272,19 +1273,39 @@ self.user = user self.library = library self.folder = folder - self.state = state self.samples_list = [] + def state(self): + if self.events: + return self.events[0].state + return None + def last_comment(self): + if self.events: + if self.events[0].comment: + return self.events[0].comment + else: + return '' + return 'No comment' def has_sample(self, sample_name): for s in self.samples: if s.name == sample_name: return s return False + def unsubmitted(self): + return self.state() in [ self.states.REJECTED, self.states.NEW ] + def rejected(self): + return self.state() == self.states.REJECTED def submitted(self): - return self.state == self.states.SUBMITTED - def unsubmitted(self): - return self.state == self.states.UNSUBMITTED + return self.state() == self.states.SUBMITTED + def new(self): + return self.state() == self.states.NEW def complete(self): - return self.state == self.states.COMPLETE + return self.state() == self.states.COMPLETE + +class RequestEvent( object ): + def __init__(self, request=None, request_state=None, comment=''): + self.request = request + self.state = request_state + self.comment = comment class RequestType( object ): def __init__(self, name=None, desc=None, request_form=None, sample_form=None): diff -r 5761948422a8 -r 8d149264b777 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 24 14:53:19 2009 -0500 +++ b/lib/galaxy/model/mapping.py Wed Nov 25 14:06:28 2009 -0500 @@ -618,8 +618,15 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ), Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), + Column( "deleted", Boolean, index=True, default=False ) ) + +RequestEvent.table = Table('request_event', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), Column( "state", TrimmedString( 255 ), index=True ), - Column( "deleted", Boolean, index=True, default=False ) ) + Column( "comment", TEXT ) ) Sample.table = Table('sample', metadata, Column( "id", Integer, primary_key=True ), @@ -768,9 +775,14 @@ folder=relation( LibraryFolder, primaryjoin=( Request.table.c.folder_id == LibraryFolder.table.c.id ) ), library=relation( Library, - primaryjoin=( Request.table.c.library_id == Library.table.c.id ) ) + primaryjoin=( Request.table.c.library_id == Library.table.c.id ) ), + events=relation( RequestEvent, backref="request", + order_by=desc(RequestEvent.table.c.update_time) ) ) ) +assign_mapper( context, RequestEvent, RequestEvent.table, + properties=None ) + assign_mapper( context, RequestType, RequestType.table, properties=dict( states=relation( SampleState, backref="request_type", diff -r 5761948422a8 -r 8d149264b777 lib/galaxy/model/migrate/versions/0027_request_events.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0027_request_events.py Wed Nov 25 14:06:28 2009 -0500 @@ -0,0 +1,94 @@ +""" +This migration script adds the request_event table and +removes the state field in the request table +""" +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exc import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def display_migration_details(): + print "========================================" + print "This migration script adds the request_event table and" + print "removes the state field in the request table" + print "========================================" + +def localtimestamp(): + if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +def nextval( table, col='id' ): + if migrate_engine.name == 'postgres': + return "nextval('%s_%s_seq')" % ( table, col ) + elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "null" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + + +RequestEvent_table = Table('request_event', metadata, + Column( "id", Integer, primary_key=True), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "request_id", Integer, ForeignKey( "request.id" ), index=True ), + Column( "state", TrimmedString( 255 ), index=True ), + Column( "comment", TEXT ) ) + +def upgrade(): + display_migration_details() + # Load existing tables + metadata.reflect() + # Add new request_event table + try: + RequestEvent_table.create() + except Exception, e: + log.debug( "Creating request_event table failed: %s" % str( e ) ) + # move the current state of all existing requests to the request_event table + cmd = \ + "INSERT INTO request_event " + \ + "SELECT %s AS id," + \ + "%s AS create_time," + \ + "%s AS update_time," + \ + "request.id AS request_id," + \ + "request.state AS state " + \ + "FROM request;" + cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp() ) + db_session.execute( cmd ) + + # Delete the state column + try: + Request_table = Table( "request", metadata, autoload=True ) + except NoSuchTableError: + Request_table = None + log.debug( "Failed loading table request" ) + if Request_table: + try: + Request_table.c.state.drop() + except Exception, e: + log.debug( "Deleting column 'state' to request table failed: %s" % ( str( e ) ) ) + +def downgrade(): + pass \ No newline at end of file diff -r 5761948422a8 -r 8d149264b777 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Nov 24 14:53:19 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Wed Nov 25 14:06:28 2009 -0500 @@ -28,27 +28,57 @@ return request.type.name class LastUpdateColumn( grids.TextColumn ): def get_value(self, trans, grid, request): - return request.update_time + delta = datetime.utcnow() - request.update_time + if delta > timedelta( minutes=60 ): + last_update = '%s hours' % int( delta.seconds / 60 / 60 ) + else: + last_update = '%s minutes' % int( delta.seconds / 60 ) + return last_update class StateColumn( grids.GridColumn ): + def __init__( self, col_name, key, model_class, event_class, filterable, link ): + grids.GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable, link=link) + self.event_class = event_class + def get_value(self, trans, grid, request): + if request.state() == request.states.REJECTED: + return '<div class="count-box state-color-error">%s</div>' % request.state() + elif request.state() == request.states.NEW: + return '<div class="count-box state-color-queued">%s</div>' % request.state() + elif request.state() == request.states.SUBMITTED: + return '<div class="count-box state-color-running">%s</div>' % request.state() + elif request.state() == request.states.COMPLETE: + return '<div class="count-box state-color-ok">%s</div>' % request.state() + return request.state() def filter( self, db_session, query, column_filter ): """ Modify query to filter request by state. """ if column_filter == "All": return query if column_filter: - query = query.filter( model.Request.state == column_filter ) - return query + # select r.id, r.name, re.id, re.state + # from request as r, request_event as re + # where re.request_id=r.id and re.state='Complete' and re.create_time in + # (select MAX( create_time) + # from request_event + # group by request_id) + q = query.join(self.event_class.table)\ + .filter( self.model_class.table.c.id==self.event_class.table.c.request_id )\ + .filter( self.event_class.table.c.state==column_filter )\ + .filter( self.event_class.table.c.id.in_(select(columns=[func.max(self.event_class.table.c.id)], + from_obj=self.event_class.table, + group_by=self.event_class.table.c.request_id))) + return q def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = [ model.Request.states.UNSUBMITTED, - model.Request.states.SUBMITTED, - model.Request.states.COMPLETE, - "All"] - accepted_filters = [] - for val in accepted_filter_labels_and_vals: - label = val.lower() - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = [ model.Request.states.NEW, + model.Request.states.REJECTED, + model.Request.states.SUBMITTED, + model.Request.states.COMPLETE, + "All"] + accepted_filters = [] + for val in accepted_filter_labels_and_vals: + label = val.lower() + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ @@ -66,7 +96,7 @@ num_rows_per_page = 50 preserve_state = True use_paging = True - default_filter = dict( deleted="False", state=model.Request.states.UNSUBMITTED) + default_filter = dict( deleted="False", state=model.Request.states.NEW) columns = [ NameColumn( "Name", key="name", @@ -83,23 +113,27 @@ TypeColumn( "Type" ), LastUpdateColumn( "Last update", format=time_ago ), - StateColumn( "State", - key='state', - filterable="advanced"), DeletedColumn( "Deleted", key="deleted", - visible=True, - filterable="advanced" ) + visible=False, + filterable="advanced" ), + StateColumn( "State", + model_class=model.Request, + event_class=model.RequestEvent, + key='state', + filterable="advanced", + link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ) ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[0], columns[1], columns[6] ], key="free-text-search", visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ) ), + grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ), + confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." ), grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() ) ), - grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted and item.unsubmitted() ) ), + grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted and item.new() ) ), grids.GridOperation( "Undelete", allow_multiple=True, condition=( lambda item: item.deleted ) ) ] @@ -145,9 +179,23 @@ return self.__undelete_request( trans, **kwd ) elif operation == "edit": return self.__edit_request( trans, **kwd ) + elif operation == "events": + return self.__request_events( trans, **kwd ) + # if there are one or more requests that has been rejected by the admin + # recently, then show a msg as a reminder to the user + rlist = trans.sa_session.query( trans.app.model.Request ) \ + .filter( trans.app.model.Request.table.c.deleted==False ) \ + .filter( trans.app.model.Request.table.c.user_id==trans.user.id ) + rejected = 0 + for r in rlist: + if r.rejected(): + rejected = rejected + 1 + if rejected: + kwd['status'] = 'warning' + kwd['message'] = "%d requests (highlighted in red) were rejected, click on the request name for details." \ + % rejected # Render the list view return self.request_grid( trans, **kwd ) - def __show_request(self, trans, **kwd): params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) @@ -172,6 +220,28 @@ sample_copy=self.__copy_sample(current_samples), details='hide', edit_mode='False', msg=msg, messagetype=messagetype ) + def __request_events(self, trans, **kwd): + try: + request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests', + action='list', + status='error', + message=msg, + **kwd) ) + events_list = [] + all_events = request.events + for event in all_events: + delta = datetime.utcnow() - event.update_time + if delta > timedelta( minutes=60 ): + last_update = '%s hours' % int( delta.seconds / 60 / 60 ) + else: + last_update = '%s minutes' % int( delta.seconds / 60 ) + events_list.append((event.state, last_update, event.comment)) + return trans.fill_template( '/requests/events.mako', + events_list=events_list, request=request) def request_details(self, trans, id): ''' Shows the request details @@ -187,7 +257,7 @@ value=request.type.name, helptext='')) request_details.append(dict(label='State', - value=request.state, + value=request.state(), helptext='')) request_details.append(dict(label='Date created', value=request.create_time, @@ -366,9 +436,9 @@ trans.sa_session.add( sample ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests', - action='list', - operation='show_request', - id=trans.security.encode_id(request.id)) ) + action='list', + operation='show_request', + id=trans.security.encode_id(request.id)) ) elif params.get('edit_samples_button', False) == 'Edit samples': edit_mode = 'True' return trans.fill_template( '/requests/show_request.mako', @@ -700,10 +770,15 @@ if not request: request = trans.app.model.Request(name, desc, request_type, trans.user, form_values, - library=library, folder=folder, - state=trans.app.model.Request.states.UNSUBMITTED) + library=library, folder=folder) trans.sa_session.add( request ) trans.sa_session.flush() + trans.sa_session.refresh( request ) + # create an event with state 'New' for this new request + comments = "Request created." + event = trans.app.model.RequestEvent(request, request.states.NEW, comments) + trans.sa_session.add( event ) + trans.sa_session.flush() else: request.name = name request.desc = desc @@ -712,7 +787,6 @@ request.values = form_values request.library = library request.folder = folder - request.state = trans.app.model.Request.states.UNSUBMITTED trans.sa_session.add( request ) trans.sa_session.flush() return request @@ -731,7 +805,7 @@ message="Invalid request ID", **kwd) ) if params.get('show', False) == 'True': - return self.__edit_request(trans, **kwd) + return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) elif params.get('save_changes_request_button', False) == 'Save changes' \ or params.get('edit_samples_button', False) == 'Edit samples': request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) @@ -760,7 +834,7 @@ messagetype='done', **new_kwd) ) elif params.get('refresh', False) == 'true': - return self.__edit_request(trans, **kwd) + return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) def __edit_request(self, trans, **kwd): try: @@ -819,7 +893,7 @@ message=msg, **kwd) ) # a request cannot be deleted once its submitted - if not request.unsubmitted(): + if not request.new(): delete_failed.append(request.name) else: request.deleted = True @@ -870,21 +944,22 @@ msg = self.__validate(trans, request) if msg: return trans.response.send_redirect( web.url_for( controller='requests', - action='edit', + action='list', + operation='edit', messagetype = 'error', msg=msg, - request_id=request.id, - show='True') ) + id=trans.security.encode_id(request.id) )) + # change the request state to 'Submitted' + comments = "Request moved to 'Submitted' state." + event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments) + trans.sa_session.add( event ) + trans.sa_session.flush() # get the new state new_state = request.type.states[0] for s in request.samples: event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') trans.sa_session.add( event ) trans.sa_session.flush() - # change request's submitted field - request.state = request.states.SUBMITTED - trans.sa_session.add( request ) - trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests', action='list', id=trans.security.encode_id(request.id), diff -r 5761948422a8 -r 8d149264b777 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Nov 24 14:53:19 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Nov 25 14:06:28 2009 -0500 @@ -8,6 +8,8 @@ from galaxy.web.form_builder import * from datetime import datetime, timedelta from galaxy.web.controllers.forms import get_all_forms +from sqlalchemy.sql.expression import func, and_ +from sqlalchemy.sql import select log = logging.getLogger( __name__ ) @@ -31,27 +33,58 @@ return request.type.name class LastUpdateColumn( grids.TextColumn ): def get_value(self, trans, grid, request): - return request.update_time + delta = datetime.utcnow() - request.update_time + if delta > timedelta( minutes=60 ): + last_update = '%s hours' % int( delta.seconds / 60 / 60 ) + else: + last_update = '%s minutes' % int( delta.seconds / 60 ) + return last_update class StateColumn( grids.GridColumn ): + def __init__( self, col_name, key, model_class, event_class, filterable, link ): + grids.GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable, link=link) + self.event_class = event_class + def get_value(self, trans, grid, request): + if request.state() == request.states.REJECTED: + return '<div class="count-box state-color-error">%s</div>' % request.state() + elif request.state() == request.states.NEW: + return '<div class="count-box state-color-queued">%s</div>' % request.state() + elif request.state() == request.states.SUBMITTED: + return '<div class="count-box state-color-running">%s</div>' % request.state() + elif request.state() == request.states.COMPLETE: + return '<div class="count-box state-color-ok">%s</div>' % request.state() + return request.state() def filter( self, db_session, query, column_filter ): """ Modify query to filter request by state. """ if column_filter == "All": return query if column_filter: - query = query.filter( model.Request.state == column_filter ) - return query + # select r.id, r.name, re.id, re.state + # from request as r, request_event as re + # where re.request_id=r.id and re.state='Complete' and re.create_time in + # (select MAX( create_time) + # from request_event + # group by request_id) + q = query.join(self.event_class.table)\ + .filter( self.model_class.table.c.id==self.event_class.table.c.request_id )\ + .filter( self.event_class.table.c.state==column_filter )\ + .filter( self.event_class.table.c.id.in_(select(columns=[func.max(self.event_class.table.c.id)], + from_obj=self.event_class.table, + group_by=self.event_class.table.c.request_id))) + #print column_filter, q + return q def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = [ model.Request.states.UNSUBMITTED, - model.Request.states.SUBMITTED, - model.Request.states.COMPLETE, - "All"] - accepted_filters = [] - for val in accepted_filter_labels_and_vals: - label = val.lower() - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters + """ Returns a list of accepted filters for this column. """ + accepted_filter_labels_and_vals = [ model.Request.states.NEW, + model.Request.states.REJECTED, + model.Request.states.SUBMITTED, + model.Request.states.COMPLETE, + "All"] + accepted_filters = [] + for val in accepted_filter_labels_and_vals: + label = val.lower() + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args) ) + return accepted_filters class UserColumn( grids.TextColumn ): def get_value(self, trans, grid, request): return request.user.email @@ -86,20 +119,25 @@ filterable="advanced" ), SamplesColumn( "Sample(s)", link=( lambda item: iff( item.deleted, None, dict( operation="show_request", id=item.id ) ) ), ), - TypeColumn( "Type" ), + TypeColumn( "Type", + link=( lambda item: iff( item.deleted, None, dict( operation="view_type", id=item.type.id ) ) ), ), LastUpdateColumn( "Last update", format=time_ago ), - StateColumn( "State", - key='state', - filterable="advanced"), - UserColumn( "User", - key='user.email', - model_class=model.Request, - filterable="advanced" ), DeletedColumn( "Deleted", key="deleted", - visible=True, - filterable="advanced" ) + visible=False, + filterable="advanced" ), + StateColumn( "State", + model_class=model.Request, + event_class=model.RequestEvent, + key='state', + filterable="advanced", + link=( lambda item: iff( item.deleted, None, dict( operation="events", id=item.id ) ) ), + ), + UserColumn( "User", + #key='user.email', + model_class=model.Request) + ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[6] ], @@ -107,10 +145,11 @@ visible=False, filterable="standard" ) ) operations = [ - grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ) ), + grids.GridOperation( "Submit", allow_multiple=False, condition=( lambda item: not item.deleted and item.unsubmitted() and item.samples ), + confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." ), grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Reject", allow_multiple=False, condition=( lambda item: not item.deleted and item.submitted() ) ), - grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted and item.unsubmitted() ) ), + grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted and item.new() ) ), grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), ] global_actions = [ @@ -227,6 +266,11 @@ return self.__edit_request( trans, **kwd ) elif operation == "reject": return self.__reject_request( trans, **kwd ) + elif operation == "events": + return self.__request_events( trans, **kwd ) + elif operation == "view_type": + return self.__view_request_type( trans, **kwd ) + # Render the grid view return self.request_grid( trans, **kwd ) def __show_request(self, trans, **kwd): @@ -253,7 +297,52 @@ sample_copy=self.__copy_sample(current_samples), details='hide', edit_mode='False', msg=msg, messagetype=messagetype ) - + @web.expose + @web.require_admin + def edit(self, trans, **kwd): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) + except: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message="Invalid request ID", + **kwd) ) + if params.get('show', False) == 'True': + return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) + elif params.get('save_changes_request_button', False) == 'Save changes' \ + or params.get('edit_samples_button', False) == 'Edit samples': + request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) + if not util.restore_text(params.get('name', '')): + msg = 'Please enter the <b>Name</b> of the request' + kwd['messagetype'] = 'error' + kwd['msg'] = msg + kwd['show'] = 'True' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='edit', + **kwd) ) + request = self.__save_request(trans, request, **kwd) + msg = 'The changes made to the request named %s has been saved' % request.name + if params.get('save_changes_request_button', False) == 'Save changes': + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + message=msg , + status='done') ) + elif params.get('edit_samples_button', False) == 'Edit samples': + new_kwd = {} + new_kwd['request_id'] = request.id + new_kwd['edit_samples_button'] = 'Edit samples' + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_request', + msg=msg , + messagetype='done', + **new_kwd) ) + elif params.get('refresh', False) == 'true': + return self.__edit_request(trans, id=trans.security.encode_id(request.id), **kwd) + def __edit_request(self, trans, **kwd): try: request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) @@ -311,7 +400,7 @@ message=msg, **kwd) ) # a request cannot be deleted once its submitted - if not request.unsubmitted(): + if not request.new(): delete_failed.append(request.name) else: request.deleted = True @@ -362,18 +451,24 @@ msg = self.__validate(trans, request) if msg: return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='edit', + action='list', + operation='edit', messagetype = 'error', msg=msg, - request_id=request.id, - show='True') ) - # get the new state + id=trans.security.encode_id(request.id) ) ) + # change the request state to 'Submitted' + if request.user.email is not trans.user: + comments = "Request moved to 'Submitted' state by admin (%s) on behalf of %s." % (trans.user.email, request.user.email) + else: + comments = "" + event = trans.app.model.RequestEvent(request, request.states.SUBMITTED, comments) + trans.sa_session.add( event ) + trans.sa_session.flush() + # change the state of each of the samples of thus request new_state = request.type.states[0] for s in request.samples: event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') trans.sa_session.add( event ) - # change request's submitted field - request.state = request.states.SUBMITTED trans.sa_session.add( request ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -393,15 +488,64 @@ status='error', message=msg, **kwd) ) - # change request's submitted field - request.state = request.states.UNSUBMITTED - trans.sa_session.add( request ) + return trans.fill_template( '/admin/requests/reject.mako', + request=request) + @web.expose + @web.require_admin + def reject(self, trans, **kwd): + params = util.Params( kwd ) + if params.get('cancel_reject_button', False): + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + operation='show_request', + id=kwd['id'])) + try: + request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + # validate + if not params.get('comment', ''): + return trans.fill_template( '/admin/requests/reject.mako', + request=request, messagetype='error', + msg='A comment is required for rejecting a request.') + # create an event with state 'Rejected' for this request + comments = util.restore_text( params.comment ) + event = trans.app.model.RequestEvent(request, request.states.REJECTED, comments) + trans.sa_session.add( event ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', status='done', - message='The request <b>%s</b> is now unsubmitted.' % request.name - ) ) + message='Request <b>%s</b> has been rejected.' % request.name) ) + + def __request_events(self, trans, **kwd): + try: + request = trans.sa_session.query( trans.app.model.Request ).get( trans.security.decode_id(kwd['id']) ) + except: + msg = "Invalid request ID" + log.warn( msg ) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='list', + status='error', + message=msg, + **kwd) ) + events_list = [] + all_events = request.events + for event in all_events: + delta = datetime.utcnow() - event.update_time + if delta > timedelta( minutes=60 ): + last_update = '%s hours' % int( delta.seconds / 60 / 60 ) + else: + last_update = '%s minutes' % int( delta.seconds / 60 ) + events_list.append((event.state, last_update, event.comment)) + return trans.fill_template( '/admin/requests/events.mako', + events_list=events_list, request=request) # #---- Request Creation ---------------------------------------------------------- # @@ -732,9 +876,18 @@ if not request: request = trans.app.model.Request(name, desc, request_type, user, form_values, - library=library, folder=folder, - state=trans.app.model.Request.states.UNSUBMITTED) + library=library, folder=folder) trans.sa_session.add( request ) + trans.sa_session.flush() + trans.sa_session.refresh( request ) + # create an event with state 'New' for this new request + if request.user.email is not trans.user: + comments = "Request created by admin (%s) on behalf of %s." % (trans.user.email, request.user.email) + else: + comments = "Request created." + event = trans.app.model.RequestEvent(request, request.states.NEW, comments) + trans.sa_session.add( event ) + trans.sa_session.flush() else: request.name = name request.desc = desc @@ -744,58 +897,14 @@ request.library = library request.folder = folder trans.sa_session.add( request ) - trans.sa_session.flush() + trans.sa_session.flush() + return request # -#---- Request Editing ---------------------------------------------------------- +#---- Request Page ---------------------------------------------------------- # - @web.expose - @web.require_admin - def edit(self, trans, **kwd): - params = util.Params( kwd ) - msg = util.restore_text( params.get( 'msg', '' ) ) - messagetype = params.get( 'messagetype', 'done' ) - try: - request = trans.sa_session.query( trans.app.model.Request ).get( int( params.get( 'request_id', None ) ) ) - except: - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - status='error', - message="Invalid request ID", - **kwd) ) - if params.get('show', False) == 'True': - return self.__edit_request(trans, request.id, **kwd) - elif params.get('save_changes_request_button', False) == 'Save changes' \ - or params.get('edit_samples_button', False) == 'Edit samples': - request_type = trans.sa_session.query( trans.app.model.RequestType ).get( int( params.select_request_type ) ) - if not util.restore_text(params.get('name', '')): - msg = 'Please enter the <b>Name</b> of the request' - kwd['messagetype'] = 'error' - kwd['msg'] = msg - kwd['show'] = 'True' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='edit', - **kwd) ) - request = self.__save_request(trans, request, **kwd) - msg = 'The changes made to the request named %s has been saved' % request.name - if params.get('save_changes_request_button', False) == 'Save changes': - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='list', - message=msg , - status='done') ) - elif params.get('edit_samples_button', False) == 'Edit samples': - new_kwd = {} - new_kwd['request_id'] = request.id - new_kwd['edit_samples_button'] = 'Edit samples' - return trans.response.send_redirect( web.url_for( controller='requests_admin', - action='show_request', - msg=msg , - messagetype='done', - **new_kwd) ) - elif params.get('refresh', False) == 'true': - return self.__edit_request(trans, request.id, **kwd) def __update_samples(self, request, **kwd): ''' This method retrieves all the user entered sample information and @@ -1013,7 +1122,7 @@ value=request.type.name, helptext='')) request_details.append(dict(label='State', - value=request.state, + value=request.state(), helptext='')) request_details.append(dict(label='Date created', value=request.create_time, @@ -1167,11 +1276,13 @@ if s.current_state().id != request.type.states[-1].id: complete = False if complete: - request.state = request.states.COMPLETE - else: - request.state = request.states.SUBMITTED - trans.sa_session.add( request ) - trans.sa_session.flush() + # change the request state to 'Complete' + comments = "All samples of this request are in the last sample state (%s)." % request.type.states[-1].name + event = trans.app.model.RequestEvent(request, request.states.COMPLETE, comments) + trans.sa_session.add( event ) + trans.sa_session.flush() +# trans.sa_session.add( request ) +# trans.sa_session.flush() def change_state(self, trans, sample): possible_states = sample.request.type.states curr_state = sample.current_state() diff -r 5761948422a8 -r 8d149264b777 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue Nov 24 14:53:19 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Wed Nov 25 14:06:28 2009 -0500 @@ -402,7 +402,7 @@ return query.filter( complete_filter ) class GridOperation( object ): - def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False ): + def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None, async_compatible=False, confirm=None ): self.label = label self.key = key self.allow_multiple = allow_multiple @@ -411,6 +411,8 @@ self.target = target self.url_args = url_args self.async_compatible = async_compatible + # if 'confirm' is set, then ask before completing the operation + self.confirm = confirm def get_url_args( self, item ): if self.url_args: temp = dict( self.url_args ) diff -r 5761948422a8 -r 8d149264b777 templates/admin/requests/events.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/events.mako Wed Nov 25 14:06:28 2009 -0500 @@ -0,0 +1,36 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<h2>History of Sequencing Request "${request.name}"</h2> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> + <span>Browse this request</span></a> + </li> +</ul> +<h3>User: ${request.user.email}</h3> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Last Update</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for state, updated, comments in events_list: + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td><b><a>${state}</a></b></td> + <td><a>${updated}</a></td> + <td><a>${comments}</a></td> + </tr> + %endfor + </tbody> + </table> +</div> diff -r 5761948422a8 -r 8d149264b777 templates/admin/requests/reject.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/admin/requests/reject.mako Wed Nov 25 14:06:28 2009 -0500 @@ -0,0 +1,42 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<h2>Reject Sequencing Request "${request.name}"</h2> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> + <span>Browse this request</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}"> + <span>Events</span></a> + </li> +</ul> +<h3>User: ${request.user.email}</h3> + + + +<div class="toolForm"> + <div class="toolFormTitle">Reject request</div> + <form name="event" action="${h.url_for( controller='requests_admin', action='reject', id=trans.security.encode_id(request.id))}" method="post" > + <div class="form-row"> + Rejecting this request will move the request state to <b>Rejected</b>. + </div> + <div class="form-row"> + <label>Comments</label> + <textarea name="comment" rows="5" cols="40"></textarea> + <div class="toolParamHelp" style="clear: both;"> + Required + </div> + </div> + <div class="form-row"> + <input type="submit" name="reject_button" value="Reject"/> + <input type="submit" name="cancel_reject_button" value="Cancel"/> + </div> + </form> + </div> +</div> \ No newline at end of file diff -r 5761948422a8 -r 8d149264b777 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Tue Nov 24 14:53:19 2009 -0500 +++ b/templates/admin/requests/show_request.mako Wed Nov 25 14:06:28 2009 -0500 @@ -5,11 +5,16 @@ ${render_msg( msg, messagetype )} %endif +%if request.rejected(): + ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )} +%endif + <div class="grid-header"> <h2>Sequencing Request "${request.name}"</h2> </div> <ul class="manage-table-actions"> + %if request.unsubmitted() and request.samples: <li> <a class="action-button" confirm="More samples cannot be added to this request once it is submitted. Click OK to submit." href="${h.url_for( controller='requests_admin', action='list', operation='Submit', id=trans.security.encode_id(request.id) )}"> @@ -28,6 +33,10 @@ <span>Bar codes</span></a> </li> %endif + <li> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}"> + <span>History</span></a> + </li> </ul> @@ -82,7 +91,7 @@ %if grid_index == 0: <td>${sample.bar_code}</td> <td> - %if sample.request.unsubmitted(): + %if sample.request.new(): Unsubmitted %else: <a href="${h.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> @@ -117,6 +126,8 @@ %else: <i>None</i> %endif + %elif rd['label'] == 'State': + <a href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a> %else: ${rd['value']} %endif diff -r 5761948422a8 -r 8d149264b777 templates/grid_base.mako --- a/templates/grid_base.mako Tue Nov 24 14:53:19 2009 -0500 +++ b/templates/grid_base.mako Wed Nov 25 14:06:28 2009 -0500 @@ -860,7 +860,11 @@ if operation.target: target = "target='" + operation.target + "'" %> - <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> + %if operation.confirm: + <a class="action-button" ${target} confirm="${operation.confirm}" href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> + %else: + <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> + %endif %endif %endfor </div> diff -r 5761948422a8 -r 8d149264b777 templates/requests/events.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/requests/events.mako Wed Nov 25 14:06:28 2009 -0500 @@ -0,0 +1,39 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<h2>History of Sequencing Request "${request.name}"</h2> +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> + <span>Browse this request</span></a> + </li> + <li> + <a class="action-button" href="${h.url_for( controller='requests', action='list')}"> + <span>Browse all requests</span></a> + </li> +</ul> + +%if msg: + ${render_msg( msg, messagetype )} +%endif + +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Last Update</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for state, updated, comments in events_list: + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td><b><a>${state}</a></b></td> + <td><a>${updated}</a></td> + <td><a>${comments}</a></td> + </tr> + %endfor + </tbody> + </table> +</div> diff -r 5761948422a8 -r 8d149264b777 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Tue Nov 24 14:53:19 2009 -0500 +++ b/templates/requests/show_request.mako Wed Nov 25 14:06:28 2009 -0500 @@ -6,6 +6,9 @@ ${render_msg( msg, messagetype )} %endif +%if request.rejected(): + ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )} +%endif <div class="grid-header"> <h2>Sequencing Request "${request.name}"</h2> @@ -19,6 +22,10 @@ </li> %endif <li> + <a class="action-button" href="${h.url_for( controller='requests', action='list', operation='events', id=trans.security.encode_id(request.id) )}"> + <span>History</span></a> + </li> + <li> <a class="action-button" href="${h.url_for( controller='requests', action='list')}"> <span>Browse requests</span></a> </li> @@ -73,7 +80,7 @@ </td> %if grid_index == 0: <td> - %if sample.request.unsubmitted(): + %if sample.request.new(): Unsubmitted %else: <a href="${h.url_for( controller='requests', action='show_events', sample_id=sample.id)}">${sample.current_state().name}</a> @@ -105,9 +112,11 @@ %if rd['label'] == 'Data library': %if rd['value']: <a href="${h.url_for( controller='library', action='browse_library', obj_id=request.library.id )}">${rd['value']}</a> - %else: - <i>None</i> - %endif + %elif rd['label'] == 'State': + <a href="${h.url_for( controller='requests', action='list', operation='events', id=trans.security.encode_id(request.id) )}">${rd['value']}</a> + %else: + <i>None</i> + %endif %else: ${rd['value']} %endif diff -r 5761948422a8 -r 8d149264b777 templates/sample/sample_events.mako --- a/templates/sample/sample_events.mako Tue Nov 24 14:53:19 2009 -0500 +++ b/templates/sample/sample_events.mako Wed Nov 25 14:06:28 2009 -0500 @@ -21,24 +21,25 @@ ${render_msg( msg, messagetype )} %endif - -<table class="grid"> - <thead> - <tr> - <th>State</th> - <th>Description</th> - <th>Updated</th> - <th>Comments</th> - </tr> - </thead> - <tbody> - %for state, desc, updated, comments in events_list: - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td><b><a>${state}</a></b></td> - <td><a>${desc}</a></td> - <td><a>${updated}</a></td> - <td><a>${comments}</a></td> - </tr> - %endfor - </tbody> -</table> \ No newline at end of file +<div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>State</th> + <th>Description</th> + <th>Updated</th> + <th>Comments</th> + </tr> + </thead> + <tbody> + %for state, desc, updated, comments in events_list: + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td><b><a>${state}</a></b></td> + <td><a>${desc}</a></td> + <td><a>${updated}</a></td> + <td><a>${comments}</a></td> + </tr> + %endfor + </tbody> + </table> +</div> \ No newline at end of file diff -r 5761948422a8 -r 8d149264b777 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Nov 24 14:53:19 2009 -0500 +++ b/test/base/twilltestcase.py Wed Nov 25 14:06:28 2009 -0500 @@ -1298,10 +1298,15 @@ self.home() self.visit_url( "%s/requests_admin/list?operation=Submit&id=%s" % ( self.url, self.security.encode_id( request_id ) )) self.check_page_for_string( 'The request <b>%s</b> has been submitted.' % request_name ) - def reject_request( self, request_id, request_name ): + def reject_request( self, request_id, request_name, comment ): self.home() self.visit_url( "%s/requests_admin/list?operation=Reject&id=%s" % ( self.url, self.security.encode_id( request_id ) )) - self.check_page_for_string( 'The request <b>%s</b> is now unsubmitted.' % request_name ) + self.check_page_for_string( 'Reject Sequencing Request "%s"' % request_name ) + tc.fv( "1", "comment", comment ) + tc.submit( "reject_button" ) + self.check_page_for_string( 'Request <b>%s</b> has been rejected.' % request_name ) + self.visit_url( "%s/requests/list?sort=-create_time&operation=show_request&id=%s" % ( self.url, self.security.encode_id( request_id ) )) + self.check_page_for_string( comment ) def add_bar_codes( self, request_id, request_name, bar_codes ): self.home() self.visit_url( "%s/requests_admin/bar_codes?request_id=%i" % (self.url, request_id) ) diff -r 5761948422a8 -r 8d149264b777 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Tue Nov 24 14:53:19 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Wed Nov 25 14:06:28 2009 -0500 @@ -194,9 +194,9 @@ .filter( and_( galaxy.model.Request.table.c.name==request_name, galaxy.model.Request.table.c.deleted==False ) ) \ .first() - # check if the request's state is now set to 'unsubmitted' - assert request_one.state is not request_one.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" \ - % ( request_one.name, request_one.states.UNSUBMITTED ) + # check if the request's state is now set to 'new' + assert request_one.state is not request_one.states.NEW, "The state of the request '%s' should be set to '%s'" \ + % ( request_one.name, request_one.states.NEW ) # sample fields samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] @@ -207,8 +207,8 @@ self.edit_request(request_one.id, request_one.name, request_one.name+' (Renamed)', request_one.desc+' (Re-described)', library_one.id, folder_one.id, fields) sa_session.refresh( request_one ) - # check if the request is showing in the 'unsubmitted' filter - self.check_request_grid(state='Unsubmitted', request_name=request_one.name) + # check if the request is showing in the 'new' filter + self.check_request_grid(state='New', request_name=request_one.name) # submit the request self.submit_request( request_one.id, request_one.name ) sa_session.refresh( request_one ) @@ -257,11 +257,11 @@ .filter( and_( galaxy.model.Request.table.c.name==request_name, galaxy.model.Request.table.c.deleted==False ) ) \ .first() - # check if the request is showing in the 'unsubmitted' filter - self.check_request_admin_grid(state='Unsubmitted', request_name=request_two.name) - # check if the request's state is now set to 'unsubmitted' - assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" \ - % ( request_two.name, request_two.states.UNSUBMITTED ) + # check if the request is showing in the 'new' filter + self.check_request_admin_grid(state='New', request_name=request_two.name) + # check if the request's state is now set to 'new' + assert request_two.state is not request_two.states.NEW, "The state of the request '%s' should be set to '%s'" \ + % ( request_two.name, request_two.states.NEW ) # sample fields samples = [ ( 'Sample One', [ 'S1 Field 0 Value' ] ), ( 'Sample Two', [ 'S2 Field 0 Value' ] ) ] @@ -282,10 +282,10 @@ '''Testing rejecting a request''' self.logout() self.login( email='test(a)bx.psu.edu' ) - self.reject_request( request_two.id, request_two.name ) + self.reject_request( request_two.id, request_two.name, "Rejection test comment" ) sa_session.refresh( request_two ) - # check if the request is showing in the 'unsubmitted' filter - self.check_request_admin_grid(state='Unsubmitted', request_name=request_two.name) + # check if the request is showing in the 'rejected' filter + self.check_request_admin_grid(state='Rejected', request_name=request_two.name) # check if the request's state is now set to 'submitted' - assert request_two.state is not request_two.states.UNSUBMITTED, "The state of the request '%s' should be set to '%s'" \ - % ( request_two.name, request_two.states.UNSUBMITTED ) + assert request_two.state is not request_two.states.REJECTED, "The state of the request '%s' should be set to '%s'" \ + % ( request_two.name, request_two.states.REJECTED )

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