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[hg] galaxy 3511: Remove deprecated rgenetics Lmap datatype from...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/44e9b5ca9cf0 changeset: 3511:44e9b5ca9cf0 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 21:01:20 2010 -0500 description: Remove deprecated rgenetics Lmap datatype from datatypes_conf.xml.sample Was causing buildbot problems.. diffstat: datatypes_conf.xml.sample | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r 2af472aa0844 -r 44e9b5ca9cf0 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Wed Mar 10 17:10:43 2010 -0500 +++ b/datatypes_conf.xml.sample Wed Mar 10 21:01:20 2010 -0500 @@ -194,7 +194,6 @@  <datatype extension="gg" type="galaxy.datatypes.genetics:GenomeGraphs"/>  - <datatype extension="lmap" type="galaxy.datatypes.genetics:Lmap" display_in_upload="true"/> <datatype extension="malist" type="galaxy.datatypes.genetics:MAlist" display_in_upload="true"/>  <datatype extension="lped" type="galaxy.datatypes.genetics:Lped" display_in_upload="true">

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[hg] galaxy 3510: Revert the twilltestcase upload_composite code...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/2af472aa0844 changeset: 3510:2af472aa0844 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 17:10:43 2010 -0500 description: Revert the twilltestcase upload_composite code needed for lped/pbed upload testing diffstat: test/base/twilltestcase.py | 54 ++++++++++++++++++++++++++++++++++++++++ test/functional/test_get_data.py | 6 ++-- test/functional/test_toolbox.py | 1 + 3 files changed, 58 insertions(+), 3 deletions(-) diffs (100 lines): diff -r 26c40d8e8fdc -r 2af472aa0844 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Mar 10 16:23:53 2010 -0500 +++ b/test/base/twilltestcase.py Wed Mar 10 17:10:43 2010 -0500 @@ -196,6 +196,60 @@ # Wait for upload processing to finish (TODO: this should be done in each test case instead) self.wait() + def upload_composite_datatype_file( self, ftype, ped_file='', map_file='', bim_file='', bed_file='', + fped_file='',fphe_file='',pphe_file='',fam_file='',pheno_file='',eset_file='',malist_file='', + affybatch_file='', dbkey='unspecified (?)', base_name='rgenetics' ): + """Tests uploading either of 2 different composite data types ( lped and pbed )""" + self.visit_url( "%s/tool_runner/index?tool_id=upload1" % self.url ) + # Handle refresh_on_change + self.refresh_form( "file_type", ftype ) + tc.fv( "1", "dbkey", dbkey ) + tc.fv( "1", "files_metadata|base_name", base_name ) + if ftype == 'lped': + # lped data types include a ped_file and a map_file + ped_file = self.get_filename( ped_file ) + tc.formfile( "1", "files_0|file_data", ped_file ) + map_file = self.get_filename( map_file ) + tc.formfile( "1", "files_1|file_data", map_file ) + elif ftype == 'pbed': + # pbed data types include a bim_file, a bed_file and a fam_file + bim_file = self.get_filename( bim_file ) + tc.formfile( "1", "files_0|file_data", bim_file ) + bed_file = self.get_filename( bed_file ) + tc.formfile( "1", "files_1|file_data", bed_file ) + fam_file = self.get_filename( fam_file ) + tc.formfile( "1", "files_2|file_data", fam_file ) + elif ftype == 'pphe': + # pphe data types include a phe_file + pphe_file = self.get_filename( pphe_file ) + tc.formfile( "1", "files_0|file_data", pphe_file ) + elif ftype == 'fped': + # fped data types include an fped_file only + fped_file = self.get_filename( fped_file ) + tc.formfile( "1", "files_0|file_data", fped_file ) + elif ftype == 'eset': + # eset data types include a eset_file, a pheno_file + eset_file = self.get_filename( eset_file ) + tc.formfile( "1", "files_0|file_data", eset_file ) + pheno_file = self.get_filename( pheno_file ) + tc.formfile( "1", "files_1|file_data", pheno_file ) + elif ftype == 'affybatch': + # affybatch data types include an affybatch_file, and a pheno_file + affybatch_file = self.get_filename( affybatch_file ) + tc.formfile( "1", "files_0|file_data", affybatch_file ) + pheno_file = self.get_filename( pheno_file ) + tc.formfile( "1", "files_1|file_data", pheno_file ) + else: + raise AssertionError, "Unsupported composite data type (%s) received, currently only %s data types are supported."\ + % (ftype,','.join(self.composite_extensions)) + tc.submit( "runtool_btn" ) + self.check_page_for_string( 'The following job has been succesfully added to the queue:' ) + check_str = base_name #'Uploaded Composite Dataset (%s)' % ftype + self.check_page_for_string( check_str ) + # Wait for upload processing to finish (TODO: this should be done in each test case instead) + self.wait() + self.check_history_for_string( check_str ) + # Functions associated with histories def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" diff -r 26c40d8e8fdc -r 2af472aa0844 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Wed Mar 10 16:23:53 2010 -0500 +++ b/test/functional/test_get_data.py Wed Mar 10 17:10:43 2010 -0500 @@ -183,7 +183,7 @@ # We'll test against the resulting ped file and map file for correctness self.verify_composite_datatype_file_content( 'rgenetics.ped', str( hda.id ) ) self.verify_composite_datatype_file_content( 'rgenetics.map', str( hda.id ) ) - self.check_history_for_string( "Uploaded Composite Dataset (lped)" ) + self.check_history_for_string( "rgenetics" ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0060_upload_file( self ): """Test uploading pbed composite datatype file, manually setting the file format""" @@ -205,7 +205,7 @@ self.verify_composite_datatype_file_content( 'rgenetics.bim', str( hda.id ) ) self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda.id ) ) self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda.id ) ) - self.check_history_for_string( "Uploaded Composite Dataset (pbed)" ) + self.check_history_for_string( "rgenetics" ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_0065_upload_file( self ): """Test uploading asian_chars_1.txt, NOT setting the file format""" @@ -576,4 +576,4 @@ self.check_history_for_string( 'hello world' ) self.delete_history( id=self.security.encode_id( history.id ) ) def test_9999_clean_up( self ): - self.logout() \ No newline at end of file + self.logout() diff -r 26c40d8e8fdc -r 2af472aa0844 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Wed Mar 10 16:23:53 2010 -0500 +++ b/test/functional/test_toolbox.py Wed Mar 10 17:10:43 2010 -0500 @@ -161,3 +161,4 @@ m.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) d['test_tool_%06d' % j] = m G[ n ] = new.classobj( n, s, d ) +

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[hg] galaxy 3509: Updated functional tests for \"multivariate st...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/26c40d8e8fdc changeset: 3509:26c40d8e8fdc user: gua110 date: Wed Mar 10 16:23:53 2010 -0500 description: Updated functional tests for \"multivariate statistics\" tools, by shortening the number of decimal places displayed, so that they pass on all test platforms. diffstat: test-data/cca_out1.tabular | 30 +- test-data/cca_out2.pdf | 4 +- test-data/kcca_out1.tabular | 602 +++++++++++++++++++------------------- test-data/kcca_out2.tabular | 602 +++++++++++++++++++------------------- test-data/kpca_out1.tabular | 602 +++++++++++++++++++------------------- test-data/kpca_out2.pdf | 4 +- test-data/kpca_out3.tabular | 602 +++++++++++++++++++------------------- test-data/kpca_out4.pdf | 4 +- test-data/pca_out1.tabular | 312 ++++++++++---------- test-data/pca_out2.pdf | 4 +- test-data/pca_out3.tabular | 312 ++++++++++---------- test-data/pca_out4.pdf | 4 +- tools/multivariate_stats/cca.py | 18 +- tools/multivariate_stats/kcca.py | 6 +- tools/multivariate_stats/kpca.py | 6 +- tools/multivariate_stats/pca.py | 19 +- 16 files changed, 1568 insertions(+), 1563 deletions(-) diffs (truncated from 3327 to 3000 lines): diff -r 07a608852925 -r 26c40d8e8fdc test-data/cca_out1.tabular --- a/test-data/cca_out1.tabular Wed Mar 10 16:11:59 2010 -0500 +++ b/test-data/cca_out1.tabular Wed Mar 10 16:23:53 2010 -0500 @@ -1,22 +1,22 @@ #Component 1 2 -#Correlation 0.940897180432 0.131074795925 -#F-statistic 144.410560578 2.5696974623 -#p-value 6.21285598619e-68 0.111075110551 +#Correlation 0.9409 0.1311 +#F-statistic 144.4 2.57 +#p-value 6.213e-68 0.1111 #X-Coefficients 1 2 -c3 1.50661351834 -3.37790409332 -c4 -0.537226204038 3.65944099051 +c3 1.507 -3.378 +c4 -0.5372 3.659 #Y-Coefficients 1 2 -c1 6.35046749378 3.37940792566 -c2 -2.6597206473 6.66976562808 +c1 6.35 3.379 +c2 -2.66 6.67 #X-Loadings 1 2 -c3 0.989395177676 0.145248691528 -c4 0.913276653253 0.407339851504 +c3 0.9894 0.1452 +c4 0.9133 0.4073 #Y-Loadings 1 2 -c1 0.928869265104 0.370407732566 -c2 -0.469775462051 0.882785939656 +c1 0.9289 0.3704 +c2 -0.4698 0.8828 #X-CrossLoadings 1 2 -c3 0.930919133009 0.0190384426004 -c4 0.859299428 0.0533919879079 +c3 0.9309 0.01904 +c4 0.8593 0.05339 #Y-CrossLoadings 1 2 -c1 0.873970472527 0.0485511179549 -c2 -0.44201040768 0.115710986885 +c1 0.874 0.04855 +c2 -0.442 0.1157 diff -r 07a608852925 -r 26c40d8e8fdc test-data/cca_out2.pdf --- a/test-data/cca_out2.pdf Wed Mar 10 16:11:59 2010 -0500 +++ b/test-data/cca_out2.pdf Wed Mar 10 16:23:53 2010 -0500 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100303132536) -/ModDate (D:20100303132536) +/CreationDate (D:20100310155029) +/ModDate (D:20100310155029) /Title (R Graphics Output) /Producer (R 2.10.0) /Creator (R) diff -r 07a608852925 -r 26c40d8e8fdc test-data/kcca_out1.tabular --- a/test-data/kcca_out1.tabular Wed Mar 10 16:11:59 2010 -0500 +++ b/test-data/kcca_out1.tabular Wed Mar 10 16:23:53 2010 -0500 @@ -1,304 +1,304 @@ #Component 1 2 3 4 -#Correlation -0.999499965799 0.999499965799 -0.937388978867 0.937388978867 +#Correlation -0.9995 0.9995 -0.9374 0.9374 #Estimated X-coefficients 1 2 3 4 -1 -0.00159226306681 -0.00159226306681 0.0347922336733 0.0347922336734 -2 -0.00110978716164 -0.00110978716146 0.0325550634964 0.0325550634964 -3 0.000104871380431 0.00010487138039 0.0183484731624 0.0183484731623 -4 0.00102415734634 0.00102415734636 -0.00485228064778 -0.00485228064775 -5 -0.000169999236028 -0.000169999236004 0.0524192345792 0.0524192345792 -6 0.00230258587505 0.00230258587502 0.0196794881537 0.0196794881537 -7 0.00145199861756 0.00145199861756 0.00575575672441 0.00575575672438 -8 -0.00159595387536 -0.00159595387541 0.0382833844726 0.0382833844726 -9 0.00360877029314 0.00360877029312 -0.0750970801906 -0.0750970801906 -10 -0.00136083597277 -0.00136083597278 0.0318384011561 0.0318384011561 -11 -0.000806991906868 -0.000806991906869 0.00139328931528 0.00139328931529 -12 -0.000200007372161 -0.000200007372182 0.0392128558972 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-/CreationDate (D:20100303121837) -/ModDate (D:20100303121837) +/CreationDate (D:20100310154313) +/ModDate (D:20100310154313) /Title (R Graphics Output) /Producer (R 2.10.0) /Creator (R) diff -r 07a608852925 -r 26c40d8e8fdc test-data/pca_out1.tabular --- a/test-data/pca_out1.tabular Wed Mar 10 16:11:59 2010 -0500 +++ b/test-data/pca_out1.tabular Wed Mar 10 16:23:53 2010 -0500 @@ -1,159 +1,159 @@ #Component 1 2 3 4 -#Std. deviation 0.959802547771 0.143553847861 0.383866224491 1.70611197867 -#Proportion of variance explained 0.230305232677 0.00515192680891 0.0368383195763 0.727704520938 +#Std. deviation 0.9598 0.1436 0.3839 1.706 +#Proportion of variance explained 0.2303 0.005152 0.03684 0.7277 #Loadings 1 2 3 4 -c1 0.522371620408 -0.37231836335 0.721016809062 0.2619955869 -c2 -0.263354915314 -0.925556494147 -0.242032877214 -0.124134810063 -c3 0.581254005598 -0.0210947768412 -0.140892258488 -0.80115426908 -c4 0.565611049883 -0.0654157690789 -0.633801403356 0.523546271604 +c1 0.5224 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0.2213 +148 1.521 -0.2668 -0.1793 0.1189 +149 1.376 -1.016 -0.9314 0.02415 +150 0.9593 0.02228 -0.5288 -0.1637 diff -r 07a608852925 -r 26c40d8e8fdc test-data/pca_out2.pdf --- a/test-data/pca_out2.pdf Wed Mar 10 16:11:59 2010 -0500 +++ b/test-data/pca_out2.pdf Wed Mar 10 16:23:53 2010 -0500 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100303130628) -/ModDate (D:20100303130628) +/CreationDate (D:20100310155829) +/ModDate (D:20100310155829) /Title (R Graphics Output) /Producer (R 2.10.0) /Creator (R) diff -r 07a608852925 -r 26c40d8e8fdc test-data/pca_out3.tabular --- a/test-data/pca_out3.tabular Wed Mar 10 16:11:59 2010 -0500 +++ b/test-data/pca_out3.tabular Wed Mar 10 16:23:53 2010 -0500 @@ -1,159 +1,159 @@ #Component 1 2 3 4 -#Std. deviation 0.490539105967 0.153379073796 0.279285544512 2.04857881547 -#Proportion of variance explained 0.0530155678505 0.00518308545019 0.017185139525 0.924616207174 +#Std. deviation 0.4905 0.1534 0.2793 2.049 +#Proportion of variance explained 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1 0

[hg] galaxy 3508: Remove redundant composite_extensions - not ne...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/07a608852925 changeset: 3508:07a608852925 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 16:11:59 2010 -0500 description: Remove redundant composite_extensions - not needed with new composite output test framework diffstat: test/base/twilltestcase.py | 2 -- 1 files changed, 0 insertions(+), 2 deletions(-) diffs (12 lines): diff -r 70930ea26347 -r 07a608852925 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Mar 10 16:09:37 2010 -0500 +++ b/test/base/twilltestcase.py Wed Mar 10 16:11:59 2010 -0500 @@ -23,8 +23,6 @@ log = logging.getLogger( __name__ ) class TwillTestCase( unittest.TestCase ): - composite_extensions = ['html','lped','pbed','fped','pphe','eigenstratgeno','eset','affybatch','malist','test-data' ] - def setUp( self ): # Security helper

1 0

[hg] galaxy 3507: Cleanup genetics.py
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/70930ea26347 changeset: 3507:70930ea26347 user: fubar: ross Lazarus at gmail period com date: Wed Mar 10 16:09:37 2010 -0500 description: Cleanup genetics.py Allow download of composite objects from libraries so content is in the archive Allow download of composite objects from histories ditto (current default is zip) Small fix to missing param in download from library Small fix to twilltestcase when testing a tool with hidden form fields diffstat: lib/galaxy/datatypes/genetics.py | 468 ++++++++++++++------------ lib/galaxy/tools/parameters/grouping.py | 10 +- lib/galaxy/web/controllers/dataset.py | 142 +++++++- lib/galaxy/web/controllers/library_common.py | 1 + test/base/twilltestcase.py | 57 +-- 5 files changed, 414 insertions(+), 264 deletions(-) diffs (1190 lines): diff -r 9701e5ee128d -r 70930ea26347 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Wed Mar 10 14:25:34 2010 -0500 +++ b/lib/galaxy/datatypes/genetics.py Wed Mar 10 16:09:37 2010 -0500 @@ -1,5 +1,6 @@ """ rgenetics datatypes +Use at your peril Ross Lazarus for the rgenetics and galaxy projects @@ -10,6 +11,7 @@ ross lazarus for rgenetics august 20 2007 """ + import logging, os, sys, time, tempfile, shutil, string, glob import data from galaxy import util @@ -24,186 +26,172 @@ from galaxy.datatypes.interval import Interval from galaxy.util.hash_util import * -log = logging.getLogger(__name__) +gal_Log = logging.getLogger(__name__) +verbose = False -class GenomeGraphs(Interval): +class GenomeGraphs( Tabular ): + """ + Tab delimited data containing a marker id and any number of numeric values + """ - """gg version viewable at ucsc of Gff format""" - file_ext = "gg" - column_names = [ 'Seqname', 'Source', 'Feature', 'Start', 'End', 'Score', 'Strand', 'Frame', 'Group' ] + MetadataElement( name="markerCol", default=1, desc="Marker ID column", param=metadata.ColumnParameter ) + MetadataElement( name="columns", default=3, desc="Number of columns", readonly=True ) + MetadataElement( name="column_types", default=[], desc="Column types", readonly=True, visible=False ) + file_ext = 'gg' - """Add metadata elements""" - MetadataElement( name="columns", default=9, desc="Number of columns", readonly=True, visible=False ) - MetadataElement( name="column_types", default=['str','str','str','int','int','int','str','str','str'], param=metadata.ColumnTypesParameter, desc="Column types", readonly=True, visible=False ) - MetadataElement( name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter ) - MetadataElement( name="startCol", default=4, desc="Start column", param=metadata.ColumnParameter ) - MetadataElement( name="endCol", default=5, desc="End column", param=metadata.ColumnParameter ) - MetadataElement( name="strandCol", desc="Strand column (click box & select)", param=metadata.ColumnParameter, optional=True, no_value=0 ) - ###do we need to repeat these? they are the same as should be inherited from interval type + def __init__(self, **kwd): + """ + Initialize gg datatype, by adding UCSC display apps + """ + Tabular.__init__(self, **kwd) + self.add_display_app ( 'ucsc', 'Genome Graph', 'as_ucsc_display_file', 'ucsc_links' ) + - def __init__(self, **kwd): - """Initialize datatype, by adding GBrowse display app""" - Interval.__init__(self, **kwd) - self.add_display_app ( 'ucsc', 'display at UCSC', 'as_ucsc_display_file', 'ucsc_links' ) + def set_meta(self,dataset,**kwd): + Tabular.set_meta( self, dataset, **kwd) + dataset.metadata.markerCol = 1 + header = file(dataset.file_name,'r').readlines()[0].strip().split('\t') + dataset.metadata.columns = len(header) + t = ['numeric' for x in header] + t[0] = 'string' + dataset.metadata.column_types = t + return True + def as_ucsc_display_file( self, dataset, **kwd ): - return open( dataset.file_name ) - def set_meta( self, dataset, overwrite = True, **kwd ): - i = 0 - for i, line in enumerate( file ( dataset.file_name ) ): - line = line.rstrip('\r\n') - if line and not line.startswith( '#' ): - elems = line.split( '\t' ) - if len(elems) == 9: - try: - int( elems[3] ) - int( elems[4] ) - break - except: - pass - Interval.set_meta( self, dataset, overwrite = overwrite, skip = i ) + """ + Returns file + """ + return file(dataset.file_name,'r') + + def ucsc_links( self, dataset, type, app, base_url ): + """ + from the ever-helpful angie hinrichs angie(a)soe.ucsc.edu + a genome graphs call looks like this + http://genome.ucsc.edu/cgi-bin/hgGenome?clade=mammal&org=Human&db=hg18&hgGe… + &hgGenome_dataSetDescription=test&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess + &hgGenome_columnLabels=best%20guess&hgGenome_maxVal=&hgGenome_labelVals= + &hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=http://galaxy.esphealth.org/datasets/333/display/index + &hgGenome_doSubmitUpload=submit + Galaxy gives this for an interval file + http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr1:1-1000&hgt.cu… + http%3A%2F%2Fgalaxy.esphealth.org%2Fdisplay_as%3Fid%3D339%26display_app%3Ducsc + """ + ret_val = [] + ggtail = 'hgGenome_doSubmitUpload=submit' + if not dataset.dbkey: + dataset.dbkey = 'hg18' # punt! + if dataset.has_data: + for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): + if site_name in app.config.ucsc_display_sites: + site_url = site_url.replace('/hgTracks?','/hgGenome?') # for genome graphs + internal_url = "%s" % url_for( controller='dataset', + dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) + display_url = urllib.quote_plus( display_url ) + # was display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + #redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) + sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] + #sl.append("&hgt.customText=%s") + sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) + sl.append("&hgGenome_formatType=best guess&hgGenome_markerType=best guess") + sl.append("&hgGenome_columnLabels=first row&hgGenome_maxVal=&hgGenome_labelVals=") + sl.append("&hgGenome_doSubmitUpload=submit") + sl.append("&hgGenome_maxGapToFill=25000000&hgGenome_uploadFile=%s" % display_url) + s = ''.join(sl) + s = urllib.quote_plus(s) + redirect_url = s + log.debug('## rg gg ucsc rdurl=%s; s = %s' % (redirect_url,s)) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( (site_name, link) ) + return ret_val + def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" + """ + Create HTML table, used for displaying peek + """ + npeek = 5 out = ['<table cellspacing="0" cellpadding="3">'] - comments = [] + f = open(dataset.file_name,'r') + d = [f.next() for x in range(npeek)] + hasheader = 0 + try: + test = ['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics + except: + hasheader = 1 try: # Generate column header out.append( '<tr>' ) - for i, name in enumerate( self.column_names ): - out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) + if hasheader: + for i, name in enumerate(d[0].split() ): + out.append( '<th>%s.%s</th>' % ( str( i+1 ), name ) ) + d.pop(0) + out.append('</tr>') + for row in d: + out.append('<tr>') + out.append(''.join(['<td>%s</td>' % x for x in row.split()])) + out.append('</tr>') out.append( '</table>' ) out = "".join( out ) except Exception, exc: out = "Can't create peek %s" % exc return out - def get_estimated_display_viewport( self, dataset ): + + def validate( self, dataset ): """ - Return a chrom, start, stop tuple for viewing a file. There are slight differences between gff 2 and gff 3 - formats. This function should correctly handle both... + Validate a gg file - all numeric after header row """ - if True or (dataset.has_data() and dataset.state == dataset.states.OK): - try: - seqid = '' - start = 2147483647 # Maximum value of a signed 32 bit integer ( 2**31 - 1 ) - stop = 0 - for i, line in enumerate( file( dataset.file_name ) ): - if i == 0: # track stuff there - continue - line = line.rstrip( '\r\n' ) - if not line: - continue - if not line.startswith( '#' ): - elems = line.split( '\t' ) - if not seqid: - # We can only set the viewport for a single chromosome - seqid = elems[0] - if seqid == elems[0]: - # Make sure we have not spanned chromosomes - start = min( start, int( elems[3] ) ) - stop = max( stop, int( elems[4] ) ) - else: - # We've spanned a chromosome - break - if i > 10: # span 10 features - break - except: - seqid, start, stop = ( '', '', '' ) - return ( seqid, str( start ), str( stop ) ) - else: - return ( '', '', '' ) - def gbrowse_links( self, dataset, type, app, base_url ): - ret_val = [] - if dataset.has_data: - viewport_tuple = self.get_estimated_display_viewport( dataset ) - seqid = viewport_tuple[0] - start = viewport_tuple[1] - stop = viewport_tuple[2] - if seqid and start and stop: - for site_name, site_url in util.get_gbrowse_sites_by_build( dataset.dbkey ): - if site_name in app.config.gbrowse_display_sites: - link = "%s?start=%s&stop=%s&ref=%s&dbkey=%s" % ( site_url, start, stop, seqid, dataset.dbkey ) - ret_val.append( ( site_name, link ) ) - return ret_val - def ucsc_links( self, dataset, type, app, base_url ): - ret_val = [] - if dataset.has_data: - viewport_tuple = self.get_estimated_display_viewport(dataset) - if viewport_tuple: - chrom = viewport_tuple[0] - start = viewport_tuple[1] - stop = viewport_tuple[2] - if start == '' or int(start) < 1: - start='1' - if stop == '' or int(stop) <= start: - stop = '%d' % (int(start) + 10000) - for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: - # HACK: UCSC doesn't support https, so force http even - # if our URL scheme is https. Making this work - # requires additional hackery in your upstream proxy. - # If UCSC ever supports https, remove this hack. - internal_url = "%s" % url_for( controller='dataset', - dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) - redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop) ) - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) - else: - log.debug('@@@ gg ucsc_links - no viewport_tuple') - return ret_val + errors = list() + infile = open(dataset.file_name, "r") + header= infile.next() # header + for i,row in enumerate(infile): + ll = row.strip().split('\t')[1:] # first is alpha feature identifier + badvals = [] + for j,x in enumerate(ll): + try: + x = float(x) + except: + badval.append('col%d:%s' % (j+1,x)) + if len(badvals) > 0: + errors.append('row %d, %s' % (' '.join(badvals))) + return errors + def sniff( self, filename ): """ - Determines whether the file is in gff format - - GFF lines have nine required fields that must be tab-separated. + Determines whether the file is in gg format """ f = open(filename,'r') - headers = f.readline().split - if headers[0].lower() == 'track': - headers = f.readline.split() + headers = f.readline().split() + rows = [f.readline().split()[1:] for x in range(3)] # small sample #headers = get_headers( filename, '\t' ) - try: - if len(headers) < 2: - return False - for hdr in headers: - if hdr and hdr[0].startswith( '##gff-version' ) and hdr[0].find( '2' ) < 0: - return False - if hdr and hdr[0] and not hdr[0].startswith( '#' ): - if len(hdr) != 9: - return False - try: - int( hdr[3] ) - int( hdr[4] ) - except: - return False - if hdr[5] != '.': - try: - score = int(hdr[5]) - except: - return False - if (score < 0 or score > 1000): - return False - if hdr[6] not in data.valid_strand: - return False - return True - except: - return False + for row in rows: + try: + nums = [float(x) for x in row] # first col has been removed + except: + return false + return true + class rgTabList(Tabular): - """ + """ for sampleid and for featureid lists of exclusions or inclusions in the clean tool featureid subsets on statistical criteria -> specialized display such as gg """ file_ext = "rgTList" + def __init__(self, **kwd): - """Initialize featurelistt datatype""" + """ + Initialize featurelistt datatype + """ Tabular.__init__( self, **kwd ) self.column_names = [] + def make_html_table( self, dataset, skipchars=[] ): - """Create HTML table, used for displaying peek""" + """ + Create HTML table, used for displaying peek + """ out = ['<table cellspacing="0" cellpadding="3">'] comments = [] try: @@ -222,8 +210,9 @@ out = "Can't create peek %s" % exc return out + class rgSampleList(rgTabList): - """ + """ for sampleid exclusions or inclusions in the clean tool output from QC eg excess het, gender error, ibd pair member,eigen outlier,excess mendel errors,... since they can be uploaded, should be flexible @@ -240,9 +229,8 @@ self.column_names[0] = 'FID' self.column_names[1] = 'IID' # this is what Plink wants as at 2009 + def sniff(self,filename): - """ - """ infile = open(dataset.file_name, "r") header= infile.next() # header if header[0] == 'FID' and header[1] == 'IID': @@ -264,12 +252,17 @@ rgTabList.__init__( self, **kwd ) for i,s in enumerate(['#FeatureId', 'Chr', 'Genpos', 'Mappos']): self.column_names[i] = s + class Rgenetics(Html): """ - class to use for rgenetics + base class to use for rgenetics datatypes + derived from html - composite datatype elements + stored in extra files path """ - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="rgenetics", readonly=True, set_in_upload=True) + + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="rgenetics", + readonly=True, set_in_upload=True) composite_type = 'auto_primary_file' allow_datatype_change = False @@ -279,16 +272,22 @@ rval = ['<html><head><title>Rgenetics Galaxy Composite Dataset </title></head><p/>'] rval.append('<div>This composite dataset is composed of the following files:<p/><ul>') for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): + fn = composite_name opt_text = '' if composite_file.optional: opt_text = ' (optional)' - rval.append( '<li><a href="%s" type="application/binary">%s</a>%s' % ( composite_name, composite_name, opt_text ) ) + if composite_file.get('description'): + rval.append( '<li><a href="%s" type="application/binary">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) ) + else: + rval.append( '<li><a href="%s" type="application/binary">%s</a>%s</li>' % ( fn, fn, opt_text ) ) rval.append( '</ul></div></html>' ) return "\n".join( rval ) + def regenerate_primary_file(self,dataset): """ cannot do this until we are setting metadata """ + guessmt = {'.log':'text/plain','.ped':'text/plain', '.map':'text/plain','.out':'text/plain','.in':'text/plain'} def fix(oldpath,newbase): old,e = os.path.splitext(oldpath) head,rest = os.path.split(old) @@ -301,44 +300,45 @@ efp = dataset.extra_files_path flist = os.listdir(efp) proper_base = bn - rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Comprises the following files:<p/><ul>' % (bn)] + rval = ['<html><head><title>Files for Composite Dataset %s</title></head><p/>Composite %s contains the following files:<p/><ul>' % (dataset.name,dataset.name)] for i,fname in enumerate(flist): newpath = fix(os.path.join(efp,fname),proper_base) sfname = os.path.split(newpath)[-1] - rval.append( '<li><a href="%s">%s</a>' % ( sfname, sfname ) ) + f,e = os.path.splitext(fname) + mt = guessmt.get(e,'application/binary') + rval.append( '<li><a href="%s" mimetype="%s">%s</a></li>' % ( sfname, mt, sfname) ) rval.append( '</ul></html>' ) f = file(dataset.file_name,'w') f.write("\n".join( rval )) f.write('\n') f.close() + def set_meta( self, dataset, **kwd ): + """ for lped/pbed eg + """ + Html.set_meta( self, dataset, **kwd ) if kwd.get('overwrite') == False: - #log.debug('@@@ rgenetics set_meta called with overwrite = False') + if verbose: + gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False') return True try: efp = dataset.extra_files_path except: - #log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name)) + if verbose: + gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name)) return False try: flist = os.listdir(efp) except: - #log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name)) + if verbose: gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name)) return False if len(flist) == 0: - #log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp)) + if verbose: + gal_Log.debug('@@@rgenetics set_meta failed - %s efp %s is empty?' % (dataset.name,efp)) return False - bn = None - for f in flist: - n,e = os.path.splitext(f)[0] - if (not bn) and e in ('.ped','.map','.bim','.fam'): - bn = n - dataset.metadata.base_name = bn - if not bn: - bn = '?' self.regenerate_primary_file(dataset) if not dataset.info: dataset.info = 'Galaxy genotype datatype object' @@ -346,22 +346,23 @@ dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit' return True + class SNPMatrix(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + BioC SNPMatrix Rgenetics data collections """ file_ext="snpmatrix" - def set_peek( self, dataset, is_multi_byte=False ): + def set_peek( self, dataset, **kwd ): if not dataset.dataset.purged: dataset.peek = "Binary RGenetics file" dataset.blurb = data.nice_size( dataset.get_size() ) else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + def sniff(self,filename): - """ - need to check the file header hex code + """ need to check the file header hex code """ infile = open(dataset.file_name, "b") head = infile.read(16) @@ -371,9 +372,10 @@ else: return True + class Lped(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + linkage pedigree (ped,map) Rgenetics data collections """ file_ext="lped" @@ -382,25 +384,24 @@ self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = True ) self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = True ) + class Pphe(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + Plink phenotype file - header must have FID\tIID... Rgenetics data collections """ file_ext="pphe" def __init__( self, **kwd ): Rgenetics.__init__(self, **kwd) - self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.pphe', description = 'Plink Phenotype File', substitute_name_with_metadata = 'base_name', is_binary = True ) -class Lmap(Rgenetics): - """ - fake class to distinguish different species of Rgenetics data collections - """ - file_ext="lmap" + + class Fphe(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + fbat pedigree file - mad format with ! as first char on header row + Rgenetics data collections """ file_ext="fphe" @@ -410,7 +411,7 @@ class Phe(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + Phenotype file """ file_ext="phe" @@ -418,9 +419,12 @@ Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.phe', description = 'Phenotype File', substitute_name_with_metadata = 'base_name' ) + + class Fped(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + FBAT pedigree format - single file, map is header row of rs numbers. Strange. + Rgenetics data collections """ file_ext="fped" @@ -428,9 +432,10 @@ Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.fped', description = 'FBAT format pedfile', substitute_name_with_metadata = 'base_name' ) + class Pbed(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + Plink Binary compressed 2bit/geno Rgenetics data collections """ file_ext="pbed" @@ -442,7 +447,9 @@ class Eigenstratgeno(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + Eigenstrat format - may be able to get rid of this + if we move to shellfish + Rgenetics data collections """ file_ext="eigenstratgeno" @@ -451,10 +458,13 @@ self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name', is_binary = True ) self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name', is_binary = True ) self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name', is_binary = True ) + + class Eigenstratpca(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + Eigenstrat PCA file for case control adjustment + Rgenetics data collections """ file_ext="eigenstratpca" @@ -462,18 +472,21 @@ Rgenetics.__init__(self, **kwd) self.add_composite_file( '%s.eigenstratpca', description = 'Eigenstrat PCA file', substitute_name_with_metadata = 'base_name' ) + class Snptest(Rgenetics): """ - fake class to distinguish different species of Rgenetics data collections + BioC snptest Rgenetics data collections """ file_ext="snptest" + class Pheno(Tabular): """ base class for pheno files """ file_ext = 'pheno' + class RexpBase( Html ): """ base class for BioC data structures in Galaxy @@ -492,16 +505,19 @@ composite_type = 'auto_primary_file' allow_datatype_change = False + def __init__( self, **kwd ): Html.__init__(self,**kwd) self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file', substitute_name_with_metadata = 'base_name', is_binary=True) + def generate_primary_file( self, dataset = None ): - """ + """ This is called only at upload to write the html file cannot rename the datasets here - they come with the default unfortunately """ return '<html><head></head><body>AutoGenerated Primary File for Composite Dataset</body></html>' + def get_phecols(self, phenolist=[], maxConc=20): """ sept 2009: cannot use whitespace to split - make a more complex structure here @@ -527,7 +543,7 @@ else: for col,code in enumerate(row): # keep column order correct if col >= totcols: - log.warning('### get_phecols error in pheno file - row %d col %d (%s) longer than header %s' % (nrows, col, row, head)) + gal_Log.warning('### get_phecols error in pheno file - row %d col %d (%s) longer than header %s' % (nrows, col, row, head)) else: concordance[col].setdefault(code,0) # first one is zero concordance[col][code] += 1 @@ -573,6 +589,8 @@ res = [('no usable phenotype columns found',[('?',0),]),] return res + + def get_pheno(self,dataset): """ expects a .pheno file in the extra_files_dir - ugh @@ -591,12 +609,12 @@ else: p = [] return '\n'.join(p) - def set_peek( self, dataset, is_multi_byte=False ): + + def set_peek( self, dataset, **kwd ): """ expects a .pheno file in the extra_files_dir - ugh note that R is wierd and does not include the row.name in - the header. why? - """ + the header. why?""" if not dataset.dataset.purged: pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name) try: @@ -608,14 +626,18 @@ else: dataset.peek = 'file does not exist\n' dataset.blurb = 'file purged from disk' + def get_peek( self, dataset ): - """expects a .pheno file in the extra_files_dir - ugh""" + """ + expects a .pheno file in the extra_files_dir - ugh + """ pp = os.path.join(dataset.extra_files_path,'%s.pheno' % dataset.metadata.base_name) try: p = file(pp,'r').readlines() except: p = ['##failed to find %s' % pp] return ''.join(p[:5]) + def get_file_peek(self,filename): """ can't really peek at a filename - need the extra_files_path and such? @@ -626,8 +648,10 @@ except: pass return ''.join(h[:5]) + def regenerate_primary_file(self,dataset): - """cannot do this until we are setting metadata + """ + cannot do this until we are setting metadata """ bn = dataset.metadata.base_name flist = os.listdir(dataset.extra_files_path) @@ -640,28 +664,34 @@ f.write("\n".join( rval )) f.write('\n') f.close() + def init_meta( self, dataset, copy_from=None ): - """Add metadata elements""" if copy_from: dataset.metadata = copy_from.metadata + def set_meta( self, dataset, **kwd ): + """ NOTE we apply the tabular machinary to the phenodata extracted from a BioC eSet or affybatch. + """ + Html.set_meta(self, dataset, **kwd) try: flist = os.listdir(dataset.extra_files_path) except: - #log.debug('@@@rexpression set_meta failed - no dataset?') + if verbose: + gal_Log.debug('@@@rexpression set_meta failed - no dataset?') return False - bn = None - for f in flist: - n = os.path.splitext(f)[0] - if not bn: - bn = n - dataset.metadata.base_name = bn + bn = dataset.metadata.base_name + if not bn: + for f in flist: + n = os.path.splitext(f)[0] + bn = n + dataset.metadata.base_name = bn if not bn: bn = '?' + dataset.metadata.base_name = bn pn = '%s.pheno' % (bn) pp = os.path.join(dataset.extra_files_path,pn) dataset.metadata.pheno_path=pp @@ -680,7 +710,7 @@ dataset.metadata.column_names = [] dataset.metadata.columns = 0 dataset.peek = 'No pheno file found' - if len(pf) > 1: + if pf and len(pf) > 1: dataset.metadata.pheCols = self.get_phecols(phenolist=pf) else: dataset.metadata.pheCols = [('','No useable phenotypes found',False),] @@ -690,8 +720,11 @@ if not dataset.blurb: dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' return True + def make_html_table( self, pp='nothing supplied from peek\n'): - """Create HTML table, used for displaying peek""" + """ + Create HTML table, used for displaying peek + """ out = ['<table cellspacing="0" cellpadding="3">',] p = pp.split('\n') try: @@ -712,25 +745,37 @@ except Exception, exc: out = "Can't create html table %s" % str( exc ) return out + def display_peek( self, dataset ): - """Returns formatted html of peek""" + """ + Returns formatted html of peek + """ out=self.make_html_table(dataset.peek) return out + def get_mime(self): - """Returns the mime type of the datatype""" + """ + Returns the mime type of the datatype + """ return 'text/html' + class Affybatch( RexpBase ): - """derived class for BioC data structures in Galaxy """ + """ + derived class for BioC data structures in Galaxy + """ + file_ext = "affybatch" def __init__( self, **kwd ): RexpBase.__init__(self, **kwd) self.add_composite_file( '%s.affybatch', description = 'AffyBatch R object saved to file', substitute_name_with_metadata = 'base_name', is_binary=True ) - + class Eset( RexpBase ): - """derived class for BioC data structures in Galaxy """ + """ + derived class for BioC data structures in Galaxy + """ file_ext = "eset" def __init__( self, **kwd ): @@ -738,8 +783,11 @@ self.add_composite_file( '%s.eset', description = 'ESet R object saved to file', substitute_name_with_metadata = 'base_name', is_binary = True ) + class MAlist( RexpBase ): - """derived class for BioC data structures in Galaxy """ + """ + derived class for BioC data structures in Galaxy + """ file_ext = "malist" def __init__( self, **kwd ): @@ -747,6 +795,8 @@ self.add_composite_file( '%s.malist', description = 'MAlist R object saved to file', substitute_name_with_metadata = 'base_name', is_binary = True ) + if __name__ == '__main__': import doctest, sys doctest.testmod(sys.modules[__name__]) + diff -r 9701e5ee128d -r 70930ea26347 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Wed Mar 10 14:25:34 2010 -0500 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Mar 10 16:09:37 2010 -0500 @@ -99,6 +99,10 @@ self.default_file_type = 'txt' self.file_type_to_ext = { 'auto':self.default_file_type } self.metadata_ref = 'files_metadata' + def get_file_base_name( self, context ): + log.debug('### uploadDataset get base name context = %s' % str(context)) + fd = context.get('files_metadata|base_name','?') + return fd def get_file_type( self, context ): return context.get( self.file_type_name, self.default_file_type ) def get_datatype_ext( self, trans, context ): @@ -291,15 +295,13 @@ temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file( dataset ) ), prefix='upload_auto_primary_file' ) dataset.primary_file = temp_name dataset.space_to_tab = False - dataset.precreated_name = dataset.name = 'Uploaded Composite Dataset (%s)' % ( file_type ) + dataset.precreated_name = dataset.name = dataset.metadata['base_name'] # was 'Uploaded Composite Dataset (%s)' % ( file_type ) else: file_bunch, warnings = get_one_filename( groups_incoming[ 0 ] ) - if dataset.datatype.composite_type: - precreated_name = 'Uploaded Composite Dataset (%s)' % ( file_type ) writable_files_offset = 1 dataset.primary_file = file_bunch.path dataset.space_to_tab = file_bunch.space_to_tab - dataset.precreated_name = file_bunch.precreated_name + dataset.precreated_name = dataset.metadata['base_name'] # file_bunch.precreated_name dataset.name = file_bunch.precreated_name dataset.warnings.extend( file_bunch.warnings ) if dataset.primary_file is None:#remove this before finish, this should create an empty dataset diff -r 9701e5ee128d -r 70930ea26347 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Mar 10 14:25:34 2010 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Wed Mar 10 16:09:37 2010 -0500 @@ -1,4 +1,4 @@ -import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib +import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib, tempfile, zipfile, glob from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids @@ -7,11 +7,30 @@ from galaxy.datatypes.display_applications.util import encode_dataset_user, decode_dataset_user from email.MIMEText import MIMEText - import pkg_resources; pkg_resources.require( "Paste" ) import paste.httpexceptions +tmpd = tempfile.mkdtemp() +comptypes=[] +ziptype = '32' +tmpf = os.path.join( tmpd, 'compression_test.zip' ) +try: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + archive.close() + comptypes.append( 'zip' ) + ziptype = '64' +except RuntimeError: + log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +except (TypeError, zipfile.LargeZipFile): # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped + log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) + comptypes.append( 'zip' ) +try: + os.unlink( tmpf ) +except OSError: + pass +os.rmdir( tmpd ) + log = logging.getLogger( __name__ ) error_report_template = """ @@ -182,6 +201,97 @@ return 'This link may not be followed from within Galaxy.' @web.expose + def archive_composite_dataset( self, trans, data=None, **kwd ): + # save a composite object into a compressed archive for downloading + params = util.Params( kwd ) + if (params.do_action == None): + params.do_action = 'zip' # default + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + if not data: + msg = "You must select at least one dataset" + messagetype = 'error' + else: + error = False + try: + if (params.do_action == 'zip'): + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) + if ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif params.do_action == 'tgz': + archive = util.streamball.StreamBall( 'w|gz' ) + elif params.do_action == 'tbz': + archive = util.streamball.StreamBall( 'w|bz2' ) + except (OSError, zipfile.BadZipFile): + error = True + log.exception( "Unable to create archive for download" ) + msg = "Unable to create archive for %s for download, please report this error" % data.name + messagetype = 'error' + if not error: + current_user_roles = trans.get_current_user_roles() + ext = data.extension + path = data.file_name + fname = os.path.split(path)[-1] + basename = data.metadata.base_name + efp = data.extra_files_path + htmlname = os.path.splitext(data.name)[0] + if not htmlname.endswith(ext): + htmlname = '%s_%s' % (htmlname,ext) + archname = '%s.html' % htmlname # fake the real nature of the html file + try: + archive.add(data.file_name,archname) + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + flist = glob.glob(os.path.join(efp,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % fname) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue + if not error: + if params.do_action == 'zip': + archive.close() + tmpfh = open( tmpf ) + # clean up now + try: + os.unlink( tmpf ) + os.rmdir( tmpd ) + except OSError: + error = True + msg = "Unable to remove temporary library download archive and directory" + log.exception( msg ) + messagetype = 'error' + if not error: + trans.response.set_content_type( "application/x-zip-compressed" ) + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyCompositeObject.zip" + return tmpfh + else: + trans.response.set_content_type( "application/x-tar" ) + outext = 'tgz' + if params.do_action == 'tbz': + outext = 'tbz' + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % outext + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + return trans.show_error_message( msg ) + + + + @web.expose def display(self, trans, dataset_id=None, preview=False, filename=None, to_ext=None, **kwd): """Catches the dataset id and displays file contents as directed""" @@ -219,15 +329,19 @@ trans.log_event( "Display dataset id: %s" % str( dataset_id ) ) if to_ext: # Saving the file - trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) - if to_ext[0] != ".": - to_ext = "." + to_ext - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = data.name - fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, to_ext) - return open( data.file_name ) - + composite_extensions = trans.app.datatypes_registry.get_composite_extensions( ) + composite_extensions.append('html') + if data.ext in composite_extensions: + return self.archive_composite_dataset( trans, data, **kwd ) + else: + trans.response.headers['Content-Length'] = int( os.stat( data.file_name ).st_size ) + if to_ext[0] != ".": + to_ext = "." + to_ext + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = data.name + fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150] + trans.response.headers["Content-Disposition"] = "attachment; filename=GalaxyHistoryItem-%s-[%s]%s" % (data.hid, fname, to_ext) + return open( data.file_name ) if os.path.exists( data.file_name ): max_peek_size = 1000000 # 1 MB if preview and os.stat( data.file_name ).st_size > max_peek_size: @@ -367,7 +481,10 @@ raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) if 'display_url' not in kwd or 'redirect_url' not in kwd: return trans.show_error_message( 'Invalid parameters specified for "display at" link, please contact a Galaxy administrator' ) - redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) + try: + redirect_url = kwd['redirect_url'] % urllib.quote_plus( kwd['display_url'] ) + except: + redirect_url = kwd['redirect_url'] # not all will need custom text current_user_roles = trans.get_current_user_roles() if trans.app.security_agent.dataset_is_public( data.dataset ): return trans.response.send_redirect( redirect_url ) # anon access already permitted by rbac @@ -591,4 +708,3 @@ status = SUCCESS message = done_msg return status, message - \ No newline at end of file diff -r 9701e5ee128d -r 70930ea26347 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Mar 10 14:25:34 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 10 16:09:37 2010 -0500 @@ -1098,6 +1098,7 @@ def download_dataset_from_folder( self, trans, cntrller, id, library_id=None, **kwd ): """Catches the dataset id and displays file contents as directed""" show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) + params = util.Params( kwd ) use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( id ) ) if not ldda.dataset: diff -r 9701e5ee128d -r 70930ea26347 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Mar 10 14:25:34 2010 -0500 +++ b/test/base/twilltestcase.py Wed Mar 10 16:09:37 2010 -0500 @@ -23,6 +23,8 @@ log = logging.getLogger( __name__ ) class TwillTestCase( unittest.TestCase ): + composite_extensions = ['html','lped','pbed','fped','pphe','eigenstratgeno','eset','affybatch','malist','test-data' ] + def setUp( self ): # Security helper @@ -61,9 +63,10 @@ else: files_differ = True if files_differ: - allowed_diff_count = attributes.get( 'lines_diff', 0 ) + allowed_diff_count = int(attributes.get( 'lines_diff', 0 )) diff = list( difflib.unified_diff( local_file, history_data, "local_file", "history_data" ) ) diff_lines = get_lines_diff( diff ) + log.debug('## files diff on %s and %s lines_diff=%d, found diff = %d' % (file1,file2,allowed_diff_count,diff_lines)) if diff_lines > allowed_diff_count: diff_slice = diff[0:40] #FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff @@ -75,7 +78,7 @@ # PDF files contain creation dates, modification dates, ids and descriptions that change with each # new file, so we need to handle these differences. As long as the rest of the PDF file does # not differ we're ok. - valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id' ] + valid_diff_strs = [ 'description', 'createdate', 'creationdate', 'moddate', 'id', 'producer', 'creator' ] valid_diff = False for line in diff_slice: # Make sure to lower case strings before checking. @@ -109,7 +112,7 @@ attributes = {} if attributes.get( 'sort', False ): history_data.sort() - lines_diff = attributes.get( 'lines_diff', 0 ) + lines_diff = int(attributes.get( 'lines_diff', 0 )) line_diff_count = 0 diffs = [] for i in range( len( history_data ) ): @@ -194,36 +197,7 @@ raise AssertionError, "Invalid hid (%s) created when pasting %s" % ( hid, url_paste ) # Wait for upload processing to finish (TODO: this should be done in each test case instead) self.wait() - def upload_composite_datatype_file( self, ftype, ped_file='', map_file='', bim_file='', bed_file='', fam_file='', dbkey='unspecified (?)', base_name='rgenetics' ): - """Tests uploading either of 2 different composite data types ( lped and pbed )""" - self.visit_url( "%s/tool_runner/index?tool_id=upload1" % self.url ) - # Handle refresh_on_change - self.refresh_form( "file_type", ftype ) - tc.fv( "1", "dbkey", dbkey ) - tc.fv( "1", "files_metadata|base_name", base_name ) - if ftype == 'lped': - # lped data types include a ped_file and a map_file - ped_file = self.get_filename( ped_file ) - tc.formfile( "1", "files_0|file_data", ped_file ) - map_file = self.get_filename( map_file ) - tc.formfile( "1", "files_1|file_data", map_file ) - elif ftype == 'pbed': - # pbed data types include a bim_file, a bed_file and a fam_file - bim_file = self.get_filename( bim_file ) - tc.formfile( "1", "files_0|file_data", bim_file ) - bed_file = self.get_filename( bed_file ) - tc.formfile( "1", "files_1|file_data", bed_file ) - fam_file = self.get_filename( fam_file ) - tc.formfile( "1", "files_2|file_data", fam_file ) - else: - raise AssertionError, "Unsupported composite data type (%s) received, currently only lped and pbed data types are supported." % ftype - tc.submit( "runtool_btn" ) - self.check_page_for_string( 'The following job has been succesfully added to the queue:' ) - check_str = 'Uploaded Composite Dataset (%s)' % ftype - self.check_page_for_string( check_str ) - # Wait for upload processing to finish (TODO: this should be done in each test case instead) - self.wait() - self.check_history_for_string( check_str ) + # Functions associated with histories def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" @@ -672,7 +646,7 @@ def verify_composite_datatype_file_content( self, file_name, hda_id, base_name = None, attributes = None ): local_name = self.get_filename( file_name ) if base_name is None: - base_name = file_name + base_name = os.path.split(file_name)[-1] temp_name = self.get_filename( '%s_temp' % file_name ) #This is a terrible way to generate a temp name self.visit_url( "%s/datasets/%s/display/%s" % ( self.url, self.security.encode_id( hda_id ), base_name ) ) data = self.last_page() @@ -915,9 +889,14 @@ # To help with debugging a tool, print out the form controls when the test fails print "form '%s' contains the following controls ( note the values )" % f.name control_names = [] + hidden_control_names = [] # cannot change these, so ignore or many complex page tool tests will fail + hc_prefix = '<HiddenControl(' for i, control in enumerate( f.controls ): - print "control %d: %s" % ( i, str( control ) ) - try: + print "control %d: %s" % ( i, str( control ) ) + if hc_prefix in str(control): + hidden_control_names.append(control.name) # cannot do much with these + else: + try: #check if a repeat element needs to be added if control.name not in kwd and control.name.endswith( '_add' ): #control name doesn't exist, could be repeat @@ -946,12 +925,14 @@ # Submit for refresh tc.submit( '___refresh_grouping___' ) return self.submit_form( form_no=form_no, button=button, **kwd ) - except Exception, e: + except Exception, e: log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) ) continue - control_names.append( control.name ) + control_names.append( control.name ) # No refresh_on_change attribute found in current form, so process as usual for control_name, control_value in kwd.items(): + if control_name in hidden_control_names: + continue # these cannot be handled safely - cause the test to barf out if not isinstance( control_value, list ): control_value = [ control_value ] try:

1 0

[hg] galaxy 3506: Now that cntrller is passed as a POST var in t...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9701e5ee128d changeset: 3506:9701e5ee128d user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Mar 10 14:25:34 2010 -0500 description: Now that cntrller is passed as a POST var in the upload form, it's not necessary to have the library_admin and library controller upload convenience methods. This should fix broken library tests on the production buildbot. diffstat: lib/galaxy/web/controllers/library.py | 3 --- lib/galaxy/web/controllers/library_admin.py | 4 ---- lib/galaxy/web/controllers/library_common.py | 8 ++------ 3 files changed, 2 insertions(+), 13 deletions(-) diffs (39 lines): diff -r 9efe896dbb17 -r 9701e5ee128d lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Wed Mar 10 11:51:00 2010 -0500 +++ b/lib/galaxy/web/controllers/library.py Wed Mar 10 14:25:34 2010 -0500 @@ -34,6 +34,3 @@ default_action=params.get( 'default_action', None ), msg=msg, messagetype=messagetype ) - @web.expose - def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): - return trans.webapp.controllers[ 'library_common' ].upload_library_dataset( trans, 'library', library_id, folder_id, **kwd ) diff -r 9efe896dbb17 -r 9701e5ee128d lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Wed Mar 10 11:51:00 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Wed Mar 10 14:25:34 2010 -0500 @@ -235,7 +235,3 @@ show_deleted=show_deleted, msg=msg, messagetype=status ) ) - @web.expose - @web.require_admin - def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): - return trans.webapp.controllers[ 'library_common' ].upload_library_dataset( trans, 'library_admin', library_id, folder_id, **kwd ) diff -r 9efe896dbb17 -r 9701e5ee128d lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Mar 10 11:51:00 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 10 14:25:34 2010 -0500 @@ -804,12 +804,8 @@ if upload_option == 'upload_file' and trans.app.config.nginx_upload_path: # url_for is intentionally not used on the base URL here - # nginx_upload_path is expected to include the proxy prefix if the - # administrator intends for it to be part of the URL. We also - # redirect to the library or library_admin controller rather than - # library_common because GET arguments can't be used in conjunction - # with nginx upload (nginx can't do percent decoding without a - # bunch of hacky rewrite rules). - action = trans.app.config.nginx_upload_path + '?nginx_redir=' + web.url_for( controller=cntrller, action='upload_library_dataset' ) + # administrator intends for it to be part of the URL. + action = trans.app.config.nginx_upload_path + '?nginx_redir=' + web.url_for( controller='library_common', action='upload_library_dataset' ) return trans.fill_template( '/library/common/upload.mako', cntrller=cntrller, upload_option=upload_option,

1 0

[hg] galaxy 3505: Fix try-except-finally bug to be compatible wi...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/9efe896dbb17 changeset: 3505:9efe896dbb17 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed Mar 10 11:51:00 2010 -0500 description: Fix try-except-finally bug to be compatible with Python 2.4 in several tools and twilltestcase.py. Updated liftOver test to replace hard-coded (incorrect) path and modified code file to allow for new path. Improved bowtie error handling. diffstat: test/base/twilltestcase.py | 70 ++++++++++++++------------ tools/extract/liftOver_wrapper.py | 17 ++++-- tools/extract/liftOver_wrapper.xml | 9 +-- tools/extract/liftOver_wrapper_code.py | 6 +- tools/samtools/sam_pileup.py | 44 ++++++++-------- tools/sr_mapping/bowtie_wrapper.py | 72 ++++++++++++++++++--------- tools/sr_mapping/bwa_wrapper.py | 88 +++++++++++++++++---------------- 7 files changed, 171 insertions(+), 135 deletions(-) diffs (452 lines): diff -r f84112d155c0 -r 9efe896dbb17 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Mar 10 11:28:50 2010 -0500 +++ b/test/base/twilltestcase.py Wed Mar 10 11:51:00 2010 -0500 @@ -633,24 +633,26 @@ data = self.last_page() file( temp_name, 'wb' ).write(data) try: - if attributes is None: - attributes = {} - compare = attributes.get( 'compare', 'diff' ) - extra_files = attributes.get( 'extra_files', None ) - if compare == 'diff': - self.files_diff( local_name, temp_name, attributes=attributes ) - elif compare == 're_match': - self.files_re_match( local_name, temp_name, attributes=attributes ) - elif compare == 're_match_multiline': - self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) - else: - raise Exception, 'Unimplemented Compare type: %s' % compare - if extra_files: - self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) - except AssertionError, err: - errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) - errmsg += str( err ) - raise AssertionError( errmsg ) + # have to nest try-except in try-finally to handle 2.4 + try: + if attributes is None: + attributes = {} + compare = attributes.get( 'compare', 'diff' ) + extra_files = attributes.get( 'extra_files', None ) + if compare == 'diff': + self.files_diff( local_name, temp_name, attributes=attributes ) + elif compare == 're_match': + self.files_re_match( local_name, temp_name, attributes=attributes ) + elif compare == 're_match_multiline': + self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare + if extra_files: + self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) + except AssertionError, err: + errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) + errmsg += str( err ) + raise AssertionError( errmsg ) finally: os.remove( temp_name ) @@ -676,21 +678,23 @@ data = self.last_page() file( temp_name, 'wb' ).write( data ) try: - if attributes is None: - attributes = {} - compare = attributes.get( 'compare', 'diff' ) - if compare == 'diff': - self.files_diff( local_name, temp_name, attributes=attributes ) - elif compare == 're_match': - self.files_re_match( local_name, temp_name, attributes=attributes ) - elif compare == 're_match_multiline': - self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) - else: - raise Exception, 'Unimplemented Compare type: %s' % compare - except AssertionError, err: - errmsg = 'Composite file (%s) of History item %s different than expected, difference (using %s):\n' % ( base_name, hda_id, compare ) - errmsg += str( err ) - raise AssertionError( errmsg ) + # have to nest try-except in try-finally to handle 2.4 + try: + if attributes is None: + attributes = {} + compare = attributes.get( 'compare', 'diff' ) + if compare == 'diff': + self.files_diff( local_name, temp_name, attributes=attributes ) + elif compare == 're_match': + self.files_re_match( local_name, temp_name, attributes=attributes ) + elif compare == 're_match_multiline': + self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare + except AssertionError, err: + errmsg = 'Composite file (%s) of History item %s different than expected, difference (using %s):\n' % ( base_name, hda_id, compare ) + errmsg += str( err ) + raise AssertionError( errmsg ) finally: os.remove( temp_name ) diff -r f84112d155c0 -r 9efe896dbb17 tools/extract/liftOver_wrapper.py --- a/tools/extract/liftOver_wrapper.py Wed Mar 10 11:28:50 2010 -0500 +++ b/tools/extract/liftOver_wrapper.py Wed Mar 10 11:51:00 2010 -0500 @@ -4,7 +4,7 @@ Converts coordinates from one build/assembly to another using liftOver binary and mapping files downloaded from UCSC. """ -import sys, os, string +import os, string, subprocess, sys import tempfile import re @@ -51,15 +51,20 @@ if in_dbkey == "?": stop_err( "Input dataset genome build unspecified, click the pencil icon in the history item to specify it." ) - if not os.path.isfile( mapfilepath ): stop_err( "%s mapping is not currently available." % ( mapfilepath.split('/')[-1].split('.')[0] ) ) safe_infile = safe_bed_file(infile) -cmd_line = "liftOver -minMatch=" + str(minMatch) + " " + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + " > /dev/null 2>&1" +cmd_line = "liftOver -minMatch=" + str(minMatch) + " " + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + " > /dev/null" try: - os.system( cmd_line ) -except Exception, exc: - stop_err( "Exception caught attempting conversion: %s" % str( exc ) ) + # have to nest try-except in try-finally to handle 2.4 + try: + proc = subprocess.Popen( args=cmd_line, shell=True, stderr=subprocess.PIPE ) + returncode = proc.wait() + stderr = proc.stderr.read() + if returncode != 0: + raise Exception, stderr + except Exception, e: + raise Exception, 'Exception caught attempting conversion: ' + str( e ) finally: os.remove(safe_infile) diff -r f84112d155c0 -r 9efe896dbb17 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml Wed Mar 10 11:28:50 2010 -0500 +++ b/tools/extract/liftOver_wrapper.xml Wed Mar 10 11:51:00 2010 -0500 @@ -23,19 +23,16 @@ <requirements> <requirement type="binary">liftOver</requirement> </requirements> - <tests> <test> <param name="input" value="5.bed" dbkey="hg18" ftype="bed" /> - <param name="to_dbkey" value="/galaxy/data/hg18/liftOver/hg18ToPanTro2.over.chain" /> + <param name="to_dbkey" value="panTro2" /> <param name="minMatch" value="0.95" /> <output name="out_file1" file="5_liftover_mapped.bed"/> <output name="out_file2" file="5_liftover_unmapped.bed"/> </test> </tests> - <help> - .. class:: warningmark Make sure that the genome build of the input dataset is specified (click the pencil icon in the history item to set it if necessary). @@ -71,6 +68,6 @@ chrX 158279 160020 AK097346 0 + chrX 160024 169033 AK074528 0 - -</help> -<code file="liftOver_wrapper_code.py"/> + </help> + <code file="liftOver_wrapper_code.py" /> </tool> diff -r f84112d155c0 -r 9efe896dbb17 tools/extract/liftOver_wrapper_code.py --- a/tools/extract/liftOver_wrapper_code.py Wed Mar 10 11:28:50 2010 -0500 +++ b/tools/extract/liftOver_wrapper_code.py Wed Mar 10 11:51:00 2010 -0500 @@ -1,8 +1,10 @@ +import os + def exec_before_job(app, inp_data, out_data, param_dict, tool): #Assuming the path of the form liftOverDirectory/hg18ToHg17.over.chain (This is how the mapping chain files from UCSC look.) - to_dbkey = param_dict['to_dbkey'].split('.')[0].split('To')[1] + #allows for . in path + to_dbkey = os.path.split(param_dict['to_dbkey'])[1].split('.')[0].split('To')[1] to_dbkey = to_dbkey[0].lower()+to_dbkey[1:] out_data['out_file1'].set_dbkey(to_dbkey) out_data['out_file1'].name = out_data['out_file1'].name + " [ MAPPED COORDINATES ]" out_data['out_file2'].name = out_data['out_file2'].name + " [ UNMAPPED COORDINATES ]" - diff -r f84112d155c0 -r 9efe896dbb17 tools/samtools/sam_pileup.py --- a/tools/samtools/sam_pileup.py Wed Mar 10 11:28:50 2010 -0500 +++ b/tools/samtools/sam_pileup.py Wed Mar 10 11:51:00 2010 -0500 @@ -78,30 +78,32 @@ #prepare basic pileup command cmd = 'samtools pileup %s -f %s %s > %s' try: - #index reference if necessary and prepare pileup command - if options.ref == 'indexed': - if not os.path.exists( "%s.fai" % seqPath ): - raise Exception, "No sequences are available for '%s', request them by reporting this error." % options.dbkey - cmd = cmd % ( opts, seqPath, tmpf0bam_name, options.output1 ) - elif options.ref == 'history': - os.symlink( options.ownFile, tmpf1_name ) - cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) - proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) + # have to nest try-except in try-finally to handle 2.4 + try: + #index reference if necessary and prepare pileup command + if options.ref == 'indexed': + if not os.path.exists( "%s.fai" % seqPath ): + raise Exception, "No sequences are available for '%s', request them by reporting this error." % options.dbkey + cmd = cmd % ( opts, seqPath, tmpf0bam_name, options.output1 ) + elif options.ref == 'history': + os.symlink( options.ownFile, tmpf1_name ) + cmdIndex = 'samtools faidx %s' % ( tmpf1_name ) + proc = subprocess.Popen( args=cmdIndex, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) + returncode = proc.wait() + stderr = proc.stderr.read() + #did index succeed? + if returncode != 0: + raise Exception, 'Error creating index file\n' + stderr + cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 ) + #perform pileup command + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) returncode = proc.wait() + #did it succeed? stderr = proc.stderr.read() - #did index succeed? if returncode != 0: - raise Exception, 'Error creating index file\n' + stderr - cmd = cmd % ( opts, tmpf1_name, tmpf0bam_name, options.output1 ) - #perform pileup command - proc = subprocess.Popen( args=cmd, shell=True, cwd=tmpDir, stderr=subprocess.PIPE ) - returncode = proc.wait() - #did it succeed? - stderr = proc.stderr.read() - if returncode != 0: - raise Exception, stderr - except Exception, e: - stop_err( 'Error running Samtools pileup tool\n' + str( e ) ) + raise Exception, stderr + except Exception, e: + stop_err( 'Error running Samtools pileup tool\n' + str( e ) ) finally: #clean up temp files if os.path.exists( tmpDir ): diff -r f84112d155c0 -r 9efe896dbb17 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Wed Mar 10 11:28:50 2010 -0500 +++ b/tools/sr_mapping/bowtie_wrapper.py Wed Mar 10 11:51:00 2010 -0500 @@ -2,7 +2,7 @@ """ Runs Bowtie on single-end or paired-end data. -For use with Bowtie v. 0.12.1 +For use with Bowtie v. 0.12.3 usage: bowtie_wrapper.py [options] -t, --threads=t: The number of threads to run @@ -58,12 +58,12 @@ -H, --suppressHeader=H: Suppress header """ -import optparse, os, shutil, sys, tempfile +import optparse, os, shutil, subprocess, sys, tempfile def stop_err( msg ): - sys.stderr.write( "%s\n" % msg ) + sys.stderr.write( '%s\n' % msg ) sys.exit() - + def __main__(): #Parse Command Line parser = optparse.OptionParser() @@ -119,6 +119,7 @@ parser.add_option( '-x', '--indexSettings', dest='index_settings', help='Whether or not indexing options are to be set' ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) (options, args) = parser.parse_args() + stdout = '' # make temp directory for placement of indices and copy reference file there if necessary tmp_index_dir = tempfile.mkdtemp() # get type of data (solid or solexa) @@ -187,17 +188,25 @@ iseed, icutoff, colorspace ) except ValueError: indexing_cmds = '%s' % colorspace + ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir ) + ref_file_name = ref_file.name + ref_file.close() + os.symlink( options.ref, ref_file_name ) + cmd1 = 'bowtie-build %s -f %s %s' % ( indexing_cmds, ref_file_name, ref_file_name ) try: - shutil.copy( options.ref, tmp_index_dir ) + proc = subprocess.Popen( args=cmd1, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE, stdout=subprocess.PIPE ) + returncode = proc.wait() + stderr = proc.stderr.read() + if returncode != 0: + raise Exception, stderr except Exception, e: - stop_err( 'Error creating temp directory for indexing purposes\n' + str( e ) ) - options.ref = os.path.join( tmp_index_dir, os.path.split( options.ref )[1] ) - cmd1 = 'bowtie-build %s -f %s %s 2> /dev/null' % ( indexing_cmds, options.ref, options.ref ) - try: - os.chdir( tmp_index_dir ) - os.system( cmd1 ) - except Exception, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) stop_err( 'Error indexing reference sequence\n' + str( e ) ) + stdout += 'File indexed. ' + else: + ref_file_name = options.ref # set up aligning and generate aligning command options # automatically set threads in both cases if options.suppressHeader == 'true': @@ -328,19 +337,34 @@ best, strata, offrate, seed, colorspace, snpphred, snpfrac, keepends, options.threads, suppressHeader ) except ValueError, e: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) - # prepare actual aligning commands - if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s 2> /dev/null' % ( aligning_cmds, options.ref, options.input1, options.input2, options.output ) - else: - cmd2 = 'bowtie %s %s %s > %s 2> /dev/null' % ( aligning_cmds, options.ref, options.input1, options.output ) - # align try: - os.system( cmd2 ) - except Exception, e: - stop_err( 'Error aligning sequence\n' + str( e ) ) - # clean up temp dir - if os.path.exists( tmp_index_dir ): - shutil.rmtree( tmp_index_dir ) + # have to nest try-except in try-finally to handle 2.4 + try: + # prepare actual aligning commands + if options.paired == 'paired': + cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output ) + else: + cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) + # align + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_index_dir, stderr=subprocess.PIPE ) + returncode = proc.wait() + stderr = proc.stderr.read() + if returncode != 0: + raise Exception, stderr + # check that there are results in the output file + if len( open( options.output, 'rb' ).read().strip() ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + except Exception, e: + stop_err( 'Error aligning sequence. ' + str( e ) ) + finally: + # clean up temp dir + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stdout += 'Sequence file aligned.\n' + sys.stdout.write( stdout ) if __name__=="__main__": __main__() diff -r f84112d155c0 -r 9efe896dbb17 tools/sr_mapping/bwa_wrapper.py --- a/tools/sr_mapping/bwa_wrapper.py Wed Mar 10 11:28:50 2010 -0500 +++ b/tools/sr_mapping/bwa_wrapper.py Wed Mar 10 11:51:00 2010 -0500 @@ -152,55 +152,57 @@ cmd3 = 'bwa samse %s %s %s %s >> %s' % ( gen_alignment_cmds, ref_file_name, tmp_align_out_name, options.fastq, options.output ) # perform alignments try: - # align + # need to nest try-except in try-finally to handle 2.4 try: - proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) - returncode = proc.wait() - stderr = proc.stderr.read() - if returncode != 0: - raise Exception, stderr - except Exception, e: - raise Exception, 'Error aligning sequence. ' + str( e ) - # and again if paired data - try: - if cmd2b: - proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + # align + try: + proc = subprocess.Popen( args=cmd2, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) returncode = proc.wait() stderr = proc.stderr.read() if returncode != 0: raise Exception, stderr + except Exception, e: + raise Exception, 'Error aligning sequence. ' + str( e ) + # and again if paired data + try: + if cmd2b: + proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + returncode = proc.wait() + stderr = proc.stderr.read() + if returncode != 0: + raise Exception, stderr + except Exception, e: + raise Exception, 'Error aligning second sequence. ' + str( e ) + # generate align + try: + proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) + returncode = proc.wait() + stderr = proc.stderr.read() + if returncode != 0: + raise Exception, stderr + except Exception, e: + raise Exception, 'Error generating alignments. ' + str( e ) + # remove header if necessary + if options.suppressHeader == 'true': + tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir) + tmp_out_name = tmp_out.name + tmp_out.close() + try: + shutil.move( options.output, tmp_out_name ) + except Exception, e: + raise Exception, 'Error moving output file before removing headers. ' + str( e ) + fout = file( options.output, 'w' ) + for line in file( tmp_out.name, 'r' ): + if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ): + fout.write( line ) + fout.close() + # check that there are results in the output file + if os.path.getsize( options.output ) > 0: + sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType ) + else: + raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.' except Exception, e: - raise Exception, 'Error aligning second sequence. ' + str( e ) - # generate align - try: - proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=subprocess.PIPE ) - returncode = proc.wait() - stderr = proc.stderr.read() - if returncode != 0: - raise Exception, stderr - except Exception, e: - raise Exception, 'Error generating alignments. ' + str( e ) - # remove header if necessary - if options.suppressHeader == 'true': - tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir) - tmp_out_name = tmp_out.name - tmp_out.close() - try: - shutil.move( options.output, tmp_out_name ) - except Exception, e: - raise Exception, 'Error moving output file before removing headers. ' + str( e ) - fout = file( options.output, 'w' ) - for line in file( tmp_out.name, 'r' ): - if not ( line.startswith( '@HD' ) or line.startswith( '@SQ' ) or line.startswith( '@RG' ) or line.startswith( '@PG' ) or line.startswith( '@CO' ) ): - fout.write( line ) - fout.close() - # check that there are results in the output file - if os.path.getsize( options.output ) > 0: - sys.stdout.write( 'BWA run on %s-end data' % options.genAlignType ) - else: - raise Exception, 'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.' - except Exception, e: - stop_err( 'The alignment failed.\n' + str( e ) ) + stop_err( 'The alignment failed.\n' + str( e ) ) finally: # clean up temp dir if os.path.exists( tmp_index_dir ):

1 0

[hg] galaxy 3504: Allow renaming of uploaded files in toolbox te...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f84112d155c0 changeset: 3504:f84112d155c0 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Mar 10 11:28:50 2010 -0500 description: Allow renaming of uploaded files in toolbox tests by including a <edit_attributes type="name" value="new dataset name" /> child tag. A rename directive is automatically assigned (no xml changes required) to uploaded composite datasets, so that they can be identified uniquely. diffstat: lib/galaxy/tools/__init__.py | 23 +++++++++++++++++++++++ lib/galaxy/tools/test.py | 11 +++++++---- test/functional/test_toolbox.py | 16 ++++++++++++++-- 3 files changed, 44 insertions(+), 6 deletions(-) diffs (91 lines): diff -r c73f093219aa -r f84112d155c0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Mar 10 11:24:49 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Wed Mar 10 11:28:50 2010 -0500 @@ -510,6 +510,7 @@ store in `self.tests`. """ self.tests = [] + composite_data_names_counter = 0 #composite datasets need a unique name: each test occurs in a fresh history, but we'll keep it unique per set of tests for i, test_elem in enumerate( tests_elem.findall( 'test' ) ): name = test_elem.get( 'name', 'Test-%d' % (i+1) ) maxseconds = int( test_elem.get( 'maxseconds', '120' ) ) @@ -524,6 +525,28 @@ else: value = None attrib['children'] = list( param_elem.getchildren() ) + if attrib['children']: + #at this time, we can assume having children only occurs on DataToolParameter test items + #but this could change and would cause the below parsing to change based upon differences in children items + attrib['metadata'] = [] + attrib['composite_data'] = [] + attrib['edit_attributes'] = [] + composite_data_name = None #composite datasets need to be renamed uniquely + for child in attrib['children']: + if child.tag == 'composite_data': + attrib['composite_data'].append( child ) + if composite_data_name is None: + #generate a unique name; each test uses a fresh history + composite_data_name = '_COMPOSITE_RENAMED %i_' % ( composite_data_names_counter ) + composite_data_names_counter += 1 + elif child.tag == 'metadata': + attrib['metadata'].append( child ) + elif child.tag == 'metadata': + attrib['metadata'].append( child ) + elif child.tag == 'edit_attributes': + attrib['edit_attributes'].append( child ) + if composite_data_name: + attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) #composite datasets need implicit renaming; inserted at front of list so explicit declarations take precedence test.add_param( attrib.pop( 'name' ), value, attrib ) for output_elem in test_elem.findall( "output" ): attrib = dict( output_elem.attrib ) diff -r c73f093219aa -r f84112d155c0 lib/galaxy/tools/test.py --- a/lib/galaxy/tools/test.py Wed Mar 10 11:24:49 2010 -0500 +++ b/lib/galaxy/tools/test.py Wed Mar 10 11:28:50 2010 -0500 @@ -30,12 +30,15 @@ if isinstance( input_value, grouping.Conditional ) or isinstance( input_value, grouping.Repeat ): self.__expand_grouping_for_data_input(name, value, extra, input_name, input_value) elif isinstance( self.tool.inputs[name], parameters.DataToolParameter ) and ( value, extra ) not in self.required_files: - if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) == 0: + name_change = [ att for att in extra.get( 'edit_attributes', [] ) if att.get( 'type' ) == 'name' ] + if name_change: + name_change = name_change[-1].get( 'value' ) #only the last name change really matters + if value is None and not name_change: assert self.tool.inputs[name].optional, '%s is not optional. You must provide a valid filename.' % name else: - self.required_files.append( ( value, extra ) ) - if value is None and len( [ child for child in extra.get( 'children', [] ) if child.tag == 'composite_data' ] ) > 0: - value = extra.get( 'ftype' ) + self.required_files.append( ( value, extra ) ) #these files will be uploaded + if name_change: + value = name_change #change value for select to renamed uploaded file for e.g. composite dataset except Exception, e: log.debug( "Error in add_param for %s: %s" % ( name, e ) ) self.inputs.append( ( name, value, extra ) ) diff -r c73f093219aa -r f84112d155c0 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Wed Mar 10 11:24:49 2010 -0500 +++ b/test/functional/test_toolbox.py Wed Mar 10 11:28:50 2010 -0500 @@ -33,10 +33,22 @@ # Upload any needed files for fname, extra in testdef.required_files: children = extra.get( 'children', [] ) - metadata = [ child for child in children if child.tag == 'metadata' ] - composite_data = [ child for child in children if child.tag == 'composite_data' ] + metadata = extra.get( 'metadata', [] ) + composite_data = extra.get( 'composite_data', [] ) self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ), metadata = metadata, composite_data = composite_data ) print "Uploaded file: ", fname, ", ftype: ", extra.get( 'ftype', 'auto' ), ", extra: ", extra + #Post upload attribute editing + edit_attributes = extra.get( 'edit_attributes', [] ) + #currently only renaming is supported + for edit_att in edit_attributes: + if edit_att.get( 'type', None ) == 'name': + new_name = edit_att.get( 'value', None ) + assert new_name, 'You must supply the new dataset name as the value tag of the edit_attributes tag' + hda_id = self.get_history_as_data_list()[-1].get( 'id' ) + self.edit_hda_attribute_info( hda_id, new_name = new_name ) + print "Renamed uploaded file to:", new_name + else: + raise Exception( 'edit_attributes type (%s) is unimplemented' % edit_att.get( 'type', None ) ) # We need to handle the case where we've uploaded a valid compressed file since the upload # tool will have uncompressed it on the fly. all_inputs = {}

1 0

[hg] galaxy 3503: Fix for deleting a list of library datasets - ...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c73f093219aa changeset: 3503:c73f093219aa user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Mar 10 11:24:49 2010 -0500 description: Fix for deleting a list of library datasets - resolves ticket # 102. diffstat: lib/galaxy/web/controllers/library_admin.py | 4 ++-- lib/galaxy/web/controllers/library_common.py | 14 ++++++++------ templates/library/common/browse_library.mako | 2 +- templates/library/common/ldda_info.mako | 2 +- test/base/twilltestcase.py | 9 ++++++--- test/functional/test_security_and_libraries.py | 6 +++--- 6 files changed, 21 insertions(+), 16 deletions(-) diffs (130 lines): diff -r 34babf71a09f -r c73f093219aa lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Mar 09 16:28:04 2010 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Wed Mar 10 11:24:49 2010 -0500 @@ -169,8 +169,8 @@ # deleted / purged contents will have the same state ). When a library or folder has been deleted for # the amount of time defined in the cleanup_datasets.py script, the library or folder and all of its # contents will be purged. The association between this method and the cleanup_datasets.py script - # enables clean maintenance of libraries and library dataset disk files. This is also why the following - # 3 objects, and not any of the associations ( the cleanup_datasets.py scipot handles everything else ). + # enables clean maintenance of libraries and library dataset disk files. This is also why the item_types + # are not any of the associations ( the cleanup_datasets.py script handles everything ). show_deleted = util.string_as_bool( kwd.get( 'show_deleted', False ) ) item_types = { 'library': trans.app.model.Library, 'folder': trans.app.model.LibraryFolder, diff -r 34babf71a09f -r c73f093219aa lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Mar 09 16:28:04 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Mar 10 11:24:49 2010 -0500 @@ -1246,8 +1246,7 @@ messagetype=messagetype ) @web.expose def act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ): - # This method is used by the select list labeled "Perform action on selected datasets" - # on the analysis library browser + # Perform an action on a list of library datasets. params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -1262,7 +1261,7 @@ messagetype = 'error' else: ldda_ids = util.listify( ldda_ids ) - if action == 'add': + if action == 'import_to_history': history = trans.get_history() if history is None: # Must be a bot sending a request without having a history. @@ -1306,9 +1305,12 @@ elif action == 'delete': for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) - ldda.deleted = True - trans.sa_session.add( ldda ) - trans.sa_session.flush() + # Do not delete the association, just delete the library_dataset. The + # cleanup_datasets.py script handles everything else. + ld = ldda.library_dataset + ld.deleted = True + trans.sa_session.add( ld ) + trans.sa_session.flush() msg = "The selected datasets have been removed from this data library" else: error = False diff -r 34babf71a09f -r c73f093219aa templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Tue Mar 09 16:28:04 2010 -0500 +++ b/templates/library/common/browse_library.mako Wed Mar 10 11:24:49 2010 -0500 @@ -229,7 +229,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), replace_id=trans.security.encode_id( library_dataset.id ), show_deleted=show_deleted )}">Upload a new version of this dataset</a> %endif %if not branch_deleted( folder ) and not ldda.library_dataset.deleted and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels )}">Download this dataset</a> %endif %if cntrller in [ 'library_admin', 'requests_admin' ]: diff -r 34babf71a09f -r c73f093219aa templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Tue Mar 09 16:28:04 2010 -0500 +++ b/templates/library/common/ldda_info.mako Wed Mar 10 11:24:49 2010 -0500 @@ -57,7 +57,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), replace_id=trans.security.encode_id( ldda.library_dataset.id ) )}">Upload a new version of this dataset</a> %endif %if cntrller=='library' and ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='add', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> %endif </div> diff -r 34babf71a09f -r c73f093219aa test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Mar 09 16:28:04 2010 -0500 +++ b/test/base/twilltestcase.py Wed Mar 10 11:24:49 2010 -0500 @@ -1595,14 +1595,17 @@ self.home() def add_library_dataset( self, cntrller, filename, library_id, folder_id, folder_name, file_type='auto', dbkey='hg18', roles=[], message='', root=False, - template_field_name1='', template_field_contents1='' ): + template_field_name1='', template_field_contents1='', show_deleted='False', + upload_option='upload_file' ): """Add a dataset to a folder""" filename = self.get_filename( filename ) self.home() - self.visit_url( "%s/library_common/upload_library_dataset?cntrller=%s&upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \ - ( self.url, cntrller, library_id, folder_id, message ) ) + self.visit_url( "%s/library_common/upload_library_dataset?cntrller=%s&library_id=%s&folder_id=%s&upload_option=%s&message=%s" % \ + ( self.url, cntrller, library_id, folder_id, upload_option, message ) ) self.check_page_for_string( 'Upload files' ) + tc.fv( "1", "library_id", library_id ) tc.fv( "1", "folder_id", folder_id ) + tc.fv( "1", "show_deleted", show_deleted ) tc.formfile( "1", "files_0|file_data", filename ) tc.fv( "1", "file_type", file_type ) tc.fv( "1", "dbkey", dbkey ) diff -r 34babf71a09f -r c73f093219aa test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Mar 09 16:28:04 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Wed Mar 10 11:24:49 2010 -0500 @@ -1181,7 +1181,7 @@ # Test importing the restricted dataset into a history, can't use the # ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission # by going directly to the form action - self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=add&ldda_ids=%s&library_id=%s' \ + self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=import_to_history&ldda_ids=%s&library_id=%s' \ % ( self.url, self.security.encode_id( ldda_five.id ), self.security.encode_id( library_one.id ) ) ) self.check_page_for_string( '1 dataset(s) have been imported into your history' ) self.logout() @@ -1473,7 +1473,7 @@ for ldda in lddas: # Import each library dataset into our history self.home() - self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=add&ldda_ids=%s&library_id=%s' % \ + self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&do_action=import_to_history&ldda_ids=%s&library_id=%s' % \ ( self.url, self.security.encode_id( ldda.id ), self.security.encode_id( library_one.id ) ) ) # Determine the new HistoryDatasetAssociation id created when the library dataset was imported into our history last_hda_created = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \ @@ -1522,7 +1522,7 @@ # be all of the above on any of the 3 datasets that are imported into a history for ldda in lddas: self.home() - self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&library_id=%s&do_action=add&ldda_ids=%s' % \ + self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=library&library_id=%s&do_action=import_to_history&ldda_ids=%s' % \ ( self.url, self.security.encode_id( library_one.id ), self.security.encode_id( ldda.id ) ) ) # Determine the new HistoryDatasetAssociation id created when the library dataset was imported into our history last_hda_created = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \

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[hg] galaxy 3502: Keep the state of displaying / hiding deleted ...
by Greg Von Kuster 11 Mar '10

11 Mar '10

details: http://www.bx.psu.edu/hg/galaxy/rev/34babf71a09f changeset: 3502:34babf71a09f user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Mar 09 16:28:04 2010 -0500 description: Keep the state of displaying / hiding deleted library items whn uploading library datasets. diffstat: lib/galaxy/web/controllers/library_common.py | 7 +++++++ lib/galaxy/web/controllers/tool_runner.py | 1 - templates/base_panels.mako | 5 +++-- templates/library/common/browse_library.mako | 2 +- templates/library/common/common.mako | 3 ++- templates/library/common/upload.mako | 14 +++++++------- 6 files changed, 20 insertions(+), 12 deletions(-) diffs (161 lines): diff -r e4592fc99acc -r 34babf71a09f lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Tue Mar 09 15:25:23 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Tue Mar 09 16:28:04 2010 -0500 @@ -659,6 +659,7 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) deleted = util.string_as_bool( params.get( 'deleted', False ) ) + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) dbkey = params.get( 'dbkey', '?' ) if isinstance( dbkey, list ): last_used_build = dbkey[0] @@ -705,6 +706,7 @@ folder_id=folder_id, replace_id=replace_id, upload_option=upload_option, + show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype='error' ) ) @@ -758,6 +760,7 @@ id=library_id, default_action=default_action, created_ldda_ids=created_ldda_ids, + show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype='done' ) ) @@ -770,6 +773,7 @@ cntrller=cntrller, id=library_id, created_ldda_ids=created_ldda_ids, + show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype=messagetype ) ) # See if we have any inherited templates, but do not inherit contents. @@ -819,6 +823,7 @@ roles=roles, history=history, widgets=widgets, + show_deleted=show_deleted, msg=msg, messagetype=messagetype ) def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_dataset=None, **kwd ): @@ -834,6 +839,7 @@ dataset_upload_inputs.append( input ) # Library-specific params params = util.Params( kwd ) # is this filetoolparam safe? + show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) @@ -883,6 +889,7 @@ folder_id=folder_id, replace_id=replace_id, upload_option=upload_option, + show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype='error' ) ) json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) diff -r e4592fc99acc -r 34babf71a09f lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Tue Mar 09 15:25:23 2010 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Mar 09 16:28:04 2010 -0500 @@ -155,7 +155,6 @@ permissions, in_roles, error, msg = trans.app.security_agent.derive_roles_from_access( trans, library_id, cntrller, library=True, **vars ) if error: return [ 'error', msg ] - permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) def create_dataset( name ): ud = Bunch( name=name, file_type=None, dbkey=None ) if nonfile_params.get( 'folder_id', False ): diff -r e4592fc99acc -r 34babf71a09f templates/base_panels.mako --- a/templates/base_panels.mako Tue Mar 09 15:25:23 2010 -0500 +++ b/templates/base_panels.mako Tue Mar 09 16:28:04 2010 -0500 @@ -131,10 +131,11 @@ $(this).ajaxSubmit( { iframe: true } ); if ( $(this).find("input[name='folder_id']").val() != undefined ) { var library_id = $(this).find("input[name='library_id']").val(); + var show_deleted = $(this).find("input[name='show_deleted']").val(); if ( location.pathname.indexOf( 'admin' ) != -1 ) { - $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets); + $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library_admin&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted); } else { - $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets); + $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_common', action='browse_library' )}?cntrller=library&id=" + library_id + "&created_ldda_ids=" + async_datasets + "&show_deleted=" + show_deleted); } } else { $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); diff -r e4592fc99acc -r 34babf71a09f templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Tue Mar 09 15:25:23 2010 -0500 +++ b/templates/library/common/browse_library.mako Tue Mar 09 16:28:04 2010 -0500 @@ -404,7 +404,7 @@ <ul class="manage-table-actions"> %if not library.deleted and ( cntrller in [ 'library_admin', 'requests_admin' ] or can_add ): - <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ) )}"><span>Add datasets</span></a></li> + <li><a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}"><span>Add datasets</span></a></li> <li><a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( library.root_folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add folder</a></li> %endif </ul> diff -r e4592fc99acc -r 34babf71a09f templates/library/common/common.mako --- a/templates/library/common/common.mako Tue Mar 09 15:25:23 2010 -0500 +++ b/templates/library/common/common.mako Tue Mar 09 16:28:04 2010 -0500 @@ -87,7 +87,7 @@ %endif </%def> -<%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history )"> +<%def name="render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history, show_deleted )"> <% import os, os.path %> %if upload_option in [ 'upload_file', 'upload_directory', 'upload_paths' ]: <div class="toolForm" id="upload_library_dataset"> @@ -106,6 +106,7 @@ <input type="hidden" name="library_id" value="${library_id}"/> <input type="hidden" name="folder_id" value="${folder_id}"/> <input type="hidden" name="upload_option" value="${upload_option}"/> + <input type="hidden" name="show_deleted" value="${show_deleted}"/> %if replace_dataset not in [ None, 'None' ]: <input type="hidden" name="replace_id" value="${trans.security.encode_id( replace_dataset.id )}"/> <div class="form-row"> diff -r e4592fc99acc -r 34babf71a09f templates/library/common/upload.mako --- a/templates/library/common/upload.mako Tue Mar 09 15:25:23 2010 -0500 +++ b/templates/library/common/upload.mako Tue Mar 09 16:28:04 2010 -0500 @@ -26,26 +26,26 @@ ## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="upload-librarydataset--popup"> - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller,library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller,library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file', show_deleted=show_deleted )}">Upload files</a> %if cntrller == 'library_admin': %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory', show_deleted=show_deleted )}">Upload directory of files</a> %endif %if trans.app.config.allow_library_path_paste: - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths', show_deleted=show_deleted )}">Upload files from filesystem paths</a> %endif %elif cntrller == 'library': %if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ): - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory', show_deleted=show_deleted )}">Upload directory of files</a> %endif %endif - <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='upload_library_dataset', cntrller=cntrller, library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history', show_deleted=show_deleted )}">Import datasets from your current history</a> </div> %endif <br/><br/> <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id )}"><span>Browse this data library</span></a> + <a class="action-button" href="${h.url_for( controller='library_common', action='browse_library', cntrller=cntrller, id=library_id, show_deleted=show_deleted )}"><span>Browse this data library</span></a> </li> </ul> @@ -53,4 +53,4 @@ ${render_msg( msg, messagetype )} %endif -${render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history )} +${render_upload_form( cntrller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, widgets, roles, history, show_deleted )}

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