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[hg] galaxy 2437: Merge genetics.py
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e27e392806df changeset: 2437:e27e392806df user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Jun 09 10:28:27 2009 -0400 description: Merge genetics.py 1 file(s) affected in this change: lib/galaxy/datatypes/genetics.py diffs (159 lines): diff -r 2c6720a9130c -r e27e392806df lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Jun 08 21:02:41 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Tue Jun 09 10:28:27 2009 -0400 @@ -17,6 +17,7 @@ from galaxy import util from cgi import escape import urllib +from galaxy.web import url_for from galaxy.datatypes import metadata from galaxy.datatypes.metadata import MetadataElement #from galaxy.datatypes.data import Text @@ -80,7 +81,7 @@ 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 - display_url = urllib.quote_plus( "%s/display_as?id=%i&display_app=%s" % (base_url, dataset.id, type) ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s" % (base_url, url_for( controller='root' ), dataset.id, type)) sl = ["%sdb=%s" % (site_url,dataset.dbkey ),] sl.append("&hgGenome_dataSetName=%s&hgGenome_dataSetDescription=%s" % (dataset.name, 'GalaxyGG_data')) sl.append("&hgGenome_formatType=best%20guess&hgGenome_markerType=best%20guess") @@ -116,8 +117,8 @@ class Rgenetics(Html): """class to use for rgenetics""" """Add metadata elements""" - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True) + file_ext="html" composite_type = 'auto_primary_file' @@ -234,7 +235,128 @@ """fake class to distinguish different species of Rgenetics data collections """ file_ext="snptest" + +class RexpBase( Html ): + """base class for BioC data structures in Galaxy + must be constructed with the pheno data in place since that + goes into the metadata for each instance""" + """Add metadata elements""" + MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=False ) + MetadataElement( name="column_names", default=[], desc="Column names", readonly=True,visible=True ) + MetadataElement( name="base_name", + desc="base name for all transformed versions of this genetic dataset", readonly=True) + MetadataElement( name="pheno_path", + desc="Path to phenotype data for this experiment", readonly=True) + MetadataElement( name="pheno", + desc="Phenotype data for this experiment", readonly=True) + + file_ext = None + + def set_peek( self, dataset ): + """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?""" + p = file(dataset.metadata.pheno_path,'r').readlines() + head = p[0].strip().split('\t') + head.insert(0,'ChipFileName') # fix R write.table b0rken-ness + p[0] = '\t'.join(head) + p = '\n'.join(p) + dataset.peek = p + dataset.metadata.pheno = p + dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit' + + # stolen from Tabular + # class Tabular( data.Text ): + """Tab delimited data""" + + """Add metadata elements""" + def init_meta( self, dataset, copy_from=None ): + if copy_from: + dataset.metadata = copy_from.metadata + + + #def set_readonly_meta( self, dataset, skip=0, **kwd ): + # """Resets the values of readonly metadata elements.""" + # RexpBase.set_meta( self, dataset, skip=skip ) + + def set_readonly_meta( self, dataset, **kwd ): + """Resets the values of readonly metadata elements.""" + RexpBase.set_meta( self, dataset ) + + #def set_meta( self, dataset, skip=0, **kwd ): + def set_meta( self, dataset, **kwd ): + + """ + NOTE we apply the tabular machinary to the phenodata extracted + from a BioC eSet or affybatch. + + """ + if not dataset.peek: + dataset.set_peek() + pk = dataset.peek # use the peek which is the pheno data insead of dataset (!) + if pk: + p = pk.split('\n') + h = p[0].strip().split('\t') # hope is header + h = [escape(x) for x in h] + dataset.metadata.column_names = h + dataset.metadata.columns = len(h) + else: + dataset.metadata.column_names = [] + dataset.metadata.columns = 0 + + def make_html_table( self, dataset): + """Create HTML table, used for displaying peek""" + out = ['<table cellspacing="0" cellpadding="3">',] + try: + # Generate column header + pk = dataset.peek + p = pk.split('\n') + for i,row in enumerate(p): + lrow = row.strip().split('\t') + if i == 0: + orow = ['<th>%s</th>' % escape(x) for x in lrow] + orow.insert(0,'<tr>') + orow.append('</tr>') + else: + orow = ['<td>%s</td>' % escape(x) for x in lrow] + orow.insert(0,'<tr>') + orow.append('</tr>') + out.append(''.join(orow)) + out.append( '</table>' ) + out = "\n".join( out ) + except Exception, exc: + out = "Can't create peek %s" % str( exc ) + return out + + def display_peek( self, dataset ): + """Returns formatted html of peek""" + if not dataset.peek: + dataset.set_peek() + return self.make_html_table( dataset ) + + def get_mime(self): + """Returns the mime type of the datatype""" + return 'application/gzip' + + def sniff(self): + """ can we be bothered looking for the signature or loading via rpy? + """ + return true + +class AffyBatch( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "affybatch" + + +class ESet( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "eset" + + +class MAList( RexpBase ): + """derived class for BioC data structures in Galaxy """ + file_ext = "malist" if __name__ == '__main__':

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[hg] galaxy 2436: Functional test fixes for sniffing data format...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2c6720a9130c changeset: 2436:2c6720a9130c user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 08 21:02:41 2009 -0400 description: Functional test fixes for sniffing data formats and setting metadata. 1 file(s) affected in this change: test/functional/test_sniffing_and_metadata_settings.py diffs (229 lines): diff -r 3190f7d6b572 -r 2c6720a9130c test/functional/test_sniffing_and_metadata_settings.py --- a/test/functional/test_sniffing_and_metadata_settings.py Mon Jun 08 16:52:55 2009 -0400 +++ b/test/functional/test_sniffing_and_metadata_settings.py Mon Jun 08 21:02:41 2009 -0400 @@ -1,131 +1,122 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase class SniffingAndMetaDataSettings( TwillTestCase ): - def test_00_axt_datatype( self ): """Testing correctly sniffing axt data type upon upload""" - self.login() - self.upload_file('1.axt') - self.verify_dataset_correctness('1.axt') - self.check_history_for_string('1.axt format: <span class="axt">axt</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.axt" value="\?" Change data type selected value="axt" selected="yes"') - self.delete_history_item( 1 ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + self.new_history( name='history1' ) + global history1 + history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history1 is not None, "Problem retrieving history1 from database" + self.upload_file( '1.axt' ) + self.verify_dataset_correctness( '1.axt' ) + self.check_history_for_string( '1.axt format: <span class="axt">axt</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.axt" value="\?" Change data type selected value="axt" selected="yes"' ) def test_05_bed_datatype( self ): """Testing correctly sniffing bed data type upon upload""" - self.upload_file('1.bed') - self.verify_dataset_correctness('1.bed') - self.check_history_for_string('1.bed format: <span class="bed">bed</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.bed" value="\?"') - self.check_metadata_for_string('Chrom column: <option value="1" selected> Start column: <option value="2" selected>') - self.check_metadata_for_string('End column: <option value="3" selected> Strand column <option value="6" selected>') - self.check_metadata_for_string('Convert to new format <option value="bed">Genomic Intervals To BED <option value="gff">BED to GFF') - self.check_metadata_for_string('Change data type selected value="bed" selected="yes"') - self.delete_history_item( 1 ) + self.upload_file( '1.bed' ) + self.verify_dataset_correctness( '1.bed' ) + self.check_history_for_string( '1.bed format: <span class="bed">bed</span>, database: \? Info: uploaded file') + self.check_metadata_for_string( 'value="1.bed" value="\?"' ) + self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) + self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">Genomic Intervals To BED <option value="gff">BED to GFF' ) + self.check_metadata_for_string( 'Change data type selected value="bed" selected="yes"' ) def test_10_customtrack_datatype( self ): """Testing correctly sniffing customtrack data type upon upload""" - self.upload_file('1.customtrack') - self.verify_dataset_correctness('1.customtrack') - self.check_history_for_string('1.customtrack format: <span class="customtrack">customtrack</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.customtrack" value="\?" Change data type selected value="customtrack" selected="yes"') - self.delete_history_item( 1 ) + self.upload_file( '1.customtrack' ) + self.verify_dataset_correctness( '1.customtrack' ) + self.check_history_for_string( '1.customtrack format: <span class="customtrack">customtrack</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.customtrack" value="\?" Change data type selected value="customtrack" selected="yes"' ) def test_15_fasta_datatype( self ): """Testing correctly sniffing fasta data type upon upload""" - self.upload_file('1.fasta') - self.verify_dataset_correctness('1.fasta') - self.check_history_for_string('1.fasta format: <span class="fasta">fasta</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.fasta" value="\?" Change data type selected value="fasta" selected="yes"') - self.delete_history_item( 1 ) + self.upload_file( '1.fasta' ) + self.verify_dataset_correctness( '1.fasta' ) + self.check_history_for_string( '1.fasta format: <span class="fasta">fasta</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.fasta" value="\?" Change data type selected value="fasta" selected="yes"' ) def test_18_fastqsolexa_datatype( self ): """Testing correctly sniffing fastqsolexa ( the Solexa variant ) data type upon upload""" - self.upload_file('1.fastqsolexa') - self.verify_dataset_correctness('1.fastqsolexa') - self.check_history_for_string('1.fastqsolexa format: <span class="fastqsolexa">fastqsolexa</span>, database: \? Info: uploaded fastqsolexa file') - self.delete_history_item( 1 ) + self.upload_file( '1.fastqsolexa' ) + self.verify_dataset_correctness( '1.fastqsolexa' ) + self.check_history_for_string( '1.fastqsolexa format: <span class="fastqsolexa">fastqsolexa</span>, database: \? Info: uploaded fastqsolexa file' ) def test_20_gff_datatype( self ): """Testing correctly sniffing gff data type upon upload""" - self.upload_file('5.gff') - self.verify_dataset_correctness('5.gff') - self.check_history_for_string('5.gff format: <span class="gff">gff</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="5.gff" value="\?"') - self.check_metadata_for_string('Convert to new format <option value="bed">GFF to BED') - self.check_metadata_for_string('Change data type selected value="gff" selected="yes"') - self.delete_history_item( 1 ) + self.upload_file( '5.gff' ) + self.verify_dataset_correctness( '5.gff' ) + self.check_history_for_string( '5.gff format: <span class="gff">gff</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="5.gff" value="\?"' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">GFF to BED' ) + self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' ) def test_25_gff3_datatype( self ): """Testing correctly sniffing gff3 data type upon upload""" - self.upload_file('5.gff3') - self.verify_dataset_correctness('5.gff3') - self.check_history_for_string('5.gff3 format: <span class="gff3">gff3</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="5.gff3" value="\?"') - self.check_metadata_for_string('Convert to new format <option value="bed">GFF to BED') - self.check_metadata_for_string('Change data type selected value="gff3" selected="yes"') - self.delete_history_item( 1 ) - def test_30_html_datatype( self ): - """Testing correctly sniffing html data type upon upload""" - self.upload_file('html_file.txt') - self.check_history_for_string('No data: attempted to upload an empty or inappropriate file') - self.delete_history_item( 1 ) - def test_35_interval_datatype( self ): + self.upload_file( '5.gff3' ) + self.verify_dataset_correctness( '5.gff3' ) + self.check_history_for_string( '5.gff3 format: <span class="gff3">gff3</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="5.gff3" value="\?"' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">GFF to BED' ) + self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' ) + def test_30_interval_datatype( self ): """Testing correctly sniffing interval data type upon upload""" - self.upload_file('1.interval') - self.verify_dataset_correctness('1.interval') - self.check_history_for_string('1.interval format: <span class="interval">interval</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.interval" value="\?"') - self.check_metadata_for_string('Chrom column: <option value="1" selected> Start column: <option value="2" selected>') - self.check_metadata_for_string('End column: <option value="3" selected> Strand column <option value="6" selected>') - self.check_metadata_for_string('Convert to new format <option value="bed">Genomic Intervals To BED') - self.check_metadata_for_string('Change data type selected value="interval" selected="yes"') - self.delete_history_item( 1 ) - def test_40_lav_datatype( self ): + self.upload_file( '1.interval' ) + self.verify_dataset_correctness( '1.interval' ) + self.check_history_for_string( '1.interval format: <span class="interval">interval</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.interval" value="\?"' ) + self.check_metadata_for_string( 'Chrom column: <option value="1" selected> Start column: <option value="2" selected>' ) + self.check_metadata_for_string( 'End column: <option value="3" selected> Strand column <option value="6" selected>' ) + self.check_metadata_for_string( 'Convert to new format <option value="bed">Genomic Intervals To BED' ) + self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' ) + def test_35_lav_datatype( self ): """Testing correctly sniffing lav data type upon upload""" - self.upload_file('1.lav') - self.verify_dataset_correctness('1.lav') - self.check_history_for_string('1.lav format: <span class="lav">lav</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.lav" value="\?"') - self.check_metadata_for_string('Change data type selected value="lav" selected="yes"') - self.delete_history_item( 1 ) - def test_45_maf_datatype( self ): + self.upload_file( '1.lav' ) + self.verify_dataset_correctness( '1.lav' ) + self.check_history_for_string( '1.lav format: <span class="lav">lav</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.lav" value="\?"' ) + self.check_metadata_for_string( 'Change data type selected value="lav" selected="yes"' ) + def test_40_maf_datatype( self ): """Testing correctly sniffing maf data type upon upload""" - self.upload_file('3.maf') - self.verify_dataset_correctness('3.maf') - self.check_history_for_string('3.maf format: <span class="maf">maf</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="3.maf" value="\?"') - self.check_metadata_for_string('Convert to new format <option value="interval">MAF to Genomic Intervals <option value="fasta">MAF to Fasta') - self.check_metadata_for_string('Change data type selected value="maf" selected="yes"') - self.delete_history_item( 1 ) - def test_50_tabular_datatype( self ): + self.upload_file( '3.maf' ) + self.verify_dataset_correctness( '3.maf' ) + self.check_history_for_string( '3.maf format: <span class="maf">maf</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="3.maf" value="\?"' ) + self.check_metadata_for_string( 'Convert to new format <option value="interval">MAF to Genomic Intervals <option value="fasta">MAF to Fasta' ) + self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' ) + def test_45_tabular_datatype( self ): """Testing correctly sniffing tabular data type upon upload""" - self.upload_file('1.tabular') - self.verify_dataset_correctness('1.tabular') - self.check_history_for_string('1.tabular format: <span class="tabular">tabular</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.tabular" value="\?"') - self.check_metadata_for_string('Change data type selected value="tabular" selected="yes"') - self.delete_history_item( 1 ) - def test_55_wig_datatype( self ): + self.upload_file( '1.tabular' ) + self.verify_dataset_correctness( '1.tabular' ) + self.check_history_for_string( '1.tabular format: <span class="tabular">tabular</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.tabular" value="\?"' ) + self.check_metadata_for_string( 'Change data type selected value="tabular" selected="yes"' ) + def test_50_wig_datatype( self ): """Testing correctly sniffing wig data type upon upload""" - self.upload_file('1.wig') - self.verify_dataset_correctness('1.wig') - self.check_history_for_string('1.wig format: <span class="wig">wig</span>, database: \? Info: uploaded file') - self.check_metadata_for_string('value="1.wig" value="\?"') - self.check_metadata_for_string('Change data type selected value="wig" selected="yes"') - self.delete_history_item( 1 ) - def test_60_blastxml_datatype( self ): + self.upload_file( '1.wig' ) + self.verify_dataset_correctness( '1.wig' ) + self.check_history_for_string( '1.wig format: <span class="wig">wig</span>, database: \? Info: uploaded file' ) + self.check_metadata_for_string( 'value="1.wig" value="\?"' ) + self.check_metadata_for_string( 'Change data type selected value="wig" selected="yes"' ) + def test_55_blastxml_datatype( self ): """Testing correctly sniffing blastxml data type upon upload""" self.upload_file( 'megablast_xml_parser_test1.gz' ) self.check_history_for_string( 'NCBI Blast XML data' ) self.check_history_for_string( 'format: <span class="blastxml">blastxml</span>' ) - self.delete_history_item( 1 ) - def test_65_qualsolid_datatype( self ): - """Testing correctly sniffing qualsolid data type upon upload""" - self.upload_file( 'qualscores.qualsolid' ) - self.verify_dataset_correctness('qualscores.qualsolid') - self.check_history_for_string('qualscores.qualsolid format: <span class="qualsolid">qualsolid</span>, database: \? Info: uploaded qualsolid file') - self.delete_history_item( 1 ) - def test_70_qual454_datatype( self ): - """Testing correctly sniffing qual454 data type upon upload""" - self.upload_file( 'qualscores.qual454' ) - self.verify_dataset_correctness('qualscores.qual454') - self.check_history_for_string('qualscores.qual454 format: <span class="qual454">qual454</span>, database: \? Info: uploaded qual454 file') - self.delete_history_item( 1 ) + """ + TODO: It is currently not even possible to set the following format on upload. They + should be included in the File Format select list on the upload form if they are to + be tested here... + def test_60_qualsolid_datatype( self ): + Testing correctly sniffing qualsolid data type upon upload + self.upload_file( 'qualscores.qualsolid' ) + self.verify_dataset_correctness('qualscores.qualsolid' ) + self.check_history_for_string('2.5 Kb, format: <span class="fasta">fasta</span>, database: \? Info: uploaded file' ) + def test_65_qual454_datatype( self ): + Testing correctly sniffing qual454 data type upon upload + self.upload_file( 'qualscores.qual454' ) + self.verify_dataset_correctness( 'qualscores.qual454' ) + self.check_history_for_string( '5.6 Kb, format: <span class="qual454">qual454</span>, database: \? Info: uploaded qual454 file' ) + """ def test_9999_clean_up( self ): - self.delete_history() + self.delete_history( id=str( history1.id ) ) self.logout()

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[hg] galaxy 2433: Allow the uploading of composite datatypes. A...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/73a8b43f1d97 changeset: 2433:73a8b43f1d97 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jun 08 12:49:26 2009 -0400 description: Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged. A more structured way of storing these files (rather than dumping in a directory) is worth considering. 15 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/genetics.py lib/galaxy/datatypes/registry.py lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/upload.py lib/galaxy/tools/parameters/__init__.py lib/galaxy/tools/parameters/basic.py lib/galaxy/tools/parameters/grouping.py lib/galaxy/tools/parameters/validation.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/tool_runner.py lib/galaxy/web/form_builder.py templates/base_panels.mako templates/tool_form.mako tools/data_source/upload.xml diffs (1641 lines): diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Mon Jun 08 12:49:26 2009 -0400 @@ -1,5 +1,7 @@ import logging, os, sys, time, sets, tempfile from galaxy import util +from galaxy.util.odict import odict +from galaxy.util.bunch import Bunch from cgi import escape import metadata from metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions @@ -48,10 +50,16 @@ """If False, the peek is regenerated whenever a dataset of this type is copied""" copy_safe_peek = True + #Composite datatypes + composite_type = None + composite_files = odict() + primary_file_name = 'index' + def __init__(self, **kwd): """Initialize the datatype""" object.__init__(self, **kwd) self.supported_display_apps = self.supported_display_apps.copy() + self.composite_files = self.composite_files.copy() def write_from_stream(self, dataset, stream): """Writes data from a stream""" fd = open(dataset.file_name, 'wb') @@ -242,7 +250,49 @@ def after_edit( self, dataset ): """This function is called on the dataset after metadata is edited.""" dataset.clear_associated_files( metadata_safe = True ) - + def __new_composite_file( self, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, **kwds ): + kwds[ 'optional' ] = optional + kwds[ 'mimetype' ] = mimetype + kwds[ 'description' ] = description + kwds[ 'substitute_name_with_metadata' ] = substitute_name_with_metadata + return Bunch( **kwds ) + def add_composite_file( self, name, **kwds ): + #self.composite_files = self.composite_files.copy() + self.composite_files[ name ] = self.__new_composite_file( **kwds ) + + + def __substitute_composite_key( self, key, composite_file, dataset = None ): + if composite_file.substitute_name_with_metadata: + if dataset: + meta_value = str( dataset.metadata.get( composite_file.substitute_name_with_metadata ) ) + else: + meta_value = self.spec[composite_file.substitute_name_with_metadata].default + return key % meta_value + return key + @property + def writable_files( self, dataset = None ): + files = odict() + if self.composite_type != 'auto_primary_file': + files[ self.primary_file_name ] = self.__new_composite_file() + for key, value in self.get_composite_files( dataset = dataset ).iteritems(): + files[ key ] = value + return files + def get_composite_files( self, dataset = None ): + def substitute_composite_key( key, composite_file ): + if composite_file.substitute_name_with_metadata: + if dataset: + meta_value = str( dataset.metadata.get( composite_file.substitute_name_with_metadata ) ) + else: + meta_value = self.metadata_spec[ composite_file.substitute_name_with_metadata ].default + return key % meta_value + return key + files = odict() + for key, value in self.composite_files.iteritems(): + files[ substitute_composite_key( key, value ) ] = value + return files + def generate_auto_primary_file( self, dataset = None ): + raise Exception( "generate_auto_primary_file is not implemented for this datatype." ) + @property def has_resolution(self): return False diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Jun 08 12:49:26 2009 -0400 @@ -117,15 +117,26 @@ """class to use for rgenetics""" """Add metadata elements""" - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", readonly=True) + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True) file_ext="html" - + composite_type = 'auto_primary_file' + def missing_meta( self, dataset ): """Checks for empty meta values""" for key, value in dataset.metadata.items(): if not value: return True return False + + def generate_primary_file( self, dataset = None ): + rval = ['<html><head><title>Files for Composite Dataset (%s)</title></head><p/>This composite dataset is composed of the following files:<p/><ul>' % ( self.file_ext ) ] + for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): + opt_text = '' + if composite_file.optional: + opt_text = ' (optional)' + rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) ) + rval.append( '</ul></html>' ) + return "\n".join( rval ) class SNPMatrix(Rgenetics): """fake class to distinguish different species of Rgenetics data collections @@ -148,6 +159,12 @@ """fake class to distinguish different species of Rgenetics data collections """ file_ext="lped" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name' ) + class Pphe(Rgenetics): """fake class to distinguish different species of Rgenetics data collections @@ -180,11 +197,33 @@ """fake class to distinguish different species of Rgenetics data collections """ file_ext="pbed" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name' ) + class Eigenstratgeno(Rgenetics): """fake class to distinguish different species of Rgenetics data collections """ file_ext="eigenstratgeno" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s_fo.eigenstratgeno', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_fo.ind', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_fo.map', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_oo.eigenstratgeno', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_oo.ind', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_oo.map', substitute_name_with_metadata = 'base_name', optional = 'True' ) + + class Eigenstratpca(Rgenetics): """fake class to distinguish different species of Rgenetics data collections diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Jun 08 12:49:26 2009 -0400 @@ -67,6 +67,15 @@ indexer_config = indexer.get( 'file', None ) if indexer_config: self.indexers.append( (indexer_config, extension) ) + for composite_file in elem.findall( 'composite_file' ): + # add composite files + name = composite_file.get( 'name', None ) + if name is None: + log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + optional = composite_file.get( 'optional', False ) + mimetype = composite_file.get( 'mimetype', None ) + self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) + except Exception, e: self.log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) # Load datatype sniffers from the config @@ -294,3 +303,7 @@ ret_data = None return ( convert_ext, ret_data ) return ( None, None ) + + def get_composite_extensions( self ): + return [ ext for ( ext, d_type ) in self.datatypes_by_extension.iteritems() if d_type.composite_type is not None ] + diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Jun 08 12:49:26 2009 -0400 @@ -591,7 +591,7 @@ group = Repeat() group.name = elem.get( "name" ) group.title = elem.get( "title" ) - group.inputs = self.parse_input_elem( elem, enctypes, context ) + group.inputs = self.parse_input_elem( elem, enctypes, context ) rval[group.name] = group elif elem.tag == "conditional": group = Conditional() @@ -609,6 +609,16 @@ case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) rval[group.name] = group + elif elem.tag == "upload_dataset": + group = UploadDataset() + group.name = elem.get( "name" ) + group.title = elem.get( "title" ) + group.file_type_name = elem.get( 'file_type_name', group.file_type_name ) + group.default_file_type = elem.get( 'default_file_type', group.default_file_type ) + rval[ group.file_type_name ].refresh_on_change = True + rval[ group.file_type_name ].refresh_on_change_values = self.app.datatypes_registry.get_composite_extensions() + group.inputs = self.parse_input_elem( elem, enctypes, context ) + rval[ group.name ] = group elif elem.tag == "param": param = self.parse_param_elem( elem, enctypes, context ) rval[param.name] = param @@ -951,6 +961,56 @@ group_state['__current_case__'] = current_case # Store the value of the test element group_state[ input.test_param.name ] = value + elif isinstance( input, UploadDataset ): + group_state = state[input.name] + group_errors = [] + group_old_errors = old_errors.get( input.name, None ) + any_group_errors = False + d_type = input.get_datatype( trans, context ) + writable_files = d_type.writable_files + #remove extra files + while len( group_state ) > len( writable_files ): + del group_state[-1] + if group_old_errors: + del group_old_errors[-1] + # Update state + max_index = -1 + for i, rep_state in enumerate( group_state ): + rep_index = rep_state['__index__'] + max_index = max( max_index, rep_index ) + rep_prefix = "%s_%d|" % ( key, rep_index ) + if group_old_errors: + rep_old_errors = group_old_errors[i] + else: + rep_old_errors = {} + rep_errors = self.update_state( trans, + input.inputs, + rep_state, + incoming, + prefix=rep_prefix, + context=context, + update_only=update_only, + old_errors=rep_old_errors, + changed_dependencies=changed_dependencies, + item_callback=item_callback ) + if rep_errors: + any_group_errors = True + group_errors.append( rep_errors ) + else: + group_errors.append( {} ) + #add new fileupload as needed + offset = 1 + while len( writable_files ) > len( group_state ): + new_state = {} + new_state['__index__'] = max_index + offset + offset += 1 + self.fill_in_new_state( trans, input.inputs, new_state, context ) + group_state.append( new_state ) + if any_group_errors: + group_errors.append( {} ) + # Were there *any* errors for any repetition? + if any_group_errors: + errors[input.name] = group_errors else: if key not in incoming \ and "__force_update__" + key not in incoming \ diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Mon Jun 08 12:49:26 2009 -0400 @@ -19,19 +19,15 @@ except: log.exception( 'failure removing temporary file: %s' % filename ) def execute( self, tool, trans, incoming={}, set_output_hid = True ): - data_file = incoming['file_data'] - file_type = incoming['file_type'] - dbkey = incoming['dbkey'] - url_paste = incoming['url_paste'] - is_multi_byte = False - space_to_tab = False - if 'space_to_tab' in incoming: - if incoming['space_to_tab'] not in ["None", None]: - space_to_tab = True + dataset_upload_inputs = [] + for input_name, input in tool.inputs.iteritems(): + if input.type == "upload_dataset": + dataset_upload_inputs.append( input ) + assert dataset_upload_inputs, Exception( "No dataset upload groups were found." ) # Get any precreated datasets (when using asynchronous uploads) async_datasets = [] self.precreated_datasets = [] - if incoming['async_datasets'] not in ["None", "", None]: + if incoming.get( 'async_datasets', None ) not in ["None", "", None]: async_datasets = incoming['async_datasets'].split(',') for id in async_datasets: try: @@ -45,8 +41,39 @@ log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' % ( data.id, trans.user.id ) ) else: self.precreated_datasets.append( data ) - temp_name = "" data_list = [] + for dataset_upload_input in dataset_upload_inputs: + uploaded_datasets = dataset_upload_input.get_uploaded_datasets( trans, incoming ) + for uploaded_dataset in uploaded_datasets: + precreated_dataset = self.get_precreated_dataset( uploaded_dataset.precreated_name ) + dataset = self.add_file( trans, uploaded_dataset.primary_file, uploaded_dataset.name, uploaded_dataset.file_type, uploaded_dataset.is_multi_byte, uploaded_dataset.dbkey, space_to_tab = uploaded_dataset.space_to_tab, info = uploaded_dataset.info, precreated_dataset = precreated_dataset ) + if uploaded_dataset.composite_files: + os.mkdir( dataset.extra_files_path ) #make extra files path + for name, value in uploaded_dataset.composite_files.iteritems(): + #what about binary files here, need to skip converting newlines + if value is None and not dataset.datatype.writable_files[ name ].optional: + dataset.info = "A required composite data file was not provided (%s)" % name + dataset.state = dataset.states.ERROR + break + elif value is not None: + if value.space_to_tab: + sniff.convert_newlines_sep2tabs( value.filename ) + else: + sniff.convert_newlines( value.filename ) + shutil.move( value.filename, os.path.join( dataset.extra_files_path, name ) ) + data_list.append( dataset ) + #clean up extra temp names + uploaded_dataset.clean_up_temp_files() + + #cleanup unclaimed precreated datasets: + for data in self.precreated_datasets: + log.info( 'Cleaned up unclaimed precreated dataset (%s).' % ( data.id ) ) + data.state = data.states.ERROR + data.info = 'No file contents were available.' + + if data_list: + trans.app.model.flush() + # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id @@ -56,104 +83,14 @@ # For backward compatibility, some tools may not have versions yet. job.tool_version = tool.version except: - job.tool_version = "1.0.0" + job.tool_version = "1.0.1" job.state = trans.app.model.Job.states.UPLOAD job.flush() log.info( 'tool %s created job id %d' % ( tool.id, job.id ) ) trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) - if 'local_filename' in dir( data_file ): - # Use the existing file - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] - precreated_dataset = self.get_precreated_dataset( file_name ) - try: - data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, is_multi_byte, dbkey, space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using datafile.local_filename %s: %s' % ( data_file.local_filename, str( e ) ) ) - self.remove_tempfile( data_file.local_filename ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - elif 'filename' in dir( data_file ): - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] - precreated_dataset = self.get_precreated_dataset( file_name ) - try: - temp_name, is_multi_byte = sniff.stream_to_file( data_file.file, prefix='upload' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - try: - data_list.append( self.add_file( trans, temp_name, file_name, file_type, is_multi_byte, dbkey, space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using file temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - if url_paste not in [ None, "" ]: - if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ): - # If we were sent a DATA_URL from an external application in a post, NAME and INFO - # values should be in the request - if 'NAME' in incoming and incoming[ 'NAME' ] not in [ "None", None ]: - NAME = incoming[ 'NAME' ] - else: - NAME = '' - if 'INFO' in incoming and incoming[ 'INFO' ] not in [ "None", None ]: - INFO = incoming[ 'INFO' ] - else: - INFO = "uploaded url" - url_paste = url_paste.replace( '\r', '' ).split( '\n' ) - name_set_from_line = False #if we are setting the name from the line, it needs to be the line that creates that dataset - for line in url_paste: - line = line.strip() - if line: - if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ): - continue # non-url line, ignore - if not NAME or name_set_from_line: - NAME = line - name_set_from_line = True - precreated_dataset = self.get_precreated_dataset( NAME ) - try: - temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - try: - data_list.append( self.add_file( trans, temp_name, NAME, file_type, is_multi_byte, dbkey, info="uploaded url", space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using url_paste temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - else: - precreated_dataset = self.get_precreated_dataset( 'Pasted Entry' ) - is_valid = False - for line in url_paste: - line = line.rstrip( '\r\n' ) - if line: - is_valid = True - break - if is_valid: - try: - temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - try: - data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, is_multi_byte, dbkey, info="pasted entry", space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - else: - return self.upload_empty( trans, job, "No data error:", "you pasted no data.", precreated_dataset=precreated_dataset ) - if self.empty: - return self.upload_empty( trans, job, "Empty file error:", "you attempted to upload an empty file." ) - elif len( data_list ) < 1: - return self.upload_empty( trans, job, "No data error:", "either you pasted no data, the url you specified is invalid, or you have not specified a file." ) + #if we could make a 'real' job here, then metadata could be set before job.finish() is called - hda = data_list[0] #only our first hda is being added as input for the job, why? + hda = data_list[0] #only our first hda is being added as output for the job, why? job.state = trans.app.model.Job.states.OK file_size_str = datatypes.data.nice_size( hda.dataset.file_size ) job.info = "%s, size: %s" % ( hda.info, file_size_str ) @@ -162,7 +99,7 @@ log.info( 'job id %d ended ok, file size: %s' % ( job.id, file_size_str ) ) trans.log_event( 'job id %d ended ok, file size: %s' % ( job.id, file_size_str ), tool_id=tool.id ) return dict( output=hda ) - + def upload_empty(self, trans, job, err_code, err_msg, precreated_dataset = None): if precreated_dataset is not None: data = precreated_dataset @@ -188,7 +125,7 @@ trans.log_event( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ), tool_id=job.tool_id ) return dict( output=data ) - def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None ): + def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None ): data_type = None # See if we have an empty file if not os.path.getsize( temp_name ) > 0: @@ -254,7 +191,7 @@ data_type = 'binary' if not data_type: # We must have a text file - if self.check_html( temp_name ): + if trans.app.datatypes_registry.get_datatype_by_extension( file_type ).composite_type != 'auto_primary_file' and self.check_html( temp_name ): raise BadFileException( "you attempted to upload an inappropriate file." ) if data_type != 'binary' and data_type != 'zip': if space_to_tab: @@ -404,7 +341,7 @@ return self.precreated_datasets.pop( names.index( name ) ) else: return None - + class BadFileException( Exception ): pass diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/__init__.py Mon Jun 08 12:49:26 2009 -0400 @@ -20,7 +20,7 @@ be nice to unify all the places that recursively visit inputs. """ for input in inputs.itervalues(): - if isinstance( input, Repeat ): + if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): for i, d in enumerate( input_values[ input.name ] ): index = d['__index__'] new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index ) diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Jun 08 12:49:26 2009 -0400 @@ -23,6 +23,7 @@ def __init__( self, tool, param, context=None ): self.tool = tool self.refresh_on_change = False + self.refresh_on_change_values = [] self.name = param.get("name") self.type = param.get("type") self.label = util.xml_text(param, "label") @@ -301,7 +302,7 @@ self.name = elem.get( 'name' ) self.ajax = str_bool( elem.get( 'ajax-upload' ) ) def get_html_field( self, trans=None, value=None, other_values={} ): - return form_builder.FileField( self.name, self.ajax ) + return form_builder.FileField( self.name, ajax = self.ajax, value = value ) def from_html( self, value, trans=None, other_values={} ): # Middleware or proxies may encode files in special ways (TODO: this # should be pluggable) @@ -325,10 +326,11 @@ """ return "multipart/form-data" def to_string( self, value, app ): - if value is None: + if value in [ None, '' ]: return None - else: - raise Exception( "FileToolParameter cannot be persisted" ) + elif isinstance( value, unicode ) or isinstance( value, str ): + return value + raise Exception( "FileToolParameter cannot be persisted" ) def to_python( self, value, app ): if value is None: return None @@ -401,13 +403,13 @@ >>> print p.name blah >>> print p.get_html() - <select name="blah"> + <select name="blah" last_selected_value="y"> <option value="x">I am X</option> <option value="y" selected>I am Y</option> <option value="z">I am Z</option> </select> >>> print p.get_html( value="z" ) - <select name="blah"> + <select name="blah" last_selected_value="z"> <option value="x">I am X</option> <option value="y">I am Y</option> <option value="z" selected>I am Z</option> @@ -426,13 +428,13 @@ >>> print p.name blah >>> print p.get_html() - <select name="blah" multiple> + <select name="blah" multiple last_selected_value="z"> <option value="x">I am X</option> <option value="y" selected>I am Y</option> <option value="z" selected>I am Z</option> </select> >>> print p.get_html( value=["x","y"]) - <select name="blah" multiple> + <select name="blah" multiple last_selected_value="y"> <option value="x" selected>I am X</option> <option value="y" selected>I am Y</option> <option value="z">I am Z</option> @@ -520,7 +522,7 @@ return form_builder.TextField( self.name, value=(value or "") ) if value is not None: if not isinstance( value, list ): value = [ value ] - field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change ) + field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: if isinstance( optval, UnvalidatedValue ): @@ -676,7 +678,7 @@ >>> # hg17 should be selected by default >>> print p.get_html( trans ) # doctest: +ELLIPSIS - <select name="blah"> + <select name="blah" last_selected_value="hg17"> <option value="?">unspecified (?)</option> ... <option value="hg18">Human Mar. 2006 (hg18)</option> @@ -687,7 +689,7 @@ >>> # If the user selected something else already, that should be used >>> # instead >>> print p.get_html( trans, value='hg18' ) # doctest: +ELLIPSIS - <select name="blah"> + <select name="blah" last_selected_value="hg18"> <option value="?">unspecified (?)</option> ... <option value="hg18" selected>Human Mar. 2006 (hg18)</option> @@ -942,7 +944,7 @@ return form_builder.TextArea( self.name, value=value ) else: return form_builder.TextField( self.name, value=(value or "") ) - return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, self.get_options( trans, value, other_values ), value ) + return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, self.get_options( trans, value, other_values ), value, refresh_on_change_values = self.refresh_on_change_values ) def from_html( self, value, trans=None, other_values={} ): if self.need_late_validation( trans, other_values ): @@ -1108,7 +1110,7 @@ if value is not None: if type( value ) != list: value = [ value ] - field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change ) + field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): for i, hda in enumerate( hdas ): diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Mon Jun 08 12:49:26 2009 -0400 @@ -4,6 +4,14 @@ from basic import ToolParameter from galaxy.util.expressions import ExpressionContext + +import logging +log = logging.getLogger( __name__ ) + +import StringIO, os, urllib +from galaxy.datatypes import sniff +from galaxy.util.bunch import Bunch +from galaxy.util.odict import odict class Group( object ): def __init__( self ): @@ -74,7 +82,322 @@ input.visit_inputs( new_prefix, d[input.name], callback ) def get_initial_value( self, trans, context ): return [] + +class UploadDataset( Group ): + type = "upload_dataset" + def __init__( self ): + Group.__init__( self ) + self.title = None + self.inputs = None + self.file_type_name = 'file_type' + self.default_file_type = 'txt' + self.file_type_to_ext = { 'auto':self.default_file_type } + def get_file_type( self, context ): + return context.get( self.file_type_name, self.default_file_type ) + def get_datatype_ext( self, trans, context ): + ext = self.get_file_type( context ) + if ext in self.file_type_to_ext: + ext = self.file_type_to_ext[ext] #when using autodetect, we will use composite info from 'text', i.e. only the main file + return ext + def get_datatype( self, trans, context ): + ext = self.get_datatype_ext( trans, context ) + return trans.app.datatypes_registry.get_datatype_by_extension( ext ) + @property + def title_plural( self ): + if self.title.endswith( "s" ): + return self.title + else: + return self.title + "s" + def group_title( self, context ): + return "%s (%s)" % ( self.title, context.get( self.file_type_name, self.default_file_type ) ) + def title_by_index( self, trans, index, context ): + d_type = self.get_datatype( trans, context ) + for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ): + if i == index: + rval = composite_name + if composite_file.description: + rval = "%s (%s)" % ( rval, composite_file.description ) + if composite_file.optional: + rval = "%s [optional]" % rval + return rval + return None + def value_to_basic( self, value, app ): + rval = [] + for d in value: + rval_dict = {} + # Propogate __index__ + if '__index__' in d: + rval_dict['__index__'] = d['__index__'] + for input in self.inputs.itervalues(): + rval_dict[ input.name ] = input.value_to_basic( d[input.name], app ) + rval.append( rval_dict ) + return rval + def value_from_basic( self, value, app, ignore_errors=False ): + rval = [] + for i, d in enumerate( value ): + rval_dict = {} + # If the special __index__ key is not set, create it (for backward + # compatibility) + rval_dict['__index__'] = d.get( '__index__', i ) + # Restore child inputs + for input in self.inputs.itervalues(): + if ignore_errors and input.name not in d: #this wasn't tested + rval_dict[ input.name ] = input.get_initial_value( None, d ) + else: + rval_dict[ input.name ] = input.value_from_basic( d[input.name], app, ignore_errors ) + rval.append( rval_dict ) + return rval + def visit_inputs( self, prefix, value, callback ): + for i, d in enumerate( value ): + for input in self.inputs.itervalues(): + new_prefix = prefix + "%s_%d|" % ( self.name, i ) + if isinstance( input, ToolParameter ): + callback( new_prefix, input, d[input.name], parent = d ) + else: + input.visit_inputs( new_prefix, d[input.name], callback ) + def get_initial_value( self, trans, context ): + d_type = self.get_datatype( trans, context ) + rval = [] + for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ): + rval_dict = {} + rval_dict['__index__'] = i # create __index__ + for input in self.inputs.itervalues(): + rval_dict[ input.name ] = input.get_initial_value( trans, context ) #input.value_to_basic( d[input.name], app ) + rval.append( rval_dict ) + return rval + def get_uploaded_datasets( self, trans, context, override_name = None, override_info = None ): + def get_data_file_filename( data_file, is_multi_byte = False, override_name = None, override_info = None ): + dataset_name = override_name + dataset_info = override_info + def get_file_name( file_name ): + file_name = file_name.split( '\\' )[-1] + file_name = file_name.split( '/' )[-1] + return file_name + if 'local_filename' in dir( data_file ): + # Use the existing file + return data_file.local_filename, get_file_name( data_file.filename ), is_multi_byte + elif 'filename' in dir( data_file ): + #create a new tempfile + try: + temp_name, is_multi_byte = sniff.stream_to_file( data_file.file, prefix='upload' ) + precreated_name = get_file_name( data_file.filename ) + if not dataset_name: + dataset_name = precreated_name + if not dataset_info: + dataset_info = 'uploaded file' + return temp_name, get_file_name( data_file.filename ), is_multi_byte, dataset_name, dataset_info + except Exception, e: + log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) + self.remove_temp_file( temp_name ) + return None, None, is_multi_byte, None, None + def filenames_from_url_paste( url_paste, group_incoming, override_name = None, override_info = None ): + filenames = [] + if url_paste not in [ None, "" ]: + if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ): + url_paste = url_paste.replace( '\r', '' ).split( '\n' ) + for line in url_paste: + line = line.strip() + if line: + if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ): + continue # non-url line, ignore + precreated_name = line + dataset_name = override_name + if not dataset_name: + dataset_name = line + dataset_info = override_info + if not dataset_info: + dataset_info = 'uploaded url' + try: + temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) + except Exception, e: + temp_name = None + precreated_name = str( e ) + log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) + try: + self.remove_temp_file( temp_name ) + except: + pass + yield ( temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info ) + #yield ( None, str( e ), False, dataset_name, dataset_info ) + else: + dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here + if override_name: + dataset_name = override_name + if override_info: + dataset_info = override_info + is_valid = False + for line in url_paste: #Trim off empty lines from begining + line = line.rstrip( '\r\n' ) + if line: + is_valid = True + break + if is_valid: + try: + temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) + except Exception, e: + log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) + temp_name = None + precreated_name = str( e ) + try: + self.remove_temp_file( temp_name ) + except: + pass + yield ( temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info ) + #yield ( None, str( e ), False, dataset_name, dataset_info ) + def get_one_filename( context ): + data_file = context['file_data'] + url_paste = context['url_paste'] + name = context.get( 'NAME', None ) + info = context.get( 'INFO', None ) + warnings = [] + is_multi_byte = False + space_to_tab = False + if context.get( 'space_to_tab', None ) not in ["None", None]: + space_to_tab = True + temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info = get_data_file_filename( data_file, is_multi_byte = is_multi_byte, override_name = name, override_info = info ) + if temp_name: + if url_paste.strip(): + warnings.append( "All file contents specified in the paste box were ignored." ) + else: #we need to use url_paste + #file_names = filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ) + for temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info in filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ):#file_names: + if temp_name: + break + ###this check will cause an additional file to be retrieved and created...so lets not do that + #try: #check to see if additional paste contents were available + # file_names.next() + # warnings.append( "Additional file contents were specified in the paste box, but ignored." ) + #except StopIteration: + # pass + return temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings + + def get_filenames( context ): + rval = [] + data_file = context['file_data'] + url_paste = context['url_paste'] + name = context.get( 'NAME', None ) + info = context.get( 'INFO', None ) + warnings = [] + is_multi_byte = False + space_to_tab = False + if context.get( 'space_to_tab', None ) not in ["None", None]: + space_to_tab = True + temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info = get_data_file_filename( data_file, is_multi_byte = is_multi_byte, override_name = name, override_info = info ) + if temp_name: + rval.append( ( temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info ) ) + for temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info in filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ): + if temp_name: + rval.append( ( temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info ) ) + return rval + class UploadedDataset( Bunch ): + def __init__( self, **kwd ): + Bunch.__init__( self, **kwd ) + self.primary_file = None + self.composite_files = odict() + self.dbkey = None + self.warnings = [] + + self._temp_filenames = [] #store all created filenames here, delete on cleanup + def register_temp_file( self, filename ): + if isinstance( filename, list ): + self._temp_filenames.extend( filename ) + else: + self._temp_filenames.append( filename ) + def remove_temp_file( self, filename ): + try: + os.unlink( filename ) + except Exception, e: + pass + #log.warning( str( e ) ) + def clean_up_temp_files( self ): + for filename in self._temp_filenames: + self.remove_temp_file( filename ) + + file_type = self.get_file_type( context ) + d_type = self.get_datatype( trans, context ) + dbkey = context.get( 'dbkey', None ) + writable_files = d_type.writable_files + writable_files_offset = 0 + groups_incoming = [ None for filename in writable_files ] + for group_incoming in context.get( self.name, [] ): + i = int( group_incoming['__index__'] ) + groups_incoming[ i ] = group_incoming + + if d_type.composite_type is not None: + #handle uploading of composite datatypes + #Only one Dataset can be created + + dataset = UploadedDataset() + dataset.file_type = file_type + dataset.datatype = d_type + dataset.dbkey = dbkey + + temp_name = None + precreated_name = None + is_multi_byte = False + space_to_tab = False + warnings = [] + + dataset_name = None + dataset_info = None + if dataset.datatype.composite_type == 'auto_primary_file': + #replace sniff here with just creating an empty file + temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file() ), prefix='upload_auto_primary_file' ) + precreated_name = dataset_name = 'Uploaded Composite Dataset (%s)' % ( file_type ) + else: + temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings = get_one_filename( groups_incoming[ 0 ] ) + writable_files_offset = 1 + if temp_name is None:#remove this before finish, this should create an empty dataset + raise Exception( 'No primary dataset file was available for composite upload' ) + dataset.primary_file = temp_name + dataset.is_multi_byte = is_multi_byte + dataset.space_to_tab = space_to_tab + dataset.precreated_name = precreated_name + dataset.name = dataset_name + dataset.info = dataset_info + dataset.warnings.extend( warnings ) + dataset.register_temp_file( temp_name ) + + keys = writable_files.keys() + for i, group_incoming in enumerate( groups_incoming[ writable_files_offset : ] ): + key = keys[ i + writable_files_offset ] + if group_incoming is None and not writable_files[ key ].optional: + dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) + dataset.composite_files[ key ] = None + else: + temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings = get_one_filename( group_incoming ) + if temp_name: + dataset.composite_files[ key ] = Bunch( filename = temp_name, precreated_name = precreated_name, is_multi_byte = is_multi_byte, space_to_tab = space_to_tab, warnings = warnings, info = dataset_info, name = dataset_name ) + dataset.register_temp_file( temp_name ) + else: + dataset.composite_files[ key ] = None + if not writable_files[ key ].optional: + dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) + return [ dataset ] + else: + rval = [] + for temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, in get_filenames( context[ self.name ][0] ): + dataset = UploadedDataset() + dataset.file_type = file_type + dataset.datatype = d_type + dataset.dbkey = dbkey + dataset.primary_file = temp_name + dataset.is_multi_byte = is_multi_byte + dataset.space_to_tab = space_to_tab + dataset.name = dataset_name + dataset.info = dataset_info + dataset.precreated_name = precreated_name + dataset.register_temp_file( temp_name ) + rval.append( dataset ) + return rval + def remove_temp_file( self, filename ): + try: + os.unlink( filename ) + except Exception, e: + log.warning( str( e ) ) + + class Conditional( Group ): type = "conditional" def __init__( self ): diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Mon Jun 08 12:49:26 2009 -0400 @@ -72,14 +72,18 @@ """ @classmethod def from_element( cls, param, elem ): - return cls( elem.get( 'message' ), elem.text ) - def __init__( self, message, expression ): + return cls( elem.get( 'message' ), elem.text, elem.get( 'substitute_value_in_message' ) ) + def __init__( self, message, expression, substitute_value_in_message ): self.message = message + self.substitute_value_in_message = substitute_value_in_message # Save compiled expression, code objects are thread safe (right?) - self.expression = compile( expression, '<string>', 'eval' ) + self.expression = compile( expression, '<string>', 'eval' ) def validate( self, value, history=None ): if not( eval( self.expression, dict( value=value ) ) ): - raise ValueError( self.message ) + message = self.message + if self.substitute_value_in_message: + message = message % value + raise ValueError( message ) class InRangeValidator( Validator ): """ diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/util/__init__.py Mon Jun 08 12:49:26 2009 -0400 @@ -146,6 +146,7 @@ elif isinstance( value, list ): return map(sanitize_text, value) else: + print value raise Exception, 'Unknown parameter type (%s)' % ( type( value ) ) class Params: @@ -222,7 +223,7 @@ pass if not value and not new_value: new_value = tool.param_trans_dict[ key ][1] - if key not in self.NEVER_SANITIZE and sanitize: + if sanitize and not ( key in self.NEVER_SANITIZE or True in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ] ): #sanitize check both ungrouped and grouped parameters by name self.__dict__[ new_key ] = sanitize_param( new_value ) else: self.__dict__[ new_key ] = new_value diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Mon Jun 08 12:49:26 2009 -0400 @@ -3,6 +3,8 @@ """ from galaxy.web.base.controller import * +from galaxy.util.bunch import Bunch +from galaxy.tools import DefaultToolState import logging log = logging.getLogger( __name__ ) @@ -75,32 +77,51 @@ tool = self.get_toolbox().tools_by_id.get( tool_id, None ) if not tool: return False # bad tool_id - params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool ) + #params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool ) + if "tool_state" in kwd: + encoded_state = util.string_to_object( kwd["tool_state"] ) + tool_state = DefaultToolState() + tool_state.decode( encoded_state, tool, trans.app ) + else: + tool_state = tool.new_state( trans ) + errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True ) datasets = [] - if params.file_data not in [ None, "" ]: - name = params.file_data - if name.count('/'): - name = name.rsplit('/',1)[1] - if name.count('\\'): - name = name.rsplit('\\',1)[1] - datasets.append( create_dataset( name, trans.history ) ) - if params.url_paste not in [ None, "" ]: - url_paste = params.url_paste.replace( '\r', '' ).split( '\n' ) - url = False - for line in url_paste: - line = line.rstrip( '\r\n' ).strip() - if not line: - continue - elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ): - url = True - datasets.append( create_dataset( line, trans.history ) ) - else: - if url: - continue # non-url when we've already processed some urls - else: - # pasted data - datasets.append( create_dataset( 'Pasted Entry', trans.history ) ) - break + dataset_upload_inputs = [] + for input_name, input in tool.inputs.iteritems(): + if input.type == "upload_dataset": + dataset_upload_inputs.append( input ) + assert dataset_upload_inputs, Exception( "No dataset upload groups were found." ) + for dataset_upload_input in dataset_upload_inputs: + d_type = dataset_upload_input.get_datatype( trans, kwd ) + + if d_type.composite_type is not None: + datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ), trans.history ) ) + else: + params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] ) + if params.file_data not in [ None, "" ]: + name = params.file_data + if name.count('/'): + name = name.rsplit('/',1)[1] + if name.count('\\'): + name = name.rsplit('\\',1)[1] + datasets.append( create_dataset( name, trans.history ) ) + if params.url_paste not in [ None, "" ]: + url_paste = params.url_paste.replace( '\r', '' ).split( '\n' ) + url = False + for line in url_paste: + line = line.rstrip( '\r\n' ).strip() + if not line: + continue + elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ): + url = True + datasets.append( create_dataset( line, trans.history ) ) + else: + if url: + continue # non-url when we've already processed some urls + else: + # pasted data + datasets.append( create_dataset( 'Pasted Entry', trans.history ) ) + break if datasets: trans.model.flush() return [ d.id for d in datasets ] diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/web/form_builder.py Mon Jun 08 12:49:26 2009 -0400 @@ -78,17 +78,21 @@ >>> print FileField( "foo" ).get_html() <input type="file" name="foo"> - >>> print FileField( "foo", True ).get_html() + >>> print FileField( "foo", ajax = True ).get_html() <input type="file" name="foo" galaxy-ajax-upload="true"> """ - def __init__( self, name, ajax=False ): + def __init__( self, name, value = None, ajax=False ): self.name = name self.ajax = ajax + self.value = value def get_html( self, prefix="" ): + value_text = "" + if self.value: + value_text = ' value="%s"' % self.value + ajax_text = "" if self.ajax: - return '<input type="file" name="%s%s" galaxy-ajax-upload="true">' % ( prefix, self.name ) - else: - return '<input type="file" name="%s%s">' % ( prefix, self.name ) + ajax_text = ' galaxy-ajax-upload="true"' + return '<input type="file" name="%s%s"%s%s>' % ( prefix, self.name, ajax_text, value_text ) class HiddenField(BaseField): """ @@ -120,7 +124,7 @@ >>> t.add_option( "automatic", 3 ) >>> t.add_option( "bazooty", 4, selected=True ) >>> print t.get_html() - <select name="bar"> + <select name="bar" last_selected_value="4"> <option value="3">automatic</option> <option value="4" selected>bazooty</option> </select> @@ -140,7 +144,7 @@ <div><input type="checkbox" name="bar" value="3">automatic</div> <div><input type="checkbox" name="bar" value="4" checked>bazooty</div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False ): + def __init__( self, name, multiple=None, display=None, refresh_on_change = False, refresh_on_change_values = [] ): self.name = name self.multiple = multiple or False self.options = list() @@ -152,8 +156,11 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s"' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) else: self.refresh_on_change_text = '' def add_option( self, text, value, selected = False ): @@ -195,11 +202,17 @@ def get_html_default( self, prefix="" ): if self.multiple: multiple = " multiple" else: multiple = "" - rval = [ '<select name="%s%s"%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text ) ] + rval = [] + last_selected_value = "" for text, value, selected in self.options: - if selected: selected_text = " selected" + if selected: + selected_text = " selected" + last_selected_value = value else: selected_text = "" rval.append( '<option value="%s"%s>%s</option>' % ( value, selected_text, text ) ) + if last_selected_value: + last_selected_value = ' last_selected_value="%s"' % last_selected_value + rval.insert( 0, '<select name="%s%s"%s%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text, last_selected_value ) ) rval.append( '</select>' ) return "\n".join( rval ) @@ -253,7 +266,7 @@ </li> </ul></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, options = [], value = [] ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, options = [], value = [], refresh_on_change_values = [] ): self.name = name self.multiple = multiple or False self.options = options @@ -270,8 +283,11 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s"' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) else: self.refresh_on_change_text = '' def get_html( self, prefix="" ): @@ -308,6 +324,7 @@ rval.append( '</ul></div>' ) return '\n'.join( rval ) + def get_suite(): """Get unittest suite for this module""" import doctest, sys diff -r c0c50620b89d -r 73a8b43f1d97 templates/base_panels.mako --- a/templates/base_panels.mako Mon Jun 08 12:35:38 2009 -0400 +++ b/templates/base_panels.mako Mon Jun 08 12:49:26 2009 -0400 @@ -59,19 +59,19 @@ <script type="text/javascript" src="${h.url_for('/static/scripts/galaxy.panels.js')}"></script> <script type="text/javascript"> - ensure_dd_helper(); + ensure_dd_helper(); - %if self.has_left_panel: + %if self.has_left_panel: var lp = make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); force_left_panel = lp.force_panel; %endif - %if self.has_right_panel: + %if self.has_right_panel: var rp = make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); handle_minwidth_hint = rp.handle_minwidth_hint; force_right_panel = rp.force_panel; %endif - + </script> ## Handle AJAX (actually hidden iframe) upload tool <![if !IE]> @@ -81,34 +81,36 @@ ##$(this.contentDocument).find("input[galaxy-ajax-upload]").each( function() { ##$("iframe")[0].contentDocument.body.innerHTML = "HELLO" ##$(this.contentWindow.document).find("input[galaxy-ajax-upload]").each( function() { - $(this).contents().find("input[galaxy-ajax-upload]").each( function() { - var error_set = false; - $(this).parents("form").submit( function() { - // Make a synchronous request to create the datasets first - var async_datasets; - $.ajax( { - async: false, - type: "POST", - url: "${h.url_for(controller='tool_runner', action='upload_async_create')}", - data: $(this).formSerialize(), - dataType: "json", - success: function( d, s ) { async_datasets = d.join() } - } ); - if (async_datasets == '') { - if (! error_set) { - $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage">No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch from.</div><p/>' ); - error_set = true; + $(this).contents().find("form").each( function() { + if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){ + $(this).submit( function() { + var error_set = false; + // Make a synchronous request to create the datasets first + var async_datasets; + $.ajax( { + async: false, + type: "POST", + url: "${h.url_for(controller='tool_runner', action='upload_async_create')}", + data: $(this).formSerialize(), + dataType: "json", + success: function( d, s ) { async_datasets = d.join() } + } ); + if (async_datasets == '') { + if (! error_set) { + $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage">No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch from.</div><p/>' ); + error_set = true; + } + return false; + } else { + $(this).find("input[name=async_datasets]").val( async_datasets ); + $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); } + // iframe submit is required for nginx (otherwise the encoding is wrong) + $(this).ajaxSubmit( { iframe: true } ); + $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); return false; - } else { - $(this).find("input[name=async_datasets]").val( async_datasets ); - $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); - } - // iframe submit is required for nginx (otherwise the encoding is wrong) - $(this).ajaxSubmit( { iframe: true } ); - $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); - return false; - }); + }); + } }); }); }); @@ -120,88 +122,88 @@ <%def name="masthead()"> <div class="title" style="float: left;"> - <a target="_blank" href="${app.config.wiki_url}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> - </a> - Galaxy - %if app.config.brand: - <span class='brand'>/${app.config.brand}</span> - %endif + <a target="_blank" href="${app.config.wiki_url}"> + <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> + </a> + Galaxy + %if app.config.brand: + <span class='brand'>/${app.config.brand}</span> + %endif </div> <div style="position: absolute; left: 50%;"> <div class="tab-group" style="position: relative; left: -50%;"> - - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> - <% - cls = "tab" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - style = "" - if not visible: - style = "display: none;" - %> - <span class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></span> - </%def> - ## ${tab( "tracks", "View Data", h.url_for( controller='tracks', action='dbkeys' ), target="galaxy_main")} + <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> + <% + cls = "tab" + if extra_class: + cls += " " + extra_class + if self.active_view == id: + cls += " active" + style = "" + if not visible: + style = "display: none;" + %> + <span class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></span> + </%def> + + ## ${tab( "tracks", "View Data", h.url_for( controller='tracks', action='dbkeys' ), target="galaxy_main")} - ${tab( "analysis", "Analyze Data", h.url_for( controller='root', action='index' ))} + ${tab( "analysis", "Analyze Data", h.url_for( controller='root', action='index' ))} - ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} + ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))} - ${tab( "admin", "Admin", h.url_for( controller='admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - <span class="tab"> - <a>Help</a> - <div class="submenu"> - <ul> - <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> - <li><a target="_blank" href="${app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy Wiki</a></li> - <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li> - </ul> - </div> - </span> + ${tab( "admin", "Admin", h.url_for( controller='admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - <span class="tab"> - <a>User</a> - <% - if trans.user: - user_email = trans.user.email - style1 = "display: none;" - style2 = ""; - else: - user_email = "" - style1 = "" - style2 = "display: none;" - %> - <div class="submenu"> - <ul class="loggedout-only" style="${style1}"> - <li><a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">Login</a></li> - %if app.config.allow_user_creation: - <li><a target="galaxy_main" href="${h.url_for( controller='user', action='create' )}">Register</a></li> - %endif - </ul> - <ul class="loggedin-only" style="${style2}"> - <li>Logged in as <span id="user-email">${user_email}</span></li> - <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li> - <% - if app.config.require_login: - logout_target = "" - logout_url = h.url_for( controller='root', action='index', m_c='user', m_a='logout' ) - else: - logout_target = "galaxy_main" - logout_url = h.url_for( controller='user', action='logout' ) - %> - <li><a target="${logout_target}" href="${logout_url}">Logout</a></li> - </ul> - </div> - </span> - + <span class="tab"> + <a>Help</a> + <div class="submenu"> + <ul> + <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> + <li><a target="_blank" href="${app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy Wiki</a></li> + <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li> + </ul> + </div> + </span> + + <span class="tab"> + <a>User</a> + <% + if trans.user: + user_email = trans.user.email + style1 = "display: none;" + style2 = ""; + else: + user_email = "" + style1 = "" + style2 = "display: none;" + %> + <div class="submenu"> + <ul class="loggedout-only" style="${style1}"> + <li><a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">Login</a></li> + %if app.config.allow_user_creation: + <li><a target="galaxy_main" href="${h.url_for( controller='user', action='create' )}">Register</a></li> + %endif + </ul> + <ul class="loggedin-only" style="${style2}"> + <li>Logged in as <span id="user-email">${user_email}</span></li> + <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li> + <% + if app.config.require_login: + logout_target = "" + logout_url = h.url_for( controller='root', action='index', m_c='user', m_a='logout' ) + else: + logout_target = "galaxy_main" + logout_url = h.url_for( controller='user', action='logout' ) + %> + <li><a target="${logout_target}" href="${logout_url}">Logout</a></li> + </ul> + </div> + </span> + </div> </div> @@ -213,32 +215,32 @@ <div id="overlay" %if not self.overlay_visible: - style="display: none;" + style="display: none;" %endif > - ## - <div id="overlay-background" style="position: absolute; width: 100%; height: 100%;"></div> - - ## Need a table here for centering in IE6 - <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0" - %if not self.overlay_visible: - style="display: none;" - %endif - ><tr><td> - <div class="dialog-box-wrapper"> - <div class="dialog-box"> - <div class="unified-panel-header"> - <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> - </div> - <div class="body" style="max-height: 600px; overflow: auto;">${content}</div> - <div> - <div class="buttons" style="display: none; float: right;"></div> - <div class="extra_buttons" style="display: none; padding: 5px;"></div> - <div style="clear: both;"></div> - </div> - </div> - </div> - </td></tr></table> + ## + <div id="overlay-background" style="position: absolute; width: 100%; height: 100%;"></div> + + ## Need a table here for centering in IE6 + <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0" + %if not self.overlay_visible: + style="display: none;" + %endif + ><tr><td> + <div class="dialog-box-wrapper"> + <div class="dialog-box"> + <div class="unified-panel-header"> + <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> + </div> + <div class="body" style="max-height: 600px; overflow: auto;">${content}</div> + <div> + <div class="buttons" style="display: none; float: right;"></div> + <div class="extra_buttons" style="display: none; padding: 5px;"></div> + <div style="clear: both;"></div> + </div> + </div> + </div> + </td></tr></table> </div> </%def> @@ -268,7 +270,7 @@ ${self.message_box_content()} %endif </div> - ${self.overlay()} + ${self.overlay()} %if self.has_left_panel: <div id="left"> ${self.left_panel()} diff -r c0c50620b89d -r 73a8b43f1d97 templates/tool_form.mako --- a/templates/tool_form.mako Mon Jun 08 12:35:38 2009 -0400 +++ b/templates/tool_form.mako Mon Jun 08 12:49:26 2009 -0400 @@ -15,7 +15,39 @@ <script type="text/javascript"> $( function() { $( "select[refresh_on_change='true']").change( function() { - $( "#tool_form" ).submit(); + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( ':file' ).each( function() { + var file_value = $( this )[0].value; + if ( file_value ) { + //disable file input, since we don't want to upload the file on refresh + var file_name = $( this )[0].name; + $( this )[0].name = 'replaced_file_input_' + file_name + $( this )[0].disable = true; + //create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = document.createElement( 'input' ); + new_file_input.type = 'hidden'; + new_file_input.value = file_value; + new_file_input.name = file_name; + document.getElementById( 'tool_form' ).appendChild( new_file_input ); + } + } ); + $( "#tool_form" ).submit(); + } }); }); %if not add_frame.debug: @@ -72,6 +104,38 @@ %> ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} + %elif input.type == "upload_dataset": + %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before + <% + if input.name in errors: + rep_errors = errors[input.name][0] + else: + rep_errors = dict() + %> + ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} + %else: + <div class="repeat-group"> + <div class="form-title-row"><b>${input.group_title( other_values )}</b></div> + <% + repeat_state = tool_state[input.name] + %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><b>File Contents for ${input.title_by_index( trans, i, other_values )}</b></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %endfor + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + </div> + %endif %else: ${row_for_param( prefix, input, tool_state, errors, other_values )} %endif @@ -127,7 +191,7 @@ <br/> %endif -<div class="toolForm" id="$tool.id"> +<div class="toolForm" id="${tool.id}"> %if tool.has_multiple_pages: <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> %else: diff -r c0c50620b89d -r 73a8b43f1d97 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Mon Jun 08 12:35:38 2009 -0400 +++ b/tools/data_source/upload.xml Mon Jun 08 12:49:26 2009 -0400 @@ -1,17 +1,11 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1"> +<tool name="Upload File" id="upload1" version="1.0.1"> <description> from your computer </description> <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <inputs> - <param name="async_datasets" type="hidden" value="None"/> - <param name="file_data" type="file" size="30" label="File" ajax-upload="true"/> - <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> - <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> - <option value="Yes">Yes</option> - </param> <param name="file_type" type="select" label="File Format" help="Which format? See help below"> <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> <column name="value" index="1"/> @@ -20,6 +14,16 @@ <filter type="add_value" name="Auto-detect" value="auto" index="0"/> </options> </param> + <param name="async_datasets" type="hidden" value="None"/> + <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type"> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true"> + <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>  + </param> + <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> + <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> + <option value="Yes">Yes</option> + </param> + </upload_dataset> <param name="dbkey" type="genomebuild" label="Genome" /> </inputs> <help>

1 0

[hg] galaxy 2435: Update the way the testing framework decides w...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3190f7d6b572 changeset: 2435:3190f7d6b572 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jun 08 16:52:55 2009 -0400 description: Update the way the testing framework decides whether a refresh_on_change is required. 1 file(s) affected in this change: test/base/twilltestcase.py diffs (30 lines): diff -r 73d8b2acef0a -r 3190f7d6b572 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Jun 08 16:47:01 2009 -0400 +++ b/test/base/twilltestcase.py Mon Jun 08 16:52:55 2009 -0400 @@ -548,22 +548,11 @@ # Check for refresh_on_change attribute, submit a change if required if 'refresh_on_change' in control.attrs.keys(): changed = False - for elem in kwd[control.name]: - # For DataToolParameter, control.value is the index of the DataToolParameter select list, - # but elem is the filename. The following loop gets the filename of that index. - param_text = '' - for param in tc.show().split('<select'): - param = ('<select' + param.split('select>')[0] + 'select>').replace('selected', 'selected="yes"') - if param.find('on_chang') != -1 and param.find('name="%s"' % control.name) != -1: - tree = ElementTree.fromstring(param) - for option in tree.findall('option'): - if option.get('value') in control.value: - param_text = option.text.strip() - break - break - if elem not in control.value and param_text.find(elem) == -1 : + item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] #For DataToolParameter, control.value is the HDA id, but kwd contains the filename. This loop gets the filename/label for the selected values. + for value in kwd[ control.name ]: + if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: changed = True - break + break if changed: # Clear Control and set to proper value control.clear()

1 0

[hg] galaxy 2432: Functional test fixes for purging a user.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c0c50620b89d changeset: 2432:c0c50620b89d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 08 12:35:38 2009 -0400 description: Functional test fixes for purging a user. 2 file(s) affected in this change: test/functional/test_history_functions.py test/functional/test_security_and_libraries.py diffs (215 lines): diff -r 1a24a530a3ae -r c0c50620b89d test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Mon Jun 08 10:31:59 2009 -0400 +++ b/test/functional/test_history_functions.py Mon Jun 08 12:35:38 2009 -0400 @@ -114,11 +114,10 @@ self.login( email=regular_user1.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) + # Need to delete history3_copy1 + self.delete_history( id=str( history3_copy1.id ) ) self.logout() self.login( email=admin_user.email ) - # Need to delete history3_copy1 - history3_copy1.deleted = True - history3_copy1.flush() # Test sharing a history with an invalid user email = 'jack(a)jill.com' check_str = '%s is not a valid Galaxy user.' % email @@ -138,48 +137,55 @@ self.share_history( id, email, check_str ) # We need to keep track of all shared histories so they can later be deleted history3_copy_name = "%s from %s" % ( history3.name, admin_user.email ) - history3_copies = galaxy.model.History \ + history3_to_use_for_regular_user2 = galaxy.model.History \ .filter( and_( galaxy.model.History.table.c.name==history3_copy_name, + galaxy.model.History.table.c.user_id==regular_user2.id, galaxy.model.History.table.c.deleted==False ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .limit( 2 ) \ - .all() - history3_copy2 = history3_copies[0] - history3_copy3 = history3_copies[1] - history4_copy_name = "%s from %s" % ( history4.name, admin_user.email ) - history4_copyies = galaxy.model.History \ - .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + .first() + assert history3_to_use_for_regular_user2 is not None, "Problem retrieving history3_to_use_for_regular_user2 from database" + history3_to_use_for_regular_user3 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history3_copy_name, + galaxy.model.History.table.c.user_id==regular_user3.id, galaxy.model.History.table.c.deleted==False ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .limit( 2 ) \ - .all() - history4_copy1 = history4_copyies[0] - history4_copy2 = history4_copyies[1] + .first() + assert history3_to_use_for_regular_user3 is not None, "Problem retrieving history3_to_use_for_regular_user3 from database" + history4_copy_name = "%s from %s" % ( history4.name, admin_user.email ) + history4_to_use_for_regular_user2 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + galaxy.model.History.table.c.user_id==regular_user2.id, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert history4_to_use_for_regular_user2 is not None, "Problem retrieving history4_to_use_for_regular_user2 from database" + history4_to_use_for_regular_user3 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + galaxy.model.History.table.c.user_id==regular_user3.id, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert history4_to_use_for_regular_user3 is not None, "Problem retrieving history4_to_use_for_regular_user3 from database" self.logout() self.login( email=regular_user2.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) + # Need to delete the copied histories, so later test runs are valid + self.delete_history( id=str( history3_to_use_for_regular_user2.id ) ) + self.delete_history( id=str( history4_to_use_for_regular_user2.id ) ) self.logout() self.login( email=regular_user3.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) + # Need to delete the copied histories, so later test runs are valid + self.delete_history( id=str( history3_to_use_for_regular_user3.id ) ) + self.delete_history( id=str( history4_to_use_for_regular_user3.id ) ) self.logout() self.login( email=admin_user.email ) - # Need to delete the copied histories, so later test runs are valid - history3_copy2.deleted = True - history3_copy2.flush() - history3_copy3.deleted = True - history3_copy3.flush() - history4_copy1.deleted = True - history4_copy1.flush() - history4_copy1.deleted = True - history4_copy1.flush() - history4_copy2.deleted = True - history4_copy2.flush() def test_030_change_permissions_on_current_history( self ): """Testing changing permissions on the current history""" global history5 @@ -222,8 +228,7 @@ self.visit_url( "%s/history/list" % self.url ) self.check_page_for_string( history5_copy1.name ) # Need to delete history5_copy1 on the history list page for regular_user1 - history5_copy1.deleted = True - history5_copy1.flush() + self.delete_history( id=str( history5_copy1.id ) ) self.logout() self.login( email=admin_user.email ) def test_040_sharing_history_by_making_new_sharing_role( self ): @@ -278,8 +283,7 @@ # Make sure 2.bed is accessible since it is associated with a sharing role self.display_history_item( str( hda_2_bed.id ), check_str='chr1' ) # Need to delete history5_copy2 on the history list page for regular_user1 - history5_copy2.deleted = True - history5_copy2.flush() + self.delete_history( id=str( history5_copy2.id ) ) def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): """Testing sharing a restricted history with multiple users, making no permission changes""" self.logout() @@ -301,47 +305,44 @@ action_check_str=action_check_str ) # We need to keep track of all shared histories so they can later be deleted history5_copy_name = "%s from %s" % ( history5.name, admin_user.email ) - history5_copies = galaxy.model.History \ + history5_to_use_for_regular_user1 = galaxy.model.History \ .filter( and_( galaxy.model.History.table.c.name==history5_copy_name, + galaxy.model.History.table.c.user_id==regular_user1.id, galaxy.model.History.table.c.deleted==False ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .limit( 2 ) \ - .all() - history5_copy3 = history5_copies[0] - assert history5_copy3 is not None, "Problem retrieving history5_copy3 from database" - history5_copy4 = history5_copies[1] - assert history5_copy4 is not None, "Problem retrieving history5_copy4 from database" - # Make sure test1(a)bx.psu.edu received a copy of history5 with both datasets accessible - if history5_copy3.user_id == regular_user1.id: - history_to_use_for_regular_user_1 = history5_copy3 - history_to_use_for_regular_user_2 = history5_copy4 - elif history5_copy4.user_id == regular_user1.id: - history_to_use_for_regular_user_1 = history5_copy4 - history_to_use_for_regular_user_2 = history5_copy3 - else: - raise AssertionError, "Copies of history5 were not correctly associated with users" + .first() + assert history5_to_use_for_regular_user1 is not None, "Problem retrieving history5_to_use_for_regular_user1 from database" + history5_to_use_for_regular_user2 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history5_copy_name, + galaxy.model.History.table.c.user_id==regular_user2.id, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert history5_to_use_for_regular_user2 is not None, "Problem retrieving history5_to_use_for_regular_user2 from database" self.logout() self.login( email=regular_user1.email ) check_str = '%s from %s' % ( history5.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history_to_use_for_regular_user_1.id ), name=history_to_use_for_regular_user_1.name ) + self.switch_history( id=str( history5_to_use_for_regular_user1.id ), name=history5_to_use_for_regular_user1.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) + # Need to delete the copied histories, so later test runs are valid + self.delete_history( id=str( history5_to_use_for_regular_user1.id ) ) self.logout() # Make sure test2(a)bx.psu.edu received a copy of history5, with only 1.bed accessible self.login( email=regular_user2.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history_to_use_for_regular_user_2.id ), name=history_to_use_for_regular_user_2.name ) + self.switch_history( id=str( history5_to_use_for_regular_user2.id ), name=history5_to_use_for_regular_user2.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history hda_1_bed = galaxy.model.HistoryDatasetAssociation \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_to_use_for_regular_user1.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ .first() assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" hda_2_bed = galaxy.model.HistoryDatasetAssociation \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_to_use_for_regular_user1.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ .first() assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" @@ -355,10 +356,7 @@ pass self.check_history_for_string( 'You do not have permission to view this dataset' ) # Need to delete the copied histories, so later test runs are valid - history5_copy3.deleted = True - history5_copy3.flush() - history5_copy4.deleted = True - history5_copy4.flush() + self.delete_history( id=str( history5_to_use_for_regular_user2.id ) ) def test_050_sharing_private_history_by_choosing_to_not_share( self ): """Testing sharing a restricted history with multiple users by choosing not to share""" self.logout() diff -r 1a24a530a3ae -r c0c50620b89d test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Jun 08 10:31:59 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Mon Jun 08 12:35:38 2009 -0400 @@ -1668,16 +1668,8 @@ history.refresh() if not history.deleted: raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( regular_user3.email, hda.id ) ) - # Make sure HistoryDatasetAssociation deleted - for hda in history.datasets: - hda.refresh() - if not hda.deleted: - raise AssertionError( 'HistoryDatasetAssociation id %d was not deleted.' % hda.id ) - # Make sure Dataset deleted - d = galaxy.model.Dataset.filter( galaxy.model.Dataset.table.c.id==hda.dataset_id ).first() - d.refresh() - if not d.deleted: - raise AssertionError( 'Dataset id %d was not deleted.' % d.id ) + # NOTE: Not all hdas / datasets will be deleted at the time a history is deleted - the cleanup_datasets.py script + # is responsible for this. # Make sure UserGroupAssociations deleted if regular_user3.groups: raise AssertionError( 'User %s has active group id %d after their account was marked as purged.' % ( regular_user3.email, uga.id ) )

1 0

[hg] galaxy 2434: Allow UnvalidatedValues to be used when genera...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/73d8b2acef0a changeset: 2434:73d8b2acef0a user: James Taylor <james(a)jamestaylor.org> date: Mon Jun 08 16:47:01 2009 -0400 description: Allow UnvalidatedValues to be used when generating output labels (fixes issue #59) 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (38 lines): diff -r 73a8b43f1d97 -r 73d8b2acef0a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Jun 08 12:49:26 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Jun 08 16:47:01 2009 -0400 @@ -535,9 +535,10 @@ def from_html( self, value, trans=None, context={} ): if self.need_late_validation( trans, context ): if self.multiple: - #While it is generally allowed that a select value can be '', - #we do not allow this to be the case in a dynamically generated multiple select list being set in workflow building mode - #we instead treat '' as 'No option Selected' (None) + # While it is generally allowed that a select value can be '', + # we do not allow this to be the case in a dynamically + # generated multiple select list being set in workflow building + # mode we instead treat '' as 'No option Selected' (None) if value == '': value = None else: @@ -565,9 +566,9 @@ if isinstance( value, list ): if not(self.repeat): assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" - return self.separator.join( value ) + return self.separator.join( map( str, value ) ) else: - return value + return str(value) def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } @@ -1331,6 +1332,8 @@ """ def __init__( self, value ): self.value = value + def __str__( self ): + return str( self.value ) class RuntimeValue( object ): """

1 0

[hg] galaxy 2431: Temporarily eliminate access to templates unti...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1a24a530a3ae changeset: 2431:1a24a530a3ae user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 08 10:31:59 2009 -0400 description: Temporarily eliminate access to templates until new forms are finished, and more fixes for functional tests. 7 file(s) affected in this change: lib/galaxy/web/controllers/admin.py templates/admin/library/browse_library.mako templates/library/browse_library.mako test/base/twilltestcase.py test/functional/test_DNAse_flanked_genes.py test/functional/test_metadata_editing.py test/functional/test_security_and_libraries.py diffs (1339 lines): diff -r 373962edbe90 -r 1a24a530a3ae lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Jun 05 16:48:03 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Jun 08 10:31:59 2009 -0400 @@ -553,9 +553,7 @@ # with the user's private role in case we want the ability to unpurge the user # some time in the future. # Purging a deleted User deletes all of the following: - # - DefaultUserPermissions where user_id == User.id EXCEPT FOR THE PRIVATE ROLE # - History where user_id = User.id - # - DefaultHistoryPermissions where history_id == History.id EXCEPT FOR THE PRIVATE ROLE # - HistoryDatasetAssociation where history_id = History.id # - Dataset where HistoryDatasetAssociation.dataset_id = Dataset.id # - UserGroupAssociation where user_id == User.id @@ -568,19 +566,9 @@ msg = "User '%s' has not been deleted, so it cannot be purged." % user.email trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='error' ) ) private_role = trans.app.security_agent.get_private_user_role( user ) - # Delete DefaultUserPermissions EXCEPT FOR THE PRIVATE ROLE - for dup in user.default_permissions: - if dup.role_id != private_role.id: - dup.delete() - dup.flush() # Delete History for h in user.active_histories: h.refresh() - # Delete DefaultHistoryPermissions EXCEPT FOR THE PRIVATE ROLE - for dp in h.default_permissions: - if dp.role_id != private_role.id: - dp.delete() - dp.flush() for hda in h.active_datasets: # Delete HistoryDatasetAssociation d = trans.app.model.Dataset.get( hda.dataset_id ) diff -r 373962edbe90 -r 1a24a530a3ae templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Fri Jun 05 16:48:03 2009 -0400 +++ b/templates/admin/library/browse_library.mako Mon Jun 08 10:31:59 2009 -0400 @@ -112,13 +112,14 @@ <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> <a class="action-button" href="${h.url_for( controller='admin', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a> - %if folder.library_folder_info_template_associations: - <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, id=template.id, edit_template=True )}">Edit this folder's information template</a> - %elif not folder.library_folder_info_associations: - ## Only allow adding a new template to the folder if a previously inherited template has not already been used - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if folder.library_folder_info_template_associations: + ## <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, id=template.id, edit_template=True )}">Edit this folder's information template</a> + ##%elif not folder.library_folder_info_associations: + ## ## Only allow adding a new template to the folder if a previously inherited template has not already been used + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> + ##%endif <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Delete this folder and its contents</a> </div> @@ -199,21 +200,21 @@ library_item_ids = {} library_item_ids[ 'library' ] = library.id %> - - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this library's information</a> - %if library.library_info_template_associations: - <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> - %else: - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> - %endif - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> - <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this library and its contents</a> - %if show_deleted: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> - %else: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##<a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this library's information</a> + ##%if library.library_info_template_associations: + ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> + ##%else: + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> + ##%endif + <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this library and its contents</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> + %else: + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> + %endif %elif not library.purged: <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this library</a> %endif diff -r 373962edbe90 -r 1a24a530a3ae templates/library/browse_library.mako --- a/templates/library/browse_library.mako Fri Jun 05 16:48:03 2009 -0400 +++ b/templates/library/browse_library.mako Mon Jun 08 10:31:59 2009 -0400 @@ -150,17 +150,18 @@ %else: <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">View this folder's information</a> %endif - %if folder.library_folder_info_template_associations: - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): - <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this folder's information template</a> - %endif - %elif not folder.library_folder_info_associations: - ## Only allow adding a new template to the folder if a previously inherited template has not already been used - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> - %endif - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if folder.library_folder_info_template_associations: + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): + ## <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this folder's information template</a> + ## %endif + ##%elif not folder.library_folder_info_associations: + ## ## Only allow adding a new template to the folder if a previously inherited template has not already been used + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> + ## %endif + ##%endif %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ): <a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> %endif @@ -229,17 +230,17 @@ %else: <a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a> %endif - - %if library.library_info_template_associations: - <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> - %endif - %else: - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> - %endif - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if library.library_info_template_associations: + ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> + ## %endif + ##%else: + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> + ## %endif + ##%endif %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): <a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a> %endif diff -r 373962edbe90 -r 1a24a530a3ae test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/base/twilltestcase.py Mon Jun 08 10:31:59 2009 -0400 @@ -304,30 +304,49 @@ if check_str: self.check_page_for_string( check_str ) self.home() - def edit_metadata( self, hid=None, form_no=0, **kwd ): - """Edits the metadata associated with a history item.""" - # There are currently 4 forms on the edit page: - # 0. name="edit_attributes" - # 1. name="auto_detect" - # 2. name="convert_data" - # 3. name="change_datatype" - data_list = self.get_history() - self.assertTrue( data_list ) - if hid is None: # take last hid - elem = data_list[-1] - hid = int( elem.get('hid') ) - self.assertTrue( hid ) - self.visit_page( 'edit?hid=%d' % hid ) - if form_no == 0: - button = "save" #Edit Attributes form - elif form_no == 1: - button = "detect" #Auto-detect Metadata Attributes - elif form_no == 2: - button = "convert_data" #Convert to new format form - elif form_no == 3: - button = "change" #Change data type form - if kwd: - self.submit_form( form_no=form_no, button=button, **kwd) + def edit_hda_attribute_info( self, hda_id, new_name='', new_info='', new_dbkey='', new_startcol='' ): + """Edit history_dataset_association attribute information""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'Edit Attributes' ) + if new_name: + tc.fv( 'edit_attributes', 'name', new_name ) + if new_info: + tc.fv( 'edit_attributes', 'info', new_info ) + if new_dbkey: + tc.fv( 'edit_attributes', 'dbkey', new_dbkey ) + if new_startcol: + tc.fv( 'edit_attributes', 'startCol', new_startcol ) + tc.submit( 'save' ) + self.check_page_for_string( 'Attributes updated' ) + self.home() + def auto_detect_metadata( self, hda_id ): + """Auto-detect history_dataset_association metadata""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'This will inspect the dataset and attempt' ) + tc.fv( 'auto_detect', 'id', hda_id ) + tc.submit( 'detect' ) + self.check_page_for_string( 'Attributes updated' ) + self.home() + def convert_format( self, hda_id, target_type ): + """Auto-detect history_dataset_association metadata""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'This will inspect the dataset and attempt' ) + tc.fv( 'convert_data', 'target_type', target_type ) + tc.submit( 'convert_data' ) + self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' ) + self.home() + def change_datatype( self, hda_id, datatype ): + """Auto-detect history_dataset_association metadata""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'This will change the datatype of the existing dataset but' ) + tc.fv( 'change_datatype', 'datatype', datatype ) + tc.submit( 'change' ) + self.check_page_for_string( 'Edit Attributes' ) + self.home() def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" data_list = self.get_history() diff -r 373962edbe90 -r 1a24a530a3ae test/functional/test_DNAse_flanked_genes.py --- a/test/functional/test_DNAse_flanked_genes.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/functional/test_DNAse_flanked_genes.py Mon Jun 08 10:31:59 2009 -0400 @@ -1,16 +1,16 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase """ A sample analysis""" - - class AnalysisDNAseHSSFlankedGenes( TwillTestCase ): - def test_get_DNAseHSS_flanked_genes( self ): self.login() - self.new_history() - + global history1 + history1 = galaxy.model.History.query() \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ).first() track_params = dict( db="hg17", hgta_group="regulation", @@ -24,14 +24,21 @@ output_params = dict( fbQual="whole", ) - + # Test 1 self.run_ucsc_main( track_params, output_params ) self.wait() self.verify_dataset_correctness('DNAseHSS.dat') - - self.edit_metadata( name="DNAse HS" ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + # Due to twill not being able to handle the permissions forms, we'll eliminate + # DefaultHistoryPermissions prior to uploading a dataset so that the permission + # form will not be displayed on ted edit attributes page. + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.edit_hda_attribute_info( str( latest_hda.id ), new_name="DNAse HS" ) self.check_metadata_for_string( "DNAse HS" ) - track_params = dict( db="hg17", hgta_group="genes", @@ -45,35 +52,38 @@ output_params = dict( fbQual="whole", ) - + # Test 2 self.run_ucsc_main( track_params, output_params ) self.wait() self.verify_dataset_correctness('hg17chr22KnownGenes.dat') - - self.edit_metadata( name="Genes" ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Genes" ) self.check_metadata_for_string( "Genes" ) - - + # Test 3 self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" ) self.wait() self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' ) - - self.edit_metadata( name="Flanks" ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Flanks" ) self.check_metadata_for_string( "Flanks" ) - - + # Test 4 self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none" ) self.wait() - #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) #we cannot verify this dataset, because this tool spits out data in a non-deterministic order - - + # We cannot verify this dataset, because this tool spits out data in a non-deterministic order + #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) + # Test 5 self.run_tool( 'Filter1', input="4", cond="c17==1000" ) self.wait() self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' ) - - self.delete_history() self.logout() - - - diff -r 373962edbe90 -r 1a24a530a3ae test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/functional/test_metadata_editing.py Mon Jun 08 10:31:59 2009 -0400 @@ -1,27 +1,45 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase class TestMetadataEdit( TwillTestCase ): - def test_00_metadata_edit(self): + def test_00_metadata_edit( self ): """test_metadata_edit: Testing metadata editing""" - self.login() - self.upload_file('1.bed') - self.check_history_for_string('\? bed') - self.check_metadata_for_string('1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + self.new_history( name='Test Metadata Edit' ) + global history1 + history1 = galaxy.model.History.query() \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.upload_file( '1.bed' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + self.home() + # Due to twill not being able to handle the permissions forms, we'll eliminate + # DefaultHistoryPermissions prior to uploading a dataset so that the permission + # form will not be displayed on ted edit attributes page. + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.check_history_for_string( '1.bed' ) + self.check_metadata_for_string( '1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1 ) """test editing attributes""" - self.edit_metadata(hid=1, form_no=0, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6') - self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1) + self.edit_hda_attribute_info( hda_id=str( latest_hda.id ), + new_name='Testdata', + new_info="Uploaded my file", + new_dbkey='hg16', + new_startcol='6' ) + self.check_metadata_for_string( 'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1 ) """test Auto-detecting attributes""" - self.edit_metadata(hid=1, form_no=1) - self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1) + self.auto_detect_metadata( hda_id=str( latest_hda.id ) ) + self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1 ) """test converting formats""" - self.edit_metadata(hid=1, form_no=2, target_type='gff') - self.check_history_for_string('hg16 Testdata Convert BED to GFF') - self.check_metadata_for_string('"gff" selected="yes"', hid=1) + self.convert_format( hda_id=str( latest_hda.id ), target_type='gff' ) + self.check_metadata_for_string( '"gff" selected="yes"', hid=1 ) """test changing data type""" - self.edit_metadata(hid=1, form_no=3, datatype='gff3') - self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3') - self.delete_history_item( 1 ) - def test_9999_clean_up( self ): - self.delete_history() + self.change_datatype( hda_id=str( latest_hda.id ), datatype='gff3' ) + self.check_metadata_for_string( 'gff3', hid=1 ) + self.delete_history( id=str( history1.id ) ) self.logout() diff -r 373962edbe90 -r 1a24a530a3ae test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Mon Jun 08 10:31:59 2009 -0400 @@ -51,7 +51,7 @@ raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) # Make sure DefaultUserPermissions are correct if len( admin_user.default_permissions ) > 1: - raise AssertionError( '%d DefaultUserPermissions were created for %s when their account was created ( should have been 1 )' \ + raise AssertionError( '%d DefaultUserPermissions associated with user %s ( should be 1 )' \ % ( len( admin_user.default_permissions ), admin_user.email ) ) dup = galaxy.model.DefaultUserPermissions.filter( galaxy.model.DefaultUserPermissions.table.c.user_id==admin_user.id ).first() if not dup.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: @@ -72,6 +72,8 @@ self.logout() def test_010_login_as_regular_user1( self ): """Testing logging in as regular user test1(a)bx.psu.edu - tests private role creation, changing DefaultHistoryPermissions for new histories, and sharing histories with another user""" + # Some of the history related tests here are similar to some tests in the + # test_history_functions.py script, so we could potentially eliminate 1 or 2 of them. self.login( email='test1(a)bx.psu.edu' ) # test1(a)bx.psu.edu is not an admin user global regular_user1 regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() @@ -93,7 +95,7 @@ latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() # Make sure DatasetPermissions is correct - default is 'manage permissions' if len( latest_dataset.actions ) > 1: - raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been 1 )' \ + raise AssertionError( '%d DatasetPermissions were created for dataset id %d when it was created ( should have been 1 )' \ % ( len( latest_dataset.actions ), latest_dataset.id ) ) dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.dataset_id==latest_dataset.id ).first() if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: @@ -494,97 +496,100 @@ library_one.refresh() self.rename_library( str( library_one.id ), library_one.name, name=name, description=description ) library_one.refresh() - def test_075_library_template_features( self ): - """Testing adding a template to a library, along with template features on the admin side""" - actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] - actions.sort() - # Add a new information template to the library - template_name = 'Library Template 1' - ele_name_0 = 'Foo' - ele_name_1 = 'Doh' - self.add_library_info_template( library_one.id, library_one.name, name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_name_1=ele_name_1 ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - self.check_page_for_string( ele_name_1 ) - self.home() - # Get the template for later testing - global library_one_template - library_one_template = galaxy.model.LibraryItemInfoTemplate.query().order_by( desc( galaxy.model.LibraryItemInfoTemplate.table.c.id ) ).first() - assert library_one_template is not None, 'Problem retrieving LibraryItemInfoTemplate for library named "%s" from the database' % str( library_one.name ) - # Make sure the library permissions were inherited by the template - template_permissions = galaxy.model.LibraryItemInfoTemplatePermissions \ - .query() \ - .filter( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.library_item_info_template_id == library_one_template.id ) \ - .order_by( desc( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.id ) ) \ - .limit( 3 ) \ - .all() - template_permissions = [ litp_obj.action for litp_obj in template_permissions ] - template_permissions.sort() - assert actions == template_permissions, "Template permissions for template %s not correctly inherited from library %s" \ - % ( library_one_template.name, library_one.name ) - # Make sure that the library permissions were inherited by each of the template elements - for library_item_info in library_one_template.library_item_infos: - info_permissions = galaxy.model.LibraryItemInfoPermissions \ - .filter( galaxy.model.LibraryItemInfoPermissions.table.c.library_item_info_id == library_item_info.id ) \ + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + def test_075_library_template_features( self ): + Testing adding a template to a library, along with template features on the admin side + actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] + actions.sort() + # Add a new information template to the library + template_name = 'Library Template 1' + ele_name_0 = 'Foo' + ele_name_1 = 'Doh' + self.add_library_info_template( library_one.id, library_one.name, name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_name_1=ele_name_1 ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( ele_name_0 ) + self.check_page_for_string( ele_name_1 ) + self.home() + # Get the template for later testing + global library_one_template + library_one_template = galaxy.model.LibraryItemInfoTemplate.query().order_by( desc( galaxy.model.LibraryItemInfoTemplate.table.c.id ) ).first() + assert library_one_template is not None, 'Problem retrieving LibraryItemInfoTemplate for library named "%s" from the database' % str( library_one.name ) + # Make sure the library permissions were inherited by the template + template_permissions = galaxy.model.LibraryItemInfoTemplatePermissions \ + .query() \ + .filter( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.library_item_info_template_id == library_one_template.id ) \ + .order_by( desc( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.id ) ) \ + .limit( 3 ) \ .all() - info_permissions = [ liip_obj.action for liip_obj in info_permissions ] - info_permissions.sort() - assert actions == info_permissions, "Permissions for library_item_info id %s not correctly inherited from library %s" \ - % ( library_item_info.id, library_one.name ) - element_ids = [] - if library_one.library_info_associations: - # We have a set of LibraryItemInfoElements - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - if not last_library_item_info_element: - element_ids.append( 0 ) - element_ids.append( 1 ) + template_permissions = [ litp_obj.action for litp_obj in template_permissions ] + template_permissions.sort() + assert actions == template_permissions, "Template permissions for template %s not correctly inherited from library %s" \ + % ( library_one_template.name, library_one.name ) + # Make sure that the library permissions were inherited by each of the template elements + for library_item_info in library_one_template.library_item_infos: + info_permissions = galaxy.model.LibraryItemInfoPermissions \ + .filter( galaxy.model.LibraryItemInfoPermissions.table.c.library_item_info_id == library_item_info.id ) \ + .all() + info_permissions = [ liip_obj.action for liip_obj in info_permissions ] + info_permissions.sort() + assert actions == info_permissions, "Permissions for library_item_info id %s not correctly inherited from library %s" \ + % ( library_item_info.id, library_one.name ) + element_ids = [] + if library_one.library_info_associations: + # We have a set of LibraryItemInfoElements + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + if not last_library_item_info_element: + element_ids.append( 0 ) + element_ids.append( 1 ) + else: + element_ids.append( last_library_item_info_element.id + 1 ) + element_ids.append( last_library_item_info_element.id + 2 ) else: - element_ids.append( last_library_item_info_element.id + 1 ) - element_ids.append( last_library_item_info_element.id + 2 ) - else: - # We only have a set of LibraryItemInfoTemplateElements - for ele in library_one_template.elements: - element_ids.append( ele.id ) - element_ids.sort() - # Add information to the library using the template - ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[0] ) ) - ele_1_contents = 'hello' - ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[1] ) ) - ele_2_contents = 'world' - self.edit_library_info( str( library_one.id ), library_one.name, - ele_1_field_name, ele_1_contents, - ele_2_field_name, ele_2_contents ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( ele_1_contents ) - self.check_page_for_string( ele_2_contents ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( ele_1_contents ) - self.check_page_for_string( ele_2_contents ) - # Edit the template - new_name = 'Library Template 1 renamed' - new_ele_name_1_field = "element_name_%s" % element_ids[0] - new_ele_name_1 = 'wind' - new_ele_desc_1_field = "element_description_%s" % element_ids[0] - ele_desc_1 = 'This is the wind component' - new_ele_name_2_field = "element_name_%s" % element_ids[1] - new_ele_name_2 = 'bag' - new_ele_desc_2_field = "element_description_%s" % element_ids[1] - ele_desc_2 = 'This is the bag component' - self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, - new_ele_name_1_field, new_ele_name_1, new_ele_desc_1_field, ele_desc_1, - new_ele_name_2_field, new_ele_name_2, new_ele_desc_2_field, ele_desc_2 ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( new_ele_name_1 ) - self.check_page_for_string( ele_desc_1 ) - self.check_page_for_string( ele_1_contents ) - self.check_page_for_string( new_ele_name_2 ) - self.check_page_for_string( ele_desc_2 ) - self.check_page_for_string( ele_2_contents ) + # We only have a set of LibraryItemInfoTemplateElements + for ele in library_one_template.elements: + element_ids.append( ele.id ) + element_ids.sort() + # Add information to the library using the template + ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[0] ) ) + ele_1_contents = 'hello' + ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[1] ) ) + ele_2_contents = 'world' + self.edit_library_info( str( library_one.id ), library_one.name, + ele_1_field_name, ele_1_contents, + ele_2_field_name, ele_2_contents ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( ele_1_contents ) + self.check_page_for_string( ele_2_contents ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( ele_1_contents ) + self.check_page_for_string( ele_2_contents ) + # Edit the template + new_name = 'Library Template 1 renamed' + new_ele_name_1_field = "element_name_%s" % element_ids[0] + new_ele_name_1 = 'wind' + new_ele_desc_1_field = "element_description_%s" % element_ids[0] + ele_desc_1 = 'This is the wind component' + new_ele_name_2_field = "element_name_%s" % element_ids[1] + new_ele_name_2 = 'bag' + new_ele_desc_2_field = "element_description_%s" % element_ids[1] + ele_desc_2 = 'This is the bag component' + self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, + new_ele_name_1_field, new_ele_name_1, new_ele_desc_1_field, ele_desc_1, + new_ele_name_2_field, new_ele_name_2, new_ele_desc_2_field, ele_desc_2 ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( new_ele_name_1 ) + self.check_page_for_string( ele_desc_1 ) + self.check_page_for_string( ele_1_contents ) + self.check_page_for_string( new_ele_name_2 ) + self.check_page_for_string( ele_desc_2 ) + self.check_page_for_string( ele_2_contents ) + """ def test_080_add_public_dataset_to_root_folder( self ): """Testing adding a public dataset to the root folder""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] @@ -623,7 +628,9 @@ if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: raise AssertionError( 'The DatasetPermissions.action for dataset id %d is "%s", but it should be "manage permissions"' \ % ( ldda_one.dataset.id, dp.action ) ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the library template was inherited by the ldda + """ self.home() self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) @@ -631,6 +638,7 @@ self.check_page_for_string( 'This is the wind component' ) self.check_page_for_string( 'bag' ) self.check_page_for_string( 'This is the bag component' ) + """ # Make sure other users can access the dataset from the Libraries view self.logout() self.login( email=regular_user2.email ) @@ -640,20 +648,23 @@ self.logout() self.login( email=admin_user.email ) self.home() - def test_085_editing_dataset_information( self ): - """Testing editing dataset template element information""" - # Need the current library_item_info_element.id - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - global ldda_one_ele_2_field_name - ldda_one_ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - ele_2_contents = 'pipe' - global ldda_one_ele_1_field_name - ldda_one_ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) - ele_1_contents = 'blown' - self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), - ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents ) - self.home() + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + def test_085_editing_dataset_information( self ): + Testing editing dataset template element information + # Need the current library_item_info_element.id + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + global ldda_one_ele_2_field_name + ldda_one_ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) + ele_2_contents = 'pipe' + global ldda_one_ele_1_field_name + ldda_one_ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) + ele_1_contents = 'blown' + self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), + ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents ) + self.home() + """ def test_090_add_new_folder_to_root_folder( self ): """Testing adding a folder to a library root folder""" root_folder = library_one.root_folder @@ -669,35 +680,41 @@ self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the library template is inherited + """ self.home() self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) self.check_page_for_string( 'wind' ) self.check_page_for_string( 'This is the wind component' ) self.check_page_for_string( 'bag' ) self.check_page_for_string( 'This is the bag component' ) + """ self.home() - def test_095_add_folder_template( self ): - """Testing adding a new folder template to a folder""" - # Add a new information template to the folder - template_name = 'Folder Template 1' - ele_name_0 = 'Fu' - ele_help_0 = 'This is the Fu component'.replace( ' ', '+' ) - ele_name_1 = 'Bar' - ele_help_1 = 'This is the Bar component'.replace( ' ', '+' ) - self.home() - self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_one.id ), folder_one.name, - name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, - ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) - self.home() - self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - check_str = ele_help_0.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.check_page_for_string( ele_name_1 ) - check_str = ele_help_1.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.home() + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + def test_095_add_folder_template( self ): + Testing adding a new folder template to a folder + # Add a new information template to the folder + template_name = 'Folder Template 1' + ele_name_0 = 'Fu' + ele_help_0 = 'This is the Fu component'.replace( ' ', '+' ) + ele_name_1 = 'Bar' + ele_help_1 = 'This is the Bar component'.replace( ' ', '+' ) + self.home() + self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_one.id ), folder_one.name, + name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, + ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) + self.home() + self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) + self.check_page_for_string( ele_name_0 ) + check_str = ele_help_0.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + self.check_page_for_string( ele_name_1 ) + check_str = ele_help_1.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + self.home() + """ def test_100_add_subfolder_to_folder( self ): """Testing adding a folder to a library folder""" name = "Folder One's Subfolder" @@ -712,8 +729,10 @@ self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the parent folder's template is inherited self.home() + """ self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) @@ -726,81 +745,84 @@ except: pass self.home() - def test_105_add_template_element( self ): - """Testing adding a new element to an existing library template""" - library_one_template.refresh() - element_ids = [] - for ele in library_one_template.elements: - element_ids.append( ele.id ) - element_ids.sort() - - name = 'Library Template 1 renamed' - ele_field_name_1 = "element_name_%s" % element_ids[0] - ele_name_1 = 'wind' - ele_field_desc_1 = "element_description_%s" % element_ids[0] - ele_desc_1 = 'This is the wind component' - ele_field_name_2 = "element_name_%s" % element_ids[1] - ele_name_2 = 'bag' - ele_field_desc_2 = "element_description_%s" % element_ids[1] - ele_desc_2 = 'This is the bag component' - new_ele_name = 'Fubar' - new_ele_desc = 'This is the Fubar component' - - self.add_library_info_template_element( str( library_one.id ), - str( library_one_template.id ), - library_one_template.name, - ele_field_name_1, - ele_name_1, - ele_field_desc_1, - ele_desc_1, - ele_field_name_2, - ele_name_2, - ele_field_desc_2, - ele_desc_2, - new_ele_name=new_ele_name, - new_ele_desc=new_ele_desc ) - # Make sure the new template element shows up on the existing library info page - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( library_one.name ) - self.check_page_for_string( library_one.description ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'hello' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'world' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - # Make sure the new template element does not show up on existing info pages for folder_one since it has its own template - self.home() - self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - try: + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_105_add_template_element( self ): + Testing adding a new element to an existing library template + library_one_template.refresh() + element_ids = [] + for ele in library_one_template.elements: + element_ids.append( ele.id ) + element_ids.sort() + + name = 'Library Template 1 renamed' + ele_field_name_1 = "element_name_%s" % element_ids[0] + ele_name_1 = 'wind' + ele_field_desc_1 = "element_description_%s" % element_ids[0] + ele_desc_1 = 'This is the wind component' + ele_field_name_2 = "element_name_%s" % element_ids[1] + ele_name_2 = 'bag' + ele_field_desc_2 = "element_description_%s" % element_ids[1] + ele_desc_2 = 'This is the bag component' + new_ele_name = 'Fubar' + new_ele_desc = 'This is the Fubar component' + self.add_library_info_template_element( str( library_one.id ), + str( library_one_template.id ), + library_one_template.name, + ele_field_name_1, + ele_name_1, + ele_field_desc_1, + ele_desc_1, + ele_field_name_2, + ele_name_2, + ele_field_desc_2, + ele_desc_2, + new_ele_name=new_ele_name, + new_ele_desc=new_ele_desc ) + # Make sure the new template element shows up on the existing library info page + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( library_one.name ) + self.check_page_for_string( library_one.description ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'hello' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'world' ) + self.check_page_for_string( 'This is the bag component' ) self.check_page_for_string( 'Fubar' ) - raise AssertionError( 'Changed library template inherited by folder "%s" when folder had an associated template of its own' ) - except: - pass - # Make sure the new template element shows up on existing info pages for ldda_one since it is contained in the root folder - self.home() - self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_one.id ) ) ) - # Visiting the above page will have resulted in the creation of a new LibraryItemInfoElement, so we'll retrieve it - # for later use - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - global ldda_one_ele_3_field_name - ldda_one_ele_3_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - self.home() + self.check_page_for_string( 'This is the Fubar component' ) + # Make sure the new template element does not show up on existing info pages for folder_one since it has its own template + self.home() + self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) + self.check_page_for_string( 'Fu' ) + self.check_page_for_string( 'This is the Fu component' ) + self.check_page_for_string( 'Bar' ) + self.check_page_for_string( 'This is the Bar component' ) + try: + self.check_page_for_string( 'Fubar' ) + raise AssertionError( 'Changed library template inherited by folder "%s" when folder had an associated template of its own' ) + except: + pass + # Make sure the new template element shows up on existing info pages for ldda_one since it is contained in the root folder + self.home() + self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_one.id ) ) ) + # Visiting the above page will have resulted in the creation of a new LibraryItemInfoElement, so we'll retrieve it + # for later use + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + global ldda_one_ele_3_field_name + ldda_one_ele_3_field_name = "info_element_%s" % str( last_library_item_info_element.id ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'This is the bag component' ) + self.check_page_for_string( 'Fubar' ) + self.check_page_for_string( 'This is the Fubar component' ) + self.home() + """ def test_110_add_2nd_new_folder_to_root_folder( self ): """Testing adding a 2nd folder to a library root folder""" root_folder = library_one.root_folder @@ -816,7 +838,9 @@ self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the changed library template is inherited to the new folder + """ self.home() self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) self.check_page_for_string( 'wind' ) @@ -825,6 +849,7 @@ self.check_page_for_string( 'This is the bag component' ) self.check_page_for_string( 'Fubar' ) self.check_page_for_string( 'This is the Fubar component' ) + """ self.home() def test_115_add_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a public dataset to the root folder's 2nd sub-folder""" @@ -848,56 +873,59 @@ self.check_page_for_string( "2.bed" ) self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) - def test_120_add_template_to_root_folders_2nd_subfolder( self ): - """Testing adding a template to the root folder's 2nd sub-folder""" - # Before adding the folder template, the inherited library template should be displayed - self.home() - self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - self.home() - # Add a new folde template - template_name = 'Folder 2 Template' - ele_name_0 = 'kill' - ele_help_0 = 'This is the kill component'.replace( ' ', '+' ) - ele_name_1 = 'bill' - ele_help_1 = 'This is the bill component'.replace( ' ', '+' ) - self.home() - self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_two.id ), folder_two.name, - name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, - ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) - # Make sure the new template id displayed on the folder information page - self.home() - self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - check_str = ele_help_0.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.check_page_for_string( ele_name_1 ) - check_str = ele_help_1.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - # The library dataset ldda_two had previously inherited the library template prior to the new folder template - # being introduced, so the library template should still be displayed on the ldda information page - self.home() - self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - # Make sure the new folder template is not displayed - try: - self.check_page_for_string( 'kill' ) - raise AssertionError( 'New folder template elements incorrectly included in information page for ldda "%s"' % ldda_two.name ) - except: - pass - self.home() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_120_add_template_to_root_folders_2nd_subfolder( self ): + Testing adding a template to the root folder's 2nd sub-folder + # Before adding the folder template, the inherited library template should be displayed + self.home() + self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'This is the bag component' ) + self.check_page_for_string( 'Fubar' ) + self.check_page_for_string( 'This is the Fubar component' ) + self.home() + # Add a new folde template + template_name = 'Folder 2 Template' + ele_name_0 = 'kill' + ele_help_0 = 'This is the kill component'.replace( ' ', '+' ) + ele_name_1 = 'bill' + ele_help_1 = 'This is the bill component'.replace( ' ', '+' ) + self.home() + self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_two.id ), folder_two.name, + name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, + ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) + # Make sure the new template id displayed on the folder information page + self.home() + self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) + self.check_page_for_string( ele_name_0 ) + check_str = ele_help_0.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + self.check_page_for_string( ele_name_1 ) + check_str = ele_help_1.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + # The library dataset ldda_two had previously inherited the library template prior to the new folder template + # being introduced, so the library template should still be displayed on the ldda information page + self.home() + self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'This is the bag component' ) + self.check_page_for_string( 'Fubar' ) + self.check_page_for_string( 'This is the Fubar component' ) + # Make sure the new folder template is not displayed + try: + self.check_page_for_string( 'kill' ) + raise AssertionError( 'New folder template elements incorrectly included in information page for ldda "%s"' % ldda_two.name ) + except: + pass + self.home() + """ def test_125_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a 2nd public dataset to the root folder's 2nd sub-folder""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] @@ -920,22 +948,25 @@ self.check_page_for_string( "3.bed" ) self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) - def test_130_editing_dataset_information_with_new_folder_template( self ): - """Testing editing dataset template element information with new inherited folder template""" - # Need the current library_item_info_element.id - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - # Make sure the changed inherited template is included in the ldda information - ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - ele_2_contents = 'II' - ele_2_help = 'This is the bill component' - ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) - ele_1_contents = 'Volume' - ele_1_help = 'This is the kill component' - self.edit_ldda_template_element_info( str( library_one.id ), str( folder_two.id ), str( ldda_three.id ), - ldda_three.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, - ele_1_help=ele_1_help, ele_2_help=ele_2_help ) - self.home() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_130_editing_dataset_information_with_new_folder_template( self ): + Testing editing dataset template element information with new inherited folder template + # Need the current library_item_info_element.id + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + # Make sure the changed inherited template is included in the ldda information + ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) + ele_2_contents = 'II' + ele_2_help = 'This is the bill component' + ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) + ele_1_contents = 'Volume' + ele_1_help = 'This is the kill component' + self.edit_ldda_template_element_info( str( library_one.id ), str( folder_two.id ), str( ldda_three.id ), + ldda_three.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, + ele_1_help=ele_1_help, ele_2_help=ele_2_help ) + self.home() + """ def test_135_add_dataset_with_private_role_restriction_to_folder( self ): """Testing adding a dataset with a private role restriction to a folder""" # Add a dataset restricted by the following: @@ -954,6 +985,8 @@ message ='This is a test of the fourth dataset uploaded' ele_name_0 = 'Fu' ele_name_1 = 'Bar' + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.add_library_dataset( '4.bed', str( library_one.id ), str( folder_one.id ), @@ -965,6 +998,16 @@ root=False, check_template_str1=ele_name_0, check_template_str2=ele_name_1 ) + """ + self.add_library_dataset( '4.bed', + str( library_one.id ), + str( folder_one.id ), + folder_one.name, + file_format='bed', + dbkey='hg18', + roles=[ str( regular_user1_private_role.id ) ], + message=message.replace( ' ', '+' ), + root=False ) global ldda_four ldda_four = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1047,27 +1090,30 @@ self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ldda_four.name ) self.home() - def test_150_editing_restricted_datasets_information( self ): - """Testing editing a restricted library dataset's template element information""" - ele_1_contents = '' - ele_2_contents = '' - ele_3_contents = 'Adding Fubar text' - self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), - ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents, - ele_1_help='This is the wind component'.replace( ' ', '+' ), - ele_2_help='This is the bag component'.replace( ' ', '+' ), - ele_3_field_name=ldda_one_ele_3_field_name, ele_3_contents=ele_3_contents.replace( ' ', '+' ) ) - # Check the updated information from the libraries view - self.home() - self.visit_url( '%s/library/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s' \ - % ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) - self.check_page_for_string( ele_3_contents ) - try: - self.check_page_for_string( 'blown' ) - raise AssertionError( 'Element contents were not correctly eliminated when the information was edited for ldda %s' % ldda_one.name) - except: - pass - self.home() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_150_editing_restricted_datasets_information( self ): + Testing editing a restricted library dataset's template element information + ele_1_contents = '' + ele_2_contents = '' + ele_3_contents = 'Adding Fubar text' + self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), + ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents, + ele_1_help='This is the wind component'.replace( ' ', '+' ), + ele_2_help='This is the bag component'.replace( ' ', '+' ), + ele_3_field_name=ldda_one_ele_3_field_name, ele_3_contents=ele_3_contents.replace( ' ', '+' ) ) + # Check the updated information from the libraries view + self.home() + self.visit_url( '%s/library/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s' \ + % ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) + self.check_page_for_string( ele_3_contents ) + try: + self.check_page_for_string( 'blown' ) + raise AssertionError( 'Element contents were not correctly eliminated when the information was edited for ldda %s' % ldda_one.name) + except: + pass + self.home() + """ def test_155_add_dataset_with_role_associated_with_group_and_users( self ): """Testing adding a dataset with a role that is associated with a group and users""" self.login( email='test(a)bx.psu.edu' ) @@ -1077,6 +1123,8 @@ message = 'Testing adding a dataset with a role that is associated with a group and users' ele_name_0 = 'Fu' ele_name_1 = 'Bar' + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.add_library_dataset( '5.bed', str( library_one.id ), str( folder_one.id ), @@ -1088,6 +1136,16 @@ root=False, check_template_str1=ele_name_0, check_template_str2=ele_name_1 ) + """ + self.add_library_dataset( '5.bed', + str( library_one.id ), + str( folder_one.id ), + folder_one.name, + file_format='bed', + dbkey='hg17', + roles=[ str( role_two.id ) ], + message=message.replace( ' ', '+' ), + root=False ) global ldda_five ldda_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1194,13 +1252,16 @@ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() assert ldda_six is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six from the database' # Make sure the correct template was inherited + ## TODO: temporarily eliminating templates until we have the new forms features done self.home() + """ self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) ) self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) self.check_page_for_string( 'Bar' ) self.check_page_for_string( 'This is the Bar component' ) + """ def test_170_editing_dataset_attribute_info( self ): """Testing editing a datasets attribute information""" new_ldda_name = '6.bed ( version 1 )' @@ -1213,6 +1274,8 @@ def test_175_uploading_new_dataset_version( self ): """Testing uploading a new version of a dataset""" message = 'Testing uploading a new version of a dataset' + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.upload_new_dataset_version( '6.bed', str( library_one.id ), str( subfolder_one.id ), @@ -1224,6 +1287,16 @@ message=message.replace( ' ', '+' ), check_template_str1='Fu', check_template_str2='Bar' ) + """ + self.upload_new_dataset_version( '6.bed', + str( library_one.id ), + str( subfolder_one.id ), + str( subfolder_one.name ), + str( ldda_six.library_dataset.id ), + ldda_six.name, + file_format='auto', + dbkey='hg18', + message=message.replace( ' ', '+' ) ) global ldda_six_version_two ldda_six_version_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1233,6 +1306,8 @@ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) ) self.check_page_for_string( 'This is the latest version of this library dataset' ) # Make sure the correct template was inherited + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) self.check_page_for_string( 'Bar' ) @@ -1240,6 +1315,7 @@ check_str = 'Expired versions of %s' % ldda_six_version_two.name self.check_page_for_string( check_str ) self.check_page_for_string( ldda_six.name ) + """ self.home() # Make sure th permissions are the same ldda_six.refresh() @@ -1262,6 +1338,8 @@ """Testing uploading new versions of a dataset using a directory of files""" message = 'Testing uploading new versions of a dataset using a directory of files' ldda_six_version_two.refresh() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.upload_new_dataset_versions( str( library_one.id ), str( subfolder_one.id ), str( subfolder_one.name ), @@ -1272,6 +1350,15 @@ message=message.replace( ' ', '+' ), check_template_str1='Fu', check_template_str2='Bar' ) + """ + self.upload_new_dataset_versions( str( library_one.id ), + str( subfolder_one.id ), + str( subfolder_one.name ), + str( ldda_six_version_two.library_dataset.id ), + ldda_six_version_two.name, + file_format='auto', + dbkey='hg18', + message=message.replace( ' ', '+' ) ) global ldda_six_version_five ldda_six_version_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1281,10 +1368,13 @@ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) ) self.check_page_for_string( 'This is the latest version of this library dataset' ) # Make sure the correct template was inherited + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) self.check_page_for_string( 'Bar' ) self.check_page_for_string( 'This is the Bar component' ) + """ check_str = 'Expired versions of %s' % ldda_six_version_five.name self.check_page_for_string( check_str ) self.check_page_for_string( ldda_six.name ) @@ -1309,7 +1399,9 @@ def test_185_upload_datasets_from_library_dir( self ): """Testing uploading 3 datasets from a library directory to a root folder""" message = 'This is a test for uploading a directory of files' - roles_tuple = [ ( str( role_one.id ), role_one.name ) ] + roles_tuple = [ ( str( role_one.id ), role_one.name ) ] + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.add_datasets_from_library_dir( str( library_one.id ), str( library_one.root_folder.id ), library_one.root_folder.name, @@ -1319,6 +1411,13 @@ check_template_str1='wind', check_template_str2='bag', check_template_str3='Fubar' ) + """ + self.add_datasets_from_library_dir( str( library_one.id ), + str( library_one.root_folder.id ), + library_one.root_folder.name, + roles_tuple=roles_tuple, + message=message.replace( '+', ' ' ), + root=True ) self.home() self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) ) self.check_page_for_string( admin_user.email ) @@ -1552,6 +1651,7 @@ def test_245_purge_user( self ): """Testing purging a user account""" self.mark_user_deleted( user_id=regular_user3.id, email=regular_user3.email ) + regular_user3.refresh() self.purge_user( str( regular_user3.id ), regular_user3.email ) regular_user3.refresh() if not regular_user3.purged: @@ -1565,15 +1665,9 @@ raise AssertionError( 'DefaultUserPermissions for user %s are not related with the private role.' % regular_user3.email ) # Make sure History deleted for history in regular_user3.histories: + history.refresh() if not history.deleted: raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( regular_user3.email, hda.id ) ) - # Make sure DefaultHistoryPermissions deleted EXCEPT FOR THE PRIVATE ROLE - if len( history.default_permissions ) != 1: - raise AssertionError( 'DefaultHistoryPermissions for history id %d were not deleted.' % history.id ) - for dhp in history.default_permissions: - role = galaxy.model.Role.get( dhp.role_id ) - if role.type != 'private': - raise AssertionError( 'DefaultHistoryPermissions for history id %d are not related with the private role.' % history.id ) # Make sure HistoryDatasetAssociation deleted for hda in history.datasets: hda.refresh()

1 0

[hg] galaxy 2427: Add EuPathDb data source tool config.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/73847f425801 changeset: 2427:73847f425801 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 01 10:27:04 2009 -0400 description: Add EuPathDb data source tool config. 1 file(s) affected in this change: tools/data_source/eupathdb.xml diffs (36 lines): diff -r e50551db6e60 -r 73847f425801 tools/data_source/eupathdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/eupathdb.xml Mon Jun 01 10:27:04 2009 -0400 @@ -0,0 +1,32 @@ + +<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post"> + <description>server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> + <display>go to EuPathDB server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="dbkey" missing="?" /> + <param_from_source name="wdk_history_id" missing="" /> + <param_from_source name="wdkReportFormat" missing="tabular" /> + <param_from_source name="selectedFields" missing="" /> + <param_from_source name="includeHeader" missing="yes" /> + <param_from_source name="downloadType" missing="plain" /> + </add_to_url> + </request_param> + <request_param galaxy_name="format" remote_name="wdkReportFormat" missing="tabular" /> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

1 0

[hg] galaxy 2430: Functional test fixes.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/373962edbe90 changeset: 2430:373962edbe90 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jun 05 16:48:03 2009 -0400 description: Functional test fixes. 2 file(s) affected in this change: test/functional/test_history_functions.py test/functional/test_security_and_libraries.py diffs (173 lines): diff -r 8ac9be4bd716 -r 373962edbe90 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Fri Jun 05 11:33:19 2009 -0400 +++ b/test/functional/test_history_functions.py Fri Jun 05 16:48:03 2009 -0400 @@ -24,9 +24,9 @@ global regular_user3 regular_user3 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ).first() assert regular_user3 is not None, 'Problem retrieving user with email "test3(a)bx.psu.edu" from the database' - self.logout() def test_005_deleting_histories( self ): """Testing deleting histories""" + self.logout() self.login( email='test(a)bx.psu.edu' ) global admin_user admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() @@ -104,20 +104,18 @@ check_str = "You can't send histories to yourself." self.share_history( str( history3.id ), 'test(a)bx.psu.edu', check_str ) # Share a history with 1 valid user - name = history3.name - email = 'test1(a)bx.psu.edu' - check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) - self.share_history( str( history3.id ), email, check_str ) + check_str = 'Histories (%s) have been shared with: %s' % ( history3.name, regular_user1.email ) + self.share_history( str( history3.id ), regular_user1.email, check_str ) # We need to keep track of all shared histories so they can later be deleted global history3_copy1 history3_copy1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() assert history3_copy1 is not None, "Problem retrieving history3_copy1 from database" self.logout() - self.login( email='test1(a)bx.psu.edu' ) - check_str = '%s from test(a)bx.psu.edu' % history3.name + self.login( email=regular_user1.email ) + check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) self.logout() - self.login( email='test(a)bx.psu.edu' ) + self.login( email=admin_user.email ) # Need to delete history3_copy1 history3_copy1.deleted = True history3_copy1.flush() @@ -135,7 +133,7 @@ self.upload_file( '2.bed', dbkey='hg18' ) id = '%s,%s' % ( str( history3.id ), str( history4.id ) ) name = '%s,%s' % ( history3.name, history4.name ) - email = 'test2@bx.psu.edu,test3@bx.psu.edu' + email = '%s,%s' % ( regular_user2.email, regular_user3.email ) check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) self.share_history( id, email, check_str ) # We need to keep track of all shared histories so they can later be deleted @@ -158,19 +156,19 @@ history4_copy1 = history4_copyies[0] history4_copy2 = history4_copyies[1] self.logout() - self.login( email='test2(a)bx.psu.edu' ) + self.login( email=regular_user2.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) self.logout() - self.login( email='test3(a)bx.psu.edu' ) + self.login( email=regular_user3.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) self.logout() - self.login( email='test(a)bx.psu.edu' ) + self.login( email=admin_user.email ) # Need to delete the copied histories, so later test runs are valid history3_copy2.deleted = True history3_copy2.flush() @@ -213,6 +211,7 @@ raise AssertionError, "The 'access' permission is not set for history5_dataset1.actions" def test_035_sharing_history_by_making_datasets_public( self ): """Testing sharing a restricted history by making the datasets public""" + # We're still logged in as admin_user.email check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) self.share_history( str( history5.id ), regular_user1.email, check_str, action='public', action_check_str=action_check_str ) @@ -248,7 +247,13 @@ global sharing_role role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user1.email ) sharing_role = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==role_name ).first() - assert sharing_role is not None, "Problem retrieving sharing_role from the database" + if not sharing_role: + # May have created a sharing role in a previous functional test suite from the opposite direction. + role_name = 'Sharing role for: %s, %s' % ( regular_user1.email, admin_user.email ) + sharing_role = galaxy.model.Role.filter( and_( galaxy.model.Role.table.c.type==role_type, + galaxy.model.Role.table.c.name==role_name ) ).first() + if not sharing_role: + raise AssertionError( "Privately sharing a dataset did not properly create a sharing role" ) self.logout() self.login( email=regular_user1.email ) self.visit_url( "%s/history/list" % self.url ) @@ -275,10 +280,10 @@ # Need to delete history5_copy2 on the history list page for regular_user1 history5_copy2.deleted = True history5_copy2.flush() + def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): + """Testing sharing a restricted history with multiple users, making no permission changes""" self.logout() self.login( email=admin_user.email ) - def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): - """Testing sharing a restricted history with multiple users, making no permission changes""" # History5 can be shared with any user, since it contains a public dataset. However, only # regular_user1 should be able to access history5's 2.bed dataset since it is associated with a # sharing role, and regular_user2 should be able to access history5's 1.bed, but not 2.bed even @@ -307,17 +312,26 @@ history5_copy4 = history5_copies[1] assert history5_copy4 is not None, "Problem retrieving history5_copy4 from database" # Make sure test1(a)bx.psu.edu received a copy of history5 with both datasets accessible + if history5_copy3.user_id == regular_user1.id: + history_to_use_for_regular_user_1 = history5_copy3 + history_to_use_for_regular_user_2 = history5_copy4 + elif history5_copy4.user_id == regular_user1.id: + history_to_use_for_regular_user_1 = history5_copy4 + history_to_use_for_regular_user_2 = history5_copy3 + else: + raise AssertionError, "Copies of history5 were not correctly associated with users" + self.logout() self.login( email=regular_user1.email ) check_str = '%s from %s' % ( history5.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history5_copy3.id ), name=history5_copy3.name ) + self.switch_history( id=str( history_to_use_for_regular_user_1.id ), name=history_to_use_for_regular_user_1.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) self.logout() # Make sure test2(a)bx.psu.edu received a copy of history5, with only 1.bed accessible self.login( email=regular_user2.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history5_copy4.id ), name=history5_copy4.name ) + self.switch_history( id=str( history_to_use_for_regular_user_2.id ), name=history_to_use_for_regular_user_2.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history @@ -340,18 +354,15 @@ except: pass self.check_history_for_string( 'You do not have permission to view this dataset' ) - self.logout() - self.login( email='test(a)bx.psu.edu' ) # Need to delete the copied histories, so later test runs are valid history5_copy3.deleted = True history5_copy3.flush() history5_copy4.deleted = True history5_copy4.flush() - - - def test_050_sharing_private_history_by_choosing_to_not_share( self ): """Testing sharing a restricted history with multiple users by choosing not to share""" + self.logout() + self.login( email=admin_user.email ) self.switch_history( id=str( history5.id ), name=history5.name ) email = '%s,%s' % ( regular_user1.email, regular_user2.email ) check_str = 'The following datasets can be shared with %s with no changes' % email diff -r 8ac9be4bd716 -r 373962edbe90 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Jun 05 11:33:19 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Jun 05 16:48:03 2009 -0400 @@ -170,6 +170,11 @@ global sharing_role sharing_role = galaxy.model.Role.filter( and_( galaxy.model.Role.table.c.type==role_type, galaxy.model.Role.table.c.name==role_name ) ).first() + if not sharing_role: + # May have created a sharing role in a previous functional test suite from the opposite direction. + role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user1.email ) + sharing_role = galaxy.model.Role.filter( and_( galaxy.model.Role.table.c.type==role_type, + galaxy.model.Role.table.c.name==role_name ) ).first() if not sharing_role: raise AssertionError( "Privately sharing a dataset did not properly create a sharing role" ) if len( sharing_role.users ) != 2:

1 0

[hg] galaxy 2428: Add ability to share histories with multiple u...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9a71b89082fe changeset: 2428:9a71b89082fe user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jun 05 11:15:25 2009 -0400 description: Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features. 12 file(s) affected in this change: lib/galaxy/security/__init__.py lib/galaxy/tools/actions/upload.py lib/galaxy/web/controllers/history.py lib/galaxy/web/controllers/root.py lib/galaxy/web/framework/__init__.py scripts/cleanup_datasets/cleanup_datasets.py templates/history/rename.mako templates/history/share.mako test/base/twilltestcase.py test/functional/test_history_functions.py test/functional/test_security_and_libraries.py tool_conf.xml.sample diffs (1698 lines): diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/security/__init__.py Fri Jun 05 11:15:25 2009 -0400 @@ -51,6 +51,8 @@ def set_dataset_permission( self, dataset, permission ): raise "Unimplemented Method" def set_all_library_permissions( self, dataset, permissions ): + raise "Unimplemented Method" + def dataset_is_public( self, dataset ): raise "Unimplemented Method" def make_dataset_public( self, dataset ): raise "Unimplemented Method" @@ -296,6 +298,10 @@ # Add the new specific permission on the dataset for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: dp.flush() + def dataset_is_public( self, dataset ): + # A dataset is considered public if there are no "access" actions associated with it. Any + # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. + return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ] def make_dataset_public( self, dataset ): # A dataset is considered public if there are no "access" actions associated with it. Any # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Fri Jun 05 11:15:25 2009 -0400 @@ -245,12 +245,14 @@ parts = file_name.split( "." ) if len( parts ) > 1: ext = parts[1].strip().lower() - if not( ext == 'ab1' or ext == 'scf' ): + if not( ext == 'ab1' or ext == 'scf' or ext == 'novoindex' ): raise BadFileException( "you attempted to upload an inappropriate file." ) if ext == 'ab1' and file_type != 'ab1': raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." ) elif ext == 'scf' and file_type != 'scf': raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." ) + elif ext == 'novoindex' and file_type != 'novoindex': + raise BadFileException( "you must manually set the 'File Format' to 'NovoIndex' when uploading novoindex files." ) data_type = 'binary' if not data_type: # We must have a text file @@ -336,7 +338,7 @@ return ( False, False, None ) zip_file = zipfile.ZipFile( temp_name, "r" ) # Make sure the archive consists of valid files. The current rules are: - # 1. Archives can only include .ab1, .scf or .txt files + # 1. Archives can only include .ab1, .scf, or .txt files # 2. All file extensions within an archive must be the same name = zip_file.namelist()[0] test_ext = name.split( "." )[1].strip().lower() diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Jun 05 11:15:25 2009 -0400 @@ -1,6 +1,7 @@ from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids -import webhelpers +from galaxy import util +import webhelpers, logging from datetime import datetime from cgi import escape @@ -65,7 +66,6 @@ @web.expose def index( self, trans ): return "" - @web.expose def list_as_xml( self, trans ): """ @@ -78,9 +78,7 @@ @web.expose @web.require_login( "work with multiple histories" ) def list( self, trans, **kwargs ): - """ - List all available histories - """ + """List all available histories""" status = message = None if 'operation' in kwargs: operation = kwargs['operation'].lower() @@ -92,9 +90,7 @@ status, message = None, None refresh_history = False # Load the histories and ensure they all belong to the current user - history_ids = kwargs.get( 'id', [] ) - if type( history_ids ) is not list: - history_ids = [ history_ids ] + history_ids = util.listify( kwargs.get( 'id', [] ) ) histories = [] for hid in history_ids: history = model.History.get( hid ) @@ -117,17 +113,13 @@ trans.sa_session.flush() # Render the list view return self.list_grid( trans, status=status, message=message, **kwargs ) - def _list_delete( self, trans, histories ): """Delete histories""" n_deleted = 0 deleted_current = False for history in histories: if not history.deleted: - # Delete DefaultHistoryPermissions - for dhp in history.default_permissions: - dhp.delete() - dhp.flush() + # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later # Mark history as deleted in db history.deleted = True # If deleting the current history, make a new current. @@ -144,7 +136,6 @@ message_parts.append( "Your active history was deleted, a new empty history is now active.") status = INFO return ( status, " ".join( message_parts ) ) - def _list_undelete( self, trans, histories ): """Undelete histories""" n_undeleted = 0 @@ -154,6 +145,15 @@ n_already_purged += 1 if history.deleted: history.deleted = False + if not history.default_permissions: + # For backward compatibility - for a while we were deleting all DefaultHistoryPermissions on + # the history when we deleted the history. We are no longer doing this. + # Need to add default DefaultHistoryPermissions since they were deleted when the history was deleted + default_action = trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS + private_user_role = trans.app.security_agent.get_private_user_role( history.user ) + default_permissions = {} + default_permissions[ default_action ] = [ private_user_role ] + trans.app.security_agent.history_set_default_permissions( history, default_permissions ) n_undeleted += 1 trans.log_event( "History id %d marked as undeleted" % history.id ) status = SUCCESS @@ -164,7 +164,6 @@ message_parts.append( "%d have already been purged and cannot be undeleted." % n_already_purged ) status = WARNING return status, "".join( message_parts ) - def _list_switch( self, trans, histories ): """Switch to a new different history""" new_history = histories[0] @@ -179,13 +178,9 @@ trans.log_event( "History switched to id: %s, name: '%s'" % (str(new_history.id), new_history.name ) ) # No message return None, None - @web.expose def delete_current( self, trans ): - """ - Delete just the active history -- this does not require a logged - in user. - """ + """Delete just the active history -- this does not require a logged in user.""" history = trans.get_history() if not history.deleted: history.deleted = True @@ -195,7 +190,6 @@ # history active trans.new_history() return trans.show_ok_message( "History deleted, a new history is active" ) - @web.expose def rename_async( self, trans, id=None, new_name=None ): history = model.History.get( id ) @@ -209,11 +203,9 @@ # Rename history.name = new_name trans.sa_session.flush() - - ## These have been moved from 'root' but not cleaned up - @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): + # TODO clean this up and make sure functionally correct msg = "" user = trans.get_user() user_history = trans.get_history() @@ -262,97 +254,159 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) - @web.expose @web.require_login( "share histories with other users" ) def share( self, trans, id=None, email="", **kwd ): - send_to_err = "" - if not id: - id = trans.get_history().id - if not isinstance( id, list ): - id = [ id ] - histories = [] - history_names = [] - for hid in id: - histories.append( trans.app.model.History.get( hid ) ) - history_names.append(histories[-1].name) - if not email: - return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err) - user = trans.get_user() - send_to_user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first() + # If a history contains both datasets that can be shared and others that cannot be shared with the desired user, + # then the entire history is shared, and the protected datasets will be visible, but inaccessible ( greyed out ) + # in the shared history params = util.Params( kwd ) action = params.get( 'action', None ) if action == "no_share": - trans.response.send_redirect( url_for( action='history_options' ) ) - if not send_to_user: - send_to_err = "No such user" - elif user.email == email: - send_to_err = "You can't send histories to yourself" - else: - if 'history_share_btn' in kwd or action != 'share': - # The user is attempting to share a history whose datasets cannot all be accessed by the other user. In this case, - # the user sharing the history can chose to make the datasets public ( action == 'public' ) if he has the authority - # to do so, or automatically create a new "sharing role" that allows the user to share his private datasets only with the - # desired user ( action == 'private' ). - can_change = {} - cannot_change = {} + trans.response.send_redirect( url_for( controller='root', action='history_options' ) ) + if not id: + id = trans.get_history().id + id = util.listify( id ) + send_to_err = "" + histories = [] + for hid in id: + histories.append( trans.app.model.History.get( hid ) ) + if not email: + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) + user = trans.get_user() + send_to_users = [] + for email_address in util.listify( email ): + email_address = email_address.strip() + if email_address: + if email_address == user.email: + send_to_err += "You can't send histories to yourself. " + else: + send_to_user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email_address ).first() + if send_to_user: + send_to_users.append( send_to_user ) + else: + send_to_err += "%s is not a valid Galaxy user. " % email_address + if not send_to_users: + if not send_to_err: + send_to_err += "%s is not a valid Galaxy user. " % email + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) + if params.get( 'share_proceed_button', False ) and action == 'share': + # We need to filter out all histories that cannot be shared + filtered_histories = {} + for history in histories: + for send_to_user in send_to_users: + # Only deal with datasets that have not been purged + for hda in history.activatable_datasets: + # The history can be shared if it contains at least 1 public dataset or 1 dataset that the + # other user can access. Inaccessible datasets contained in the history will be displayed + # in the shared history, but "greyed out", so they cannot be viewed or used. + if trans.app.security_agent.dataset_is_public( hda.dataset ) or \ + trans.app.security_agent.allow_action( send_to_user, + trans.app.security_agent.permitted_actions.DATASET_ACCESS, + dataset=hda ): + if send_to_user in filtered_histories: + filtered_histories[ send_to_user ].append( history ) + else: + filtered_histories[ send_to_user ] = [ history ] + break + return self._share_histories( trans, user, send_to_users, send_to_err, filtered_histories=filtered_histories ) + elif params.get( 'history_share_btn', False ) or action != 'share': + # The user is attempting to share histories whose datasets cannot all be accessed by other users. In this case, + # the user sharing the histories can: + # 1) action=='public': chose to make the datasets public if he is permitted to do so + # 2) action=='private': automatically create a new "sharing role" allowing protected + # datasets to be accessed only by the desired users + # 3) action=='share': share only what can be shared when no permissions are changed - this case is handled above + # 4) action=='no_share': Do not share anything - this case is handled above. + can_change = {} + cannot_change = {} + no_change_needed = {} + for history in histories: + # Only deal with datasets that have not been purged + for hda in history.activatable_datasets: + if trans.app.security_agent.dataset_is_public( hda.dataset ): + if history not in no_change_needed: + no_change_needed[ history ] = [ hda ] + else: + no_change_needed[ history ].append( hda ) + elif not trans.app.security_agent.allow_action( send_to_user, + trans.app.security_agent.permitted_actions.DATASET_ACCESS, + dataset=hda ): + # The user with which we are sharing the history does not have access permission on the current dataset + if trans.app.security_agent.allow_action( user, + trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, + dataset=hda ) and not hda.dataset.library_associations: + # The current user has authority to change permissions on the current dataset because + # they have permission to manage permissions on the dataset and the dataset is not associated + # with a library. + if action == "private": + trans.app.security_agent.privately_share_dataset( hda.dataset, users=[ user, send_to_user ] ) + elif action == "public": + trans.app.security_agent.make_dataset_public( hda.dataset ) + elif history not in can_change: + # Build the set of histories / datasets on which the current user has authority + # to "manage permissions". This is used in /history/share.mako + can_change[ history ] = [ hda ] + else: + can_change[ history ].append( hda ) + else: + if action in [ "private", "public" ]: + # Don't change stuff that the user doesn't have permission to change + continue + elif history not in cannot_change: + # Build the set of histories / datasets on which the current user does + # not have authority to "manage permissions". This is used in /history/share.mako + cannot_change[ history ] = [ hda ] + else: + cannot_change[ history ].append( hda ) + if can_change or cannot_change: + return trans.fill_template( "/history/share.mako", + histories=histories, + email=email, + send_to_err=send_to_err, + can_change=can_change, + cannot_change=cannot_change, + no_change_needed=no_change_needed ) + return self._share_histories( trans, user, send_to_users, send_to_err, histories=histories ) + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) + def _share_histories( self, trans, user, send_to_users, send_to_err, histories=[], filtered_histories={} ): + msg = "" + if not send_to_users: + msg = "No users have been specified with which to share histories" + sent_to_emails = [] + for sent_to_user in send_to_users: + sent_to_emails.append( sent_to_user.email ) + emails = ",".join( e for e in sent_to_emails ) + if not histories and not filtered_histories: + msg = "No histories can be sent to (%s) without changing dataset permissions associating a sharing role with them" % emails + elif histories: + history_names = [] + for history in histories: + history_names.append( history.name ) + for send_to_user in send_to_users: + new_history = history.copy( target_user=send_to_user ) + new_history.name = history.name + " from " + user.email + new_history.user_id = send_to_user.id + self.app.model.flush() + msg = "Histories (%s) have been shared with: %s. " % ( ",".join( history_names ), emails ) + elif filtered_histories: + # filtered_histories is a dictionary like: { user: [ history, history ], user: [ history ] } + for send_to_user, histories in filtered_histories.items(): + history_names = [] for history in histories: - for hda in history.activatable_datasets: - # Only deal with datasets that have not been purged - if not trans.app.security_agent.allow_action( send_to_user, - trans.app.security_agent.permitted_actions.DATASET_ACCESS, - dataset=hda ): - # The user with which we are sharing the history does not have access permission on the current dataset - if trans.app.security_agent.allow_action( user, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=hda ) and not hda.dataset.library_associations: - # The current user has authority to change permissions on the current dataset because - # they have permission to manage permissions on the dataset and the dataset is not associated - # with a library. - if action == "private": - trans.app.security_agent.privately_share_dataset( hda.dataset, users=[ user, send_to_user ] ) - elif action == "public": - trans.app.security_agent.make_dataset_public( hda.dataset ) - elif history not in can_change: - # Build the set of histories / datasets on which the current user has authority - # to "manage permissions". This is used in /history/share.mako - can_change[ history ] = [ hda ] - else: - can_change[ history ].append( hda ) - else: - if action in [ "private", "public" ]: - # Don't change stuff that the user doesn't have permission to change - continue - elif history not in cannot_change: - # Build the set of histories / datasets on which the current user does - # not have authority to "manage permissions". This is used in /history/share.mako - cannot_change[ history ] = [ hda ] - else: - cannot_change[ history ].append( hda ) - if can_change or cannot_change: - return trans.fill_template( "/history/share.mako", - histories=histories, - email=email, - send_to_err=send_to_err, - can_change=can_change, - cannot_change=cannot_change ) - for history in histories: - new_history = history.copy( target_user=send_to_user ) - new_history.name = history.name + " from " + user.email - new_history.user_id = send_to_user.id - trans.log_event( "History share, id: %s, name: '%s': to new id: %s" % ( str( history.id ), history.name, str( new_history.id ) ) ) - self.app.model.flush() - return trans.show_message( "History (%s) has been shared with: %s" % ( ",".join( history_names ),email ) ) - return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) - + history_names.append( history.name ) + new_history = history.copy( target_user=send_to_user ) + new_history.name = history.name + " from " + user.email + new_history.user_id = send_to_user.id + self.app.model.flush() + msg += "Histories (%s) have been shared with: %s. " % ( ",".join( history_names ), send_to_user.email ) + if send_to_err: + msg += send_to_err + return trans.show_message( msg ) @web.expose @web.require_login( "rename histories" ) def rename( self, trans, id=None, name=None, **kwd ): - if trans.app.memory_usage: - # Keep track of memory usage - m0 = self.app.memory_usage.memory() user = trans.get_user() - if not isinstance( id, list ): if id != None: id = [ id ] @@ -387,7 +441,4 @@ change_msg = change_msg + "<p>You must specify a valid name for History: "+cur_names[i]+"</p>" else: change_msg = change_msg + "<p>History: "+cur_names[i]+" does not appear to belong to you.</p>" - if self.app.memory_usage: - m1 = trans.app.memory_usage.memory( m0, pretty=True ) - log.info( "End of root/history_rename, memory used increased by %s" % m1 ) - return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) \ No newline at end of file + return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri Jun 05 11:15:25 2009 -0400 @@ -349,14 +349,12 @@ """Displays a list of history related actions""" return trans.fill_template( "/history/options.mako", user = trans.get_user(), history = trans.get_history() ) - @web.expose def history_delete( self, trans, id ): """ Backward compatibility with check_galaxy script. """ return trans.webapp.controllers['history'].list( trans, id, operation='delete' ) - @web.expose def clear_history( self, trans ): """Clears the history for a user""" @@ -367,7 +365,6 @@ self.app.model.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) - @web.expose def history_import( self, trans, id=None, confirm=False, **kwd ): msg = "" @@ -417,13 +414,11 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) - @web.expose - def history_new( self, trans ): - trans.new_history() + def history_new( self, trans, name=None ): + trans.new_history( name=name ) trans.log_event( "Created new History, id: %s." % str(trans.get_history().id) ) return trans.show_message( "New history created", refresh_frames = ['history'] ) - @web.expose def history_add_to( self, trans, history_id=None, file_data=None, name="Data Added to History",info=None,ext="txt",dbkey="?",copy_access_from=None,**kwd ): """Adds a POSTed file to a History""" @@ -455,13 +450,22 @@ except Exception, e: trans.log_event( "Failed to add dataset to history: %s" % ( e ) ) return trans.show_error_message("Adding File to History has Failed") - @web.expose - def history_set_default_permissions( self, trans, **kwd ): - """Sets the user's default permissions for the current history""" + def history_set_default_permissions( self, trans, id=None, **kwd ): + """Sets the permissions on a history""" if trans.user: if 'update_roles_button' in kwd: - history = trans.get_history() + history = None + if id: + try: + id = int( id ) + except: + id = None + if id: + history = trans.app.model.History.get( id ) + if not history: + # If we haven't retrieved a history, use the current one + history = trans.get_history() p = util.Params( kwd ) permissions = {} for k, v in trans.app.model.Dataset.permitted_actions.items(): @@ -478,7 +482,6 @@ else: #user not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change a history's default permissions." ) - @web.expose def dataset_make_primary( self, trans, id=None): """Copies a dataset and makes primary""" diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Jun 05 11:15:25 2009 -0400 @@ -432,13 +432,15 @@ self.galaxy_session.current_history = history self.sa_session.flush( [ self.galaxy_session ] ) history = property( get_history, set_history ) - def new_history( self ): + def new_history( self, name=None ): """ Create a new history and associate it with the current session and its associated user (if set). """ # Create new history history = self.app.model.History() + if name: + history.name = name # Associate with session history.add_galaxy_session( self.galaxy_session ) # Make it the session's current history diff -r 73847f425801 -r 9a71b89082fe scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Mon Jun 01 10:27:04 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Fri Jun 05 11:15:25 2009 -0400 @@ -123,6 +123,11 @@ for dataset_assoc in history.datasets: _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable if not info_only: + # TODO: should the Delete DefaultHistoryPermissions be deleted here? This was incorrectly + # done in the _list_delete() method of the history controller, so copied it here. Not sure + # if we should ever delete info like this from the db though, so commented out for now... + #for dhp in history.default_permissions: + # dhp.delete() history.purged = True print "%d" % history.id history_count += 1 @@ -226,7 +231,6 @@ print "# This Dataset (%i) is not deletable, associated Metadata Files will not be removed.\n" % ( dataset.id ) else: # Mark all associated MetadataFiles as deleted and purged and remove them from disk - print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id metadata_files = [] #lets create a list of metadata files, then perform actions on them for hda in dataset.history_associations: @@ -236,6 +240,7 @@ for metadata_file in app.model.MetadataFile.filter( app.model.MetadataFile.table.c.lda_id==lda.id ).all(): metadata_files.append( metadata_file ) for metadata_file in metadata_files: + print "# The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id if not info_only: if remove_from_disk: try: @@ -248,7 +253,6 @@ print "%s" % metadata_file.file_name print dataset.deleted = True - #dataset.flush() app.model.flush() def _purge_dataset( dataset, remove_from_disk, info_only = False ): @@ -259,6 +263,7 @@ if not info_only: # Remove files from disk and update the database if remove_from_disk: + # TODO: should permissions on the dataset be deleted here? os.unlink( dataset.file_name ) # Remove associated extra files from disk if they exist if dataset.extra_files_path and os.path.exists( dataset.extra_files_path ): @@ -286,6 +291,7 @@ for sub_folder in folder.folders: _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) if not info_only: + # TODO: should the folder permissions be deleted here? folder.purged = True folder.flush() diff -r 73847f425801 -r 9a71b89082fe templates/history/rename.mako --- a/templates/history/rename.mako Mon Jun 01 10:27:04 2009 -0400 +++ b/templates/history/rename.mako Fri Jun 05 11:15:25 2009 -0400 @@ -4,17 +4,38 @@ <div class="toolForm"> <div class="toolFormTitle">${_('Rename History')}</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='rename' )}" method="post" > - <table> - <tr><th>${_('Current Name')}</th><th>${_('New Name')}</th></tr> - %for history in histories: - <tr><td>${history.name}<input type="hidden" name="id" value="${history.id}"></td><td><input type="text" name="name" value="${history.name}" size="40"></td></tr> - %endfor - <tr><td colspan="2"><input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"></td></tr> - </table> - </form> - </div> + <div class="toolFormBody"> + <form action="${h.url_for( controller='history', action='rename' )}" method="post" > + <table class="grid"> + %for history in histories: + <tr> + <td> + <div class="form-row"> + <input type="hidden" name="id" value="${history.id}"> + <label>${_('Current Name')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${history.name} + </div> + </div> + </td> + <td> + <div class="form-row"> + <label>${_('New Name')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${history.name}" size="40"> + </div> + </div> + </td> + </tr> + %endfor + <tr> + <td colspan="2"> + <div class="form-row"> + <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"> + </div> + </td> + </tr> + </table> + </form> + </div> </div> -</body> -</html> \ No newline at end of file diff -r 73847f425801 -r 9a71b89082fe templates/history/share.mako --- a/templates/history/share.mako Mon Jun 01 10:27:04 2009 -0400 +++ b/templates/history/share.mako Fri Jun 05 11:15:25 2009 -0400 @@ -2,117 +2,173 @@ <%inherit file="/base.mako"/> <%def name="title()">Share histories</%def> -%if not can_change and not cannot_change: - <div class="toolForm"> - <div class="toolFormTitle">${_('Share histories')}</div> - <table> +<div class="toolForm"> + <div class="toolFormTitle">Share ${len( histories)} histories</div> + <div class="toolFormBody"> + %if not can_change and not cannot_change: <form action="${h.url_for( controller="history", action='share' )}" method="post" > - <tr><th>${_('History Name:')}</td><th>${_('Number of Datasets:')}</th><th>${_('Share Link')}</th></tr> %for history in histories: - <tr> - <td align="center">${history.name}<input type="hidden" name="id" value="${history.id}"></td> - <td align="center"> - %if len( history.datasets ) < 1: - <div class="warningmark">${_('This history contains no data.')}</div> - %else: - ${len(history.datasets)} - %endif - </td> - <td align="center"><a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('copy link to share')}</a></td> - </tr> + <div class="toolForm"> + <div class="form-row"> + <label>${_('History Name:')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${history.name}<input type="hidden" name="id" value="${history.id}"> + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>${_('Number of Datasets:')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + %if len( history.datasets ) < 1: + <div class="warningmark">${_('This history contains no data.')}</div> + %else: + ${len(history.datasets)} + %endif + </td> + </div> + </div> + ## TODO: this feature is not currently working + ##<div style="clear: both"></div> + ##<div class="form-row"> + ## <label>${_('Share Link')}</label> + ## <div style="float: left; width: 250px; margin-right: 10px;"> + ## <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('copy link to share')}</a> + ## </div> + ##</div> + ##<div style="clear: both"></div> + <p/> + </div> %endfor - <tr><td>${_('Email of User to share with:')}</td><td><input type="text" name="email" value="${email}" size="40"></td></tr> + <p/> + <div style="clear: both"></div> + <div class="form-row"> + <label>Galaxy user emails with which to share histories</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="email" value="${email}" size="40"> + </div> + <div class="toolParamHelp" style="clear: both;"> + Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users + </div> + </div> %if send_to_err: - <tr><td colspan="100%"><div class="errormessage">${send_to_err}</div></td></tr> + <div style="clear: both"></div> + <div class="form-row"> + <div class="errormessage">${send_to_err}</div> + </div> %endif - <tr><td colspan="2" align="right"><input type="submit" name="history_share_btn" value="Submit"></td></tr> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="history_share_btn" value="Submit"> + </div> </form> - </table> + %else: + <form action="${h.url_for( controller='history', action='share' )}" method="post"> + %for history in histories: + <input type="hidden" name="id" value="${history.id}"> + %endfor + <input type="hidden" name="email" value="${email}"> + %if no_change_needed: + <div style="clear: both"></div> + <div class="form-row"> + <div class="donemessage"> + The following datasets can be shared with ${email} with no changes + </div> + </div> + %for history, hdas in no_change_needed.items(): + <div class="form-row"> + <label>History</label> + ${history.name} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Datasets</label> + </div> + %for hda in hdas: + <div class="form-row"> + ${hda.name} + </div> + %endfor + %endfor + %endif + %if can_change: + <div style="clear: both"></div> + <div class="form-row"> + <div class="warningmessage"> + The following datasets can be shared with ${email} by updating their permissions + </div> + </div> + %for history, hdas in can_change.items(): + <div class="form-row"> + <label>History</label> + ${history.name} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Datasets</label> + </div> + %for hda in hdas: + <div class="form-row"> + ${hda.name} + </div> + %endfor + %endfor + %endif + %if cannot_change: + <div style="clear: both"></div> + <div class="form-row"> + <div class="errormessage"> + The following datasets cannot be shared with ${email} because you are not authorized to + change the permissions on them + </div> + </div> + %for history, hdas in cannot_change.items(): + <div class="form-row"> + <label>History</label> + ${history.name} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Datasets</label> + </div> + %for hda in hdas: + <div class="form-row"> + ${hda.name} + </div> + %endfor + %endfor + %endif + <div class="form-row"> + <label>How would you like to proceed?</label> + </div> + %if can_change: + <div class="form-row"> + <input type="radio" name="action" value="public"> Make datasets public so anyone can access them + %if cannot_change: + (where possible) + %endif + </div> + <div class="form-row"> + <input type="radio" name="action" value="private"> Make datasets private to me and the user(s) with whom I am sharing + %if cannot_change: + (where possible) + %endif + </div> + %endif + %if no_change_needed: + <div class="form-row"> + <input type="radio" name="action" value="share"> Share anyway + %if can_change: + (don't change any permissions) + %endif + </div> + %endif + <div class="form-row"> + <input type="radio" name="action" value="no_share"> Don't share + </div> + <div class="form-row"> + <input type="submit" name="share_proceed_button" value="Go"><br/> + </div> + </form> + %endif </div> -%else: - <style type="text/css"> - th - { - text-align: left; - } - td - { - vertical-align: top; - } - </style> - <form action="${h.url_for( controller='history', action='share' )}" method="post"> - %for history in histories: - <input type="hidden" name="id" value="${history.id}"> - %endfor - <input type="hidden" name="email" value="${email}"> - <div class="warningmessage"> - The history or histories you've chosen to share contain datasets that the user with which you're sharing does not have permission to access. - These datasets are shown below. Datasets that the user has permission to access are not shown. - </div> - <p/> - %if can_change: - <div class="donemessage"> - The following datasets can be shared with ${email} by updating their permissions: - <p/> - <table cellpadding="0" cellspacing="8" border="0"> - <tr><th>Histories</th><th>Datasets</th></tr> - %for history, datasets in can_change.items(): - <tr> - <td>${history.name}</td> - <td> - %for dataset in datasets: - ${dataset.name}<br/> - %endfor - </td> - </tr> - %endfor - </table> - </div> - <p/> - %endif - %if cannot_change: - <div class="errormessage"> - The following datasets cannot be shared with ${email} because you are not authorized to change the permissions on them. - <p/> - <table cellpadding="0" cellspacing="8" border="0"> - <tr><th>Histories</th><th>Datasets</th></tr> - %for history, datasets in cannot_change.items(): - <tr> - <td>${history.name}</td> - <td> - %for dataset in datasets: - ${dataset.name}<br/> - %endfor - </td> - </tr> - %endfor - </table> - </div> - <p/> - %endif - <div> - <b>How would you like to proceed?</b> - <p/> - %if can_change: - <input type="radio" name="action" value="public"> Set datasets above to public access - %if cannot_change: - (where possible) - %endif - <br/> - <input type="radio" name="action" value="private"> Set datasets above to private access for me and the user(s) with whom I am sharing - %if cannot_change: - (where possible) - %endif - <br/> - %endif - <input type="radio" name="action" value="share"> Share anyway - %if can_change: - (don't change any permissions) - %endif - <br/> - <input type="radio" name="action" value="no_share"> Don't share<br/> - <br/> - <input type="submit" name="submit" value="Ok"><br/> - </div> - </form> -%endif +</div> diff -r 73847f425801 -r 9a71b89082fe test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Jun 01 10:27:04 2009 -0400 +++ b/test/base/twilltestcase.py Fri Jun 05 11:15:25 2009 -0400 @@ -103,41 +103,42 @@ page = self.last_page() if page.find( 'error' ) > -1: raise AssertionError('Errors in the history for user %s' % self.user ) - def check_history_for_string( self, patt ): """Looks for 'string' in history page""" self.home() self.visit_page( "history" ) for subpatt in patt.split(): tc.find(subpatt) - + self.home() def clear_history( self ): """Empties a history of all datasets""" self.visit_page( "clear_history" ) self.check_history_for_string( 'Your history is empty' ) - - def delete_history( self, id=None ): - """Deletes a history""" + self.home() + def delete_history( self, id='' ): + """Deletes one or more histories""" history_list = self.get_histories() self.assertTrue( history_list ) - if id is None: + num_deleted = 1 + if not id: history = history_list[0] id = history.get( 'id' ) - id = str( id ) - self.visit_page( "history/list?operation=delete&id=%s" %(id) ) - + else: + num_deleted = len( id.split( ',' ) ) + self.visit_page( "history/list?operation=delete&id=%s" % ( id ) ) + check_str = 'Deleted %d histories' % num_deleted + self.check_page_for_string( check_str ) + self.home() def get_histories( self ): """Returns all histories""" tree = self.histories_as_xml_tree() data_list = [ elem for elem in tree.findall("data") ] return data_list - def get_history( self, show_deleted=False ): """Returns a history""" tree = self.history_as_xml_tree( show_deleted=show_deleted ) data_list = [ elem for elem in tree.findall("data") ] return data_list - def history_as_xml_tree( self, show_deleted=False ): """Returns a parsed xml object of a history""" self.home() @@ -145,7 +146,6 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree - def histories_as_xml_tree( self ): """Returns a parsed xml object of all histories""" self.home() @@ -153,97 +153,96 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree - - def history_options( self ): + def history_options( self, check_str='', upload=False ): """Mimics user clicking on history options link""" self.visit_page( "history_options" ) - - def new_history( self ): + if check_str: + self.check_page_for_string( check_str ) + else: + self.check_page_for_string( 'Rename</a> current history' ) + self.check_page_for_string( 'List</a> previously stored histories' ) + self.check_page_for_string( 'Construct workflow</a> from the current history' ) + self.check_page_for_string( 'Share</a> current history' ) + # Tests for changing default history permissions are done in test_security_and_libraries.py + self.check_page_for_string( 'Change default permissions</a> for the current history' ) + self.check_page_for_string( 'Show deleted</a> datasets in history' ) + self.check_page_for_string( 'Delete</a> current history' ) + # Need to add a history item in order to create a new empty history + try: + self.check_page_for_string( 'Create</a> a new empty history' ) + raise AssertionError, "Incorrectly able to create a new empty history when the current history is empty." + except: + pass + if upload: + self.upload_file( '1.bed', dbkey='hg18' ) + self.home() + self.visit_page( "history_options" ) + self.check_page_for_string( 'Create</a> a new empty history' ) + self.home() + def new_history( self, name=None ): """Creates a new, empty history""" - self.visit_page( "history_new" ) + if name: + self.visit_url( "%s/history_new?name=%s" % ( self.url, str( name ) ) ) + else: + self.visit_url( "%s/history_new" % self.url ) self.check_history_for_string('Your history is empty') - - def rename_history( self, id=None, name='NewTestHistory' ): + self.home() + def rename_history( self, id, old_name, new_name ): """Rename an existing history""" - history_list = self.get_histories() - self.assertTrue( history_list ) - if id is None: # take last id - elem = history_list[-1] - else: - i = history_list.index( id ) - self.assertTrue( i ) - elem = history_list[i] - id = elem.get( 'id' ) - self.assertTrue( id ) - old_name = elem.get( 'name' ) - self.assertTrue( old_name ) - id = str( id ) - self.visit_page( "history/rename?id=%s&name=%s" %(id, name) ) - return id, old_name, name - + self.home() + self.visit_page( "history/rename?id=%s&name=%s" %( id, new_name ) ) + check_str = 'History: %s renamed to: %s' % ( old_name, new_name ) + self.check_page_for_string( check_str ) + self.home() def set_history( self ): """Sets the history (stores the cookies for this run)""" if self.history_id: self.visit_page( "history?id=%s" % self.history_id ) else: self.new_history() - def share_history( self, id=None, email='test2(a)bx.psu.edu' ): - """Share a history with a different user""" - history_list = self.get_histories() - self.assertTrue( history_list ) - if id is None: # take last id - elem = history_list[-1] - else: - i = history_list.index( id ) - self.assertTrue( i ) - elem = history_list[i] - id = elem.get( 'id' ) - self.assertTrue( id ) - id = str( id ) - name = elem.get( 'name' ) - self.assertTrue( name ) + self.home() + def share_history( self, id, email, check_str, check_str2='', action=None, action_check_str=None ): + """Share a history different users""" self.visit_url( "%s/history/share?id=%s&email=%s&history_share_btn=Submit" % ( self.url, id, email ) ) - self.check_page_for_string( 'History (%s) has been shared with: %s' % ( name, email ) ) - return id, name, email - def share_history_containing_private_datasets( self, history_id, email='test(a)bx.psu.edu' ): - """Attempt to share a history containing private datasets with a different user""" - self.visit_url( "%s/history/share?id=%s&email=%s&history_share_btn=Submit" % ( self.url, history_id, email ) ) - self.last_page() - self.check_page_for_string( "The history or histories you've chosen to share contain datasets" ) - self.check_page_for_string( "How would you like to proceed?" ) + self.check_page_for_string( check_str ) + if check_str2: + self.check_page_for_string( check_str2 ) + if action: + # If we have an action, then we are sharing datasets with users that do not have access permissions on them + tc.fv( '1', 'action', action ) + tc.submit( "share_proceed_button" ) + if action_check_str: + self.check_page_for_string( action_check_str ) self.home() - def make_datasets_public( self, history_id, email='test(a)bx.psu.edu' ): - """Make private datasets public in order to share a history with a different user""" - self.visit_url( "%s/history/share?id=%s&email=%s&action=public&submit=Ok" % ( self.url, history_id, email ) ) - self.last_page() - check_str = "History (Unnamed history) has been shared with: %s" % email - self.check_page_for_string( check_str ) - self.home() - def privately_share_dataset( self, history_id, email='test(a)bx.psu.edu' ): - """Make private datasets public in order to share a history with a different user""" - self.visit_url( "%s/history/share?id=%s&email=%s&action=private&submit=Ok" % ( self.url, history_id, email ) ) - self.last_page() - check_str = "History (Unnamed history) has been shared with: %s" % email - self.check_page_for_string( check_str ) - self.home() - def switch_history( self, hid=None ): + def switch_history( self, id='', name='' ): """Switches to a history in the current list of histories""" data_list = self.get_histories() self.assertTrue( data_list ) - if hid is None: # take last hid - elem = data_list[-1] - hid = elem.get('hid') - if hid < 0: - hid = len(data_list) + hid + 1 - hid = str(hid) - elems = [ elem for elem in data_list if elem.get('hid') == hid ] - self.assertEqual(len(elems), 1) - self.visit_page( "history/list?operation=switch&id=%s" % elems[0].get('id') ) - - def view_stored_histories( self, check_str='' ): + if not id: + history = history_list[0] + id = history.get( 'id' ) + self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) ) + if name: + self.check_history_for_string( name ) + self.home() + def view_stored_active_histories( self, check_str='' ): self.visit_page( "history/list" ) + self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( '<input type="checkbox" name="id" value=' ) + self.check_page_for_string( 'operation=Rename&id' ) + self.check_page_for_string( 'operation=Switch&id' ) + self.check_page_for_string( 'operation=Delete&id' ) if check_str: self.check_page_for_string( check_str ) + self.home() + def view_stored_deleted_histories( self, check_str='' ): + self.visit_page( "history/list?f-deleted=True" ) + self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( '<input type="checkbox" name="id" value=' ) + self.check_page_for_string( 'operation=Undelete&id' ) + if check_str: + self.check_page_for_string( check_str ) + self.home() # Functions associated with datasets (history items) and meta data def get_job_stderr( self, id ): @@ -299,9 +298,14 @@ self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, elems[0].get( 'id' ) ) ) if check_str: self.check_page_for_string( check_str ) + def display_history_item( self, id, check_str='' ): + """Displays a history item - simulates eye icon click""" + self.visit_url( '%s/datasets/%s/display/index' % ( self.url, id ) ) + if check_str: + self.check_page_for_string( check_str ) + self.home() def edit_metadata( self, hid=None, form_no=0, **kwd ): - """ - Edits the metadata associated with a history item.""" + """Edits the metadata associated with a history item.""" # There are currently 4 forms on the edit page: # 0. name="edit_attributes" # 1. name="auto_detect" @@ -324,7 +328,6 @@ button = "change" #Change data type form if kwd: self.submit_form( form_no=form_no, button=button, **kwd) - def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" data_list = self.get_history() diff -r 73847f425801 -r 9a71b89082fe test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Mon Jun 01 10:27:04 2009 -0400 +++ b/test/functional/test_history_functions.py Fri Jun 05 11:15:25 2009 -0400 @@ -4,74 +4,367 @@ class TestHistory( TwillTestCase ): - def test_00_history_options_when_not_logged_in( self ): + def test_000_history_options_when_not_logged_in( self ): """Testing history options when not logged in""" - self.logout() #Ensure we are not logged in - self.history_options() - self.check_page_for_string( 'logged in</a> to store or switch histories.' ) - self.login( email='test2(a)bx.psu.edu' ) #Just to make sure we have created this account since it is used to share histories self.logout() - def test_05_new_history_then_delete( self ): - """Testing creating a new history and then deleting it""" - self.login() - self.new_history() - if len(self.get_history()) > 0: - raise AssertionError("test_new_history_then_delete failed") - self.delete_history() - self.check_page_for_string( 'Deleted 1 histories' ) - def test_10_history_options_when_logged_in( self ): + check_str = 'logged in</a> to store or switch histories.' + self.history_options( check_str=check_str ) + # Make sure we have created the following accounts + self.login( email='test1(a)bx.psu.edu' ) + global regular_user1 + regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' + self.logout() + self.login( email='test2(a)bx.psu.edu' ) + global regular_user2 + regular_user2 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test2(a)bx.psu.edu' ).first() + assert regular_user2 is not None, 'Problem retrieving user with email "test2(a)bx.psu.edu" from the database' + self.logout() + self.login( email='test3(a)bx.psu.edu' ) + global regular_user3 + regular_user3 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ).first() + assert regular_user3 is not None, 'Problem retrieving user with email "test3(a)bx.psu.edu" from the database' + self.logout() + def test_005_deleting_histories( self ): + """Testing deleting histories""" + self.login( email='test(a)bx.psu.edu' ) + global admin_user + admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() + assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' + # Get the admin_user private role + global admin_user_private_role + admin_user_private_role = None + for role in admin_user.all_roles(): + if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email: + admin_user_private_role = role + break + if not admin_user_private_role: + raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) + latest_history = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert latest_history is not None, "Problem retrieving latest history from database" + assert not latest_history.deleted, "After login, associated history is deleted" + self.delete_history( str( latest_history.id ) ) + latest_history.refresh() + if not latest_history.deleted: + raise AssertionError, "Problem deleting history id %d" % latest_history.id + # We'll now test deleting a list of histories + # After deleting the current history, a new one should have been created + global history1 + history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history1 is not None, "Problem retrieving history1 from database" + self.upload_file( '1.bed', dbkey='hg18' ) + self.new_history( name='history2' ) + global history2 + history2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history2 is not None, "Problem retrieving history2 from database" + self.upload_file( '2.bed', dbkey='hg18' ) + ids = '%s,%s' % ( str( history1.id ), str( history2.id ) ) + self.delete_history( ids ) + try: + self.view_stored_active_histories( check_str=history1.name ) + raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history1.name + except: + pass + self.view_stored_deleted_histories( check_str=history1.name ) + try: + self.view_stored_active_histories( check_str=history2.name ) + raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history2.name + except: + pass + self.view_stored_deleted_histories( check_str=history2.name ) + history1.refresh() + if not history1.deleted: + raise AssertionError, "Problem deleting history id %d" % history1.id + if not history1.default_permissions: + raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history1.id + history2.refresh() + if not history2.deleted: + raise AssertionError, "Problem deleting history id %d" % history2.id + if not history2.default_permissions: + raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history2.id + def test_010_history_options_when_logged_in( self ): """Testing history options when logged in""" self.history_options() - self.check_page_for_string( 'Rename</a> current history' ) - self.check_page_for_string( 'List</a> previously stored histories' ) - self.check_page_for_string( 'Construct workflow</a> from the current history' ) - self.check_page_for_string( 'Share</a> current history' ) - # Tests for changing default history permissions are done in test_security_and_libraries.py - self.check_page_for_string( 'Change default permissions</a> for the current history' ) - self.check_page_for_string( 'Show deleted</a> datasets in history' ) - self.check_page_for_string( 'Delete</a> current history' ) - # Need to add a history item in order to create a new empty history + def test_015_history_rename( self ): + """Testing renaming a history""" + global history3 + history3 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history3 is not None, "Problem retrieving history3 from database" + if history3.deleted: + raise AssertionError, "History id %d deleted when it should not be" % latest_history.id + self.rename_history( str( history3.id ), history3.name, new_name='history3' ) + def test_020_history_list( self ): + """Testing viewing previously stored histories""" + self.view_stored_active_histories() + def test_025_history_share( self ): + """Testing sharing histories containing only public datasets""" + history3.refresh() + self.upload_file( '1.bed', dbkey='hg18' ) + # Test sharing a history with yourself + check_str = "You can't send histories to yourself." + self.share_history( str( history3.id ), 'test(a)bx.psu.edu', check_str ) + # Share a history with 1 valid user + name = history3.name + email = 'test1(a)bx.psu.edu' + check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) + self.share_history( str( history3.id ), email, check_str ) + # We need to keep track of all shared histories so they can later be deleted + global history3_copy1 + history3_copy1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history3_copy1 is not None, "Problem retrieving history3_copy1 from database" + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + check_str = '%s from test(a)bx.psu.edu' % history3.name + self.view_stored_active_histories( check_str=check_str ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # Need to delete history3_copy1 + history3_copy1.deleted = True + history3_copy1.flush() + # Test sharing a history with an invalid user + email = 'jack(a)jill.com' + check_str = '%s is not a valid Galaxy user.' % email + self.share_history( str( history3.id ), email, check_str ) + # Test sharing multiple histories with multiple users + self.new_history() + global history4 + history4 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history4 is not None, "Problem retrieving history4 from database" + self.rename_history( str( history4.id ), history4.name, new_name='history4' ) + history4.refresh() + self.upload_file( '2.bed', dbkey='hg18' ) + id = '%s,%s' % ( str( history3.id ), str( history4.id ) ) + name = '%s,%s' % ( history3.name, history4.name ) + email = 'test2@bx.psu.edu,test3@bx.psu.edu' + check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) + self.share_history( id, email, check_str ) + # We need to keep track of all shared histories so they can later be deleted + history3_copy_name = "%s from %s" % ( history3.name, admin_user.email ) + history3_copies = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history3_copy_name, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .limit( 2 ) \ + .all() + history3_copy2 = history3_copies[0] + history3_copy3 = history3_copies[1] + history4_copy_name = "%s from %s" % ( history4.name, admin_user.email ) + history4_copyies = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .limit( 2 ) \ + .all() + history4_copy1 = history4_copyies[0] + history4_copy2 = history4_copyies[1] + self.logout() + self.login( email='test2(a)bx.psu.edu' ) + check_str = '%s from %s' % ( history3.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + check_str = '%s from %s' % ( history4.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + self.logout() + self.login( email='test3(a)bx.psu.edu' ) + check_str = '%s from %s' % ( history3.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + check_str = '%s from %s' % ( history4.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # Need to delete the copied histories, so later test runs are valid + history3_copy2.deleted = True + history3_copy2.flush() + history3_copy3.deleted = True + history3_copy3.flush() + history4_copy1.deleted = True + history4_copy1.flush() + history4_copy1.deleted = True + history4_copy1.flush() + history4_copy2.deleted = True + history4_copy2.flush() + def test_030_change_permissions_on_current_history( self ): + """Testing changing permissions on the current history""" + global history5 + history5 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history5 is not None, "Problem retrieving history5 from database" + self.rename_history( str( history5.id ), history5.name, new_name='history5' ) + history5.refresh() + # Due to the limitations of twill ( not functional with the permissions forms ), we're forced + # to do this manually. At this point, we just want to restrict the access permission on history5 + # to the admin_user + global access_action + access_action = galaxy.model.Dataset.permitted_actions.DATASET_ACCESS.action + dhp = galaxy.model.DefaultHistoryPermissions( history5, access_action, admin_user_private_role ) + dhp.flush() + self.upload_file( '1.bed', dbkey='hg18' ) + history5_dataset1 = None + for hda in history5.datasets: + if hda.name == '1.bed': + history5_dataset1 = hda.dataset + assert history5_dataset1 is not None, "Problem retrieving history5_dataset1 from the database" + # The permissions on the dataset should be restricted from sharing with anyone due to the + # inherited history permissions + restricted = False + for action in history5_dataset1.actions: + if action.action == access_action: + restricted = True + break + if not restricted: + raise AssertionError, "The 'access' permission is not set for history5_dataset1.actions" + def test_035_sharing_history_by_making_datasets_public( self ): + """Testing sharing a restricted history by making the datasets public""" + check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) + self.share_history( str( history5.id ), regular_user1.email, check_str, action='public', action_check_str=action_check_str ) + history5_copy1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history5_copy1 is not None, "Problem retrieving history5_copy1 from database" + self.logout() + self.login( email=regular_user1.email ) + self.visit_url( "%s/history/list" % self.url ) + self.check_page_for_string( history5_copy1.name ) + # Need to delete history5_copy1 on the history list page for regular_user1 + history5_copy1.deleted = True + history5_copy1.flush() + self.logout() + self.login( email=admin_user.email ) + def test_040_sharing_history_by_making_new_sharing_role( self ): + """Testing sharing a restricted history by associating a new sharing role with protected datasets""" + self.switch_history( id=str( history5.id ), name=history5.name ) + # At this point, history5 should have 1 item, 1.bed, which is public. We'll add another + # item which will be private to admin_user due to the permissions on history5 + self.upload_file( '2.bed', dbkey='hg18' ) + check_str = 'The following datasets can be shared with %s with no changes' % regular_user1.email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) + self.share_history( str( history5.id ), + regular_user1.email, + check_str, + check_str2=check_str2, + action='private', + action_check_str=action_check_str ) + history5_copy2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history5_copy2 is not None, "Problem retrieving history5_copy2 from database" + # We should now have a new sharing role + global sharing_role + role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user1.email ) + sharing_role = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==role_name ).first() + assert sharing_role is not None, "Problem retrieving sharing_role from the database" + self.logout() + self.login( email=regular_user1.email ) + self.visit_url( "%s/history/list" % self.url ) + self.check_page_for_string( history5_copy2.name ) + self.switch_history( id=str( history5_copy2.id ), name=history5_copy2.name ) + # Make sure both datasets are in the history + self.check_history_for_string( '1.bed' ) + self.check_history_for_string( '2.bed' ) + # Get both new hdas from the db that were created for the shared history + hda_1_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ + .first() + assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" + hda_2_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ + .first() + assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" + # Make sure 1.bed is accessible since it is public + self.display_history_item( str( hda_1_bed.id ), check_str='chr1' ) + # Make sure 2.bed is accessible since it is associated with a sharing role + self.display_history_item( str( hda_2_bed.id ), check_str='chr1' ) + # Need to delete history5_copy2 on the history list page for regular_user1 + history5_copy2.deleted = True + history5_copy2.flush() + self.logout() + self.login( email=admin_user.email ) + def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): + """Testing sharing a restricted history with multiple users, making no permission changes""" + # History5 can be shared with any user, since it contains a public dataset. However, only + # regular_user1 should be able to access history5's 2.bed dataset since it is associated with a + # sharing role, and regular_user2 should be able to access history5's 1.bed, but not 2.bed even + # though they can see it in their shared history. + self.switch_history( id=str( history5.id ), name=history5.name ) + email = '%s,%s' % ( regular_user1.email, regular_user2.email ) + check_str = 'The following datasets can be shared with %s with no changes' % email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % email + action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) + self.share_history( str( history5.id ), + email, + check_str, + check_str2=check_str2, + action='share', + action_check_str=action_check_str ) + # We need to keep track of all shared histories so they can later be deleted + history5_copy_name = "%s from %s" % ( history5.name, admin_user.email ) + history5_copies = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history5_copy_name, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .limit( 2 ) \ + .all() + history5_copy3 = history5_copies[0] + assert history5_copy3 is not None, "Problem retrieving history5_copy3 from database" + history5_copy4 = history5_copies[1] + assert history5_copy4 is not None, "Problem retrieving history5_copy4 from database" + # Make sure test1(a)bx.psu.edu received a copy of history5 with both datasets accessible + self.login( email=regular_user1.email ) + check_str = '%s from %s' % ( history5.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + self.switch_history( id=str( history5_copy3.id ), name=history5_copy3.name ) + self.check_history_for_string( '1.bed' ) + self.check_history_for_string( '2.bed' ) + self.logout() + # Make sure test2(a)bx.psu.edu received a copy of history5, with only 1.bed accessible + self.login( email=regular_user2.email ) + self.view_stored_active_histories( check_str=check_str ) + self.switch_history( id=str( history5_copy4.id ), name=history5_copy4.name ) + self.check_history_for_string( '1.bed' ) + self.check_history_for_string( '2.bed' ) + # Get both new hdas from the db that were created for the shared history + hda_1_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ + .first() + assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" + hda_2_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ + .first() + assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" + # Make sure 1.bed is accessible since it is public + self.display_history_item( str( hda_1_bed.id ), check_str='chr1' ) + # Make sure 2.bed is not accessible since it is protected try: - self.check_page_for_string( 'Create</a> a new empty history' ) - raise AssertionError, "Incorrectly able to create a new empty history when the current history is empty." + self.display_history_item( str( hda_2_bed.id ), check_str='chr1' ) + raise AssertionError, "History item 2.bed is accessible by user %s when is should not be" % regular_user2.email except: pass - self.upload_file( '1.bed', dbkey='hg18' ) - self.history_options() - self.check_page_for_string( 'Create</a> a new empty history' ) - def test_15_history_rename( self ): - """Testing renaming a history""" - id, old_name, new_name = self.rename_history() - self.check_page_for_string( 'History: %s renamed to: %s' %(old_name, new_name) ) - def test_20_history_list( self ): - """Testing viewing previously stored histories""" - self.view_stored_histories() - self.check_page_for_string( 'Stored histories' ) - self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) - def test_25_history_share( self ): - """Testing sharing a history with another user""" - self.upload_file('1.bed', dbkey='hg18') - id, name, email = self.share_history() - self.logout() - self.login( email=email ) - self.home() - check_str = 'Unnamed history from test(a)bx.psu.edu' - self.view_stored_histories( check_str=check_str ) - histories = self.get_histories() - for history in histories: - if history.get( 'name' ) == 'Unnamed history from test(a)bx.psu.edu': - id = history.get( 'id' ) - break - self.assertTrue( id ) - self.delete_history( id ) + self.check_history_for_string( 'You do not have permission to view this dataset' ) self.logout() self.login( email='test(a)bx.psu.edu' ) - def test_30_history_show_and_hide_deleted_datasets( self ): + # Need to delete the copied histories, so later test runs are valid + history5_copy3.deleted = True + history5_copy3.flush() + history5_copy4.deleted = True + history5_copy4.flush() + + + + def test_050_sharing_private_history_by_choosing_to_not_share( self ): + """Testing sharing a restricted history with multiple users by choosing not to share""" + self.switch_history( id=str( history5.id ), name=history5.name ) + email = '%s,%s' % ( regular_user1.email, regular_user2.email ) + check_str = 'The following datasets can be shared with %s with no changes' % email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % email + action_check_str = 'History Options' + self.share_history( str( history5.id ), + email, + check_str, + check_str2=check_str2, + action='no_share' ) + def test_055_history_show_and_hide_deleted_datasets( self ): """Testing displaying deleted history items""" - self.new_history() + self.new_history( name='temp_history1' ) self.upload_file('1.bed', dbkey='hg18') latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -85,9 +378,9 @@ self.home() self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( 'Your history is empty' ) - def test_35_deleting_and_undeleting_history_items( self ): + def test_060_deleting_and_undeleting_history_items( self ): """Testing deleting and un-deleting history items""" - self.new_history() + self.new_history( name='temp_history2' ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) self.home() @@ -110,6 +403,8 @@ self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) - def test_9999_clean_up( self ): - self.delete_history() - self.logout() + def test_065_reset_data_for_later_test_runs( self ): + """Reseting data to enable later test runs to pass""" + self.delete_history( id=str( history3.id ) ) + self.delete_history( id=str( history4.id ) ) + self.delete_history( id=str( history5.id ) ) diff -r 73847f425801 -r 9a71b89082fe test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Jun 01 10:27:04 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Jun 05 11:15:25 2009 -0400 @@ -40,7 +40,7 @@ global admin_user admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' - # Get the admin user's privat role for later use + # Get the admin user's private role for later use global admin_user_private_role admin_user_private_role = None for role in admin_user.all_roles(): @@ -136,7 +136,7 @@ dps.append( dp.action ) # Sort actions for later comparison dps.sort() - # Compare DatasetPermissionss with permissions_in - should be the same + # Compare DatasetPermissions with permissions_in - should be the same if dps != actions_in: raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from changed default permissions "%s"' \ % ( str( dps ), latest_dataset.id, str( actions_in ) ) ) @@ -145,14 +145,26 @@ raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s" for history id %d' \ % ( str( dps ), latest_dataset.id, str( dhps ), latest_history.id ) ) # Since the dataset in the history is now private, we can test sharing with another user - self.share_history_containing_private_datasets( str( latest_history.id ), email=admin_user.email ) # Test making the dataset in the history public - self.make_datasets_public( str( latest_history.id ), email=admin_user.email ) + check_str = 'The following datasets can be shared with %s by updating their permissions' % admin_user.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( latest_history.name, admin_user.email ) + self.share_history( str( latest_history.id ), + admin_user.email, + check_str, + action='public', + action_check_str=action_check_str ) # Add another dataset to the history, it should be private since that is now our default self.upload_file( '2.bed' ) - self.share_history_containing_private_datasets( str( latest_history.id ), email=admin_user.email ) - # Test creating a new sharing role for sharing the private datasets - self.privately_share_dataset( str( latest_history.id ), email=admin_user.email ) + # Test creating a new sharing role for the private dataset + check_str = 'The following datasets can be shared with %s with no changes' % admin_user.email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % admin_user.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( latest_history.name, admin_user.email ) + self.share_history( str( latest_history.id ), + admin_user.email, + check_str, + check_str2=check_str2, + action='private', + action_check_str=action_check_str ) role_type = 'sharing' role_name = 'Sharing role for: %s, %s' % ( regular_user1.email, admin_user.email ) global sharing_role diff -r 73847f425801 -r 9a71b89082fe tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Jun 01 10:27:04 2009 -0400 +++ b/tool_conf.xml.sample Fri Jun 05 11:15:25 2009 -0400 @@ -13,6 +13,7 @@ <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/flymine_test.xml" /> + <tool file="data_source/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> <tool file="data_source/epigraph_import_test.xml" />

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