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557 lines
38 KiB
Python
557 lines
38 KiB
Python
import galaxy.model
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from galaxy.model.orm import *
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from galaxy.model.mapping import context as sa_session
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from base.twilltestcase import TwillTestCase
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class UploadData( TwillTestCase ):
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def test_0005_upload_file( self ):
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"""Test uploading 1.bed, NOT setting the file format"""
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self.logout()
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self.login( email='test@bx.psu.edu' )
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global admin_user
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admin_user = sa_session.query( galaxy.model.User ) \
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.filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ) \
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.one()
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.bed' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.bed', hid=str( hda.hid ) )
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self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0010_upload_file( self ):
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"""Test uploading 4.bed.gz, manually setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) )
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self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0015_upload_file( self ):
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"""Test uploading 1.scf, manually setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.scf', ftype='scf' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.scf', hid=str( hda.hid ) )
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self.check_history_for_string( "Binary scf sequence file</pre>" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0020_upload_file( self ):
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"""Test uploading 1.scf, NOT setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.scf' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.check_history_for_string( "File Format' to 'Scf' when uploading scf files" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0025_upload_file( self ):
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"""Test uploading 1.scf.zip, manually setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.scf.zip', ftype='binseq.zip' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.scf.zip', hid=str( hda.hid ) )
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self.check_history_for_string( "Archive of 1 binary sequence files</pre>" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0030_upload_file( self ):
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"""Test uploading 1.scf.zip, NOT setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.scf.zip' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.check_history_for_string( "'File Format' for archive consisting of binary files - use 'Binseq.zip'" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0035_upload_file( self ):
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"""Test uploading 1.sam NOT setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.sam' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.sam', hid=str( hda.hid ) )
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self.check_history_for_string( "<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0040_upload_file( self ):
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"""Test uploading 1.sff, NOT setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.sff' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.sff', hid=str( hda.hid ) )
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self.check_history_for_string( 'format: <span class="sff">sff' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0045_upload_file( self ):
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"""Test uploading 454Score.pdf, NOT setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '454Score.pdf' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.check_history_for_string( "The uploaded file contains inappropriate content" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0050_upload_file( self ):
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"""Test uploading 454Score.png, NOT setting the file format"""
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '454Score.png' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.check_history_for_string( "The uploaded file contains inappropriate content" )
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def test_0055_upload_file( self ):
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"""Test uploading lped composite datatype file, manually setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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# lped data types include a ped_file and a map_file ( which is binary )
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self.upload_composite_datatype_file( 'lped', ped_file='tinywga.ped', map_file='tinywga.map', base_name='rgenetics' )
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# Get the latest hid for testing
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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# We'll test against the resulting ped file and map file for correctness
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self.verify_composite_datatype_file_content( 'rgenetics.ped', str( hda.id ) )
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self.verify_composite_datatype_file_content( 'rgenetics.map', str( hda.id ) )
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self.check_history_for_string( "Uploaded Composite Dataset (lped)" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0060_upload_file( self ):
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"""Test uploading pbed composite datatype file, manually setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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# pbed data types include a bim_file, a bed_file and a fam_file
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self.upload_composite_datatype_file( 'pbed', bim_file='tinywga.bim', bed_file='tinywga.bed', fam_file='tinywga.fam', base_name='rgenetics' )
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# Get the latest hid for testing
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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# We'll test against the resulting ped file and map file for correctness
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self.verify_composite_datatype_file_content( 'rgenetics.bim', str( hda.id ) )
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self.verify_composite_datatype_file_content( 'rgenetics.bed', str( hda.id ) )
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self.verify_composite_datatype_file_content( 'rgenetics.fam', str( hda.id ) )
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self.check_history_for_string( "Uploaded Composite Dataset (pbed)" )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0065_upload_file( self ):
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"""Test uploading asian_chars_1.txt, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( 'asian_chars_1.txt' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda.hid ) )
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self.check_history_for_string( 'uploaded multi-byte char file' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0070_upload_file( self ):
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"""Test uploading 2gen.fastq, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '2gen.fastq' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '2gen.fastq', hid=str( hda.hid ) )
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self.check_history_for_string( '2gen.fastq format: <span class="fastq">fastq</span>, database: \? Info: uploaded fastq file' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0075_upload_file( self ):
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"""Test uploading 1.wig, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.wig' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.wig', hid=str( hda.hid ) )
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self.check_history_for_string( '1.wig format: <span class="wig">wig</span>, database: \? Info: uploaded file' )
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self.check_metadata_for_string( 'value="1.wig" value="\?"' )
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self.check_metadata_for_string( 'Change data type selected value="wig" selected="yes"' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0080_upload_file( self ):
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"""Test uploading 1.tabular, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( '1.tabular' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( '1.tabular', hid=str( hda.hid ) )
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self.check_history_for_string( '1.tabular format: <span class="tabular">tabular</span>, database: \? Info: uploaded file' )
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self.check_metadata_for_string( 'value="1.tabular" value="\?"' )
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self.check_metadata_for_string( 'Change data type selected value="tabular" selected="yes"' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0085_upload_file( self ):
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"""Test uploading qualscores.qualsolid, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( 'qualscores.qualsolid' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( 'qualscores.qualsolid', hid=str( hda.hid ) )
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self.check_history_for_string( '48 lines, format: <span class="qualsolid">qualsolid</span>, database: \? Info: uploaded file' )
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self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0090_upload_file( self ):
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"""Test uploading qualscores.qual454, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
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history = sa_session.query( galaxy.model.History ) \
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.filter( and_( galaxy.model.History.table.c.deleted==False,
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galaxy.model.History.table.c.user_id==admin_user.id ) ) \
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.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
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.first()
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self.upload_file( 'qualscores.qual454' )
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hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
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.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
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.first()
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assert hda is not None, "Problem retrieving hda from database"
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self.verify_dataset_correctness( 'qualscores.qual454', hid=str( hda.hid ) )
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self.check_history_for_string( '49 lines, format: <span class="qual454">qual454</span>, database: \?' )
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self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' )
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self.delete_history( id=self.security.encode_id( history.id ) )
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def test_0095_upload_file( self ):
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"""Test uploading 3.maf, NOT setting the file format"""
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# Logged in as admin_user
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self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '3.maf' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '3.maf', hid=str( hda.hid ) )
|
|
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">Convert MAF to Genomic Intervals <option value="fasta">Convert MAF to Fasta' )
|
|
self.check_metadata_for_string( 'Change data type selected value="maf" selected="yes"' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0100_upload_file( self ):
|
|
"""Test uploading 1.lav, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '1.lav' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '1.lav', hid=str( hda.hid ) )
|
|
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( id=self.security.encode_id( history.id ) )
|
|
def test_0105_upload_file( self ):
|
|
"""Test uploading 1.interval, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '1.interval' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '1.interval', hid=str( hda.hid ) )
|
|
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">Convert Genomic Intervals To BED' )
|
|
self.check_metadata_for_string( 'Change data type selected value="interval" selected="yes"' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0110_upload_file( self ):
|
|
"""Test uploading 5.gff3, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '5.gff3' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '5.gff3', hid=str( hda.hid ) )
|
|
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">Convert GFF to BED' )
|
|
self.check_metadata_for_string( 'Change data type selected value="gff3" selected="yes"' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0115_upload_file( self ):
|
|
"""Test uploading html_file.txt, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( 'html_file.txt' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.check_history_for_string( 'The uploaded file contains inappropriate content' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0120_upload_file( self ):
|
|
"""Test uploading 5.gff, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '5.gff' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '5.gff', hid=str( hda.hid ) )
|
|
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">Convert GFF to BED' )
|
|
self.check_metadata_for_string( 'Change data type selected value="gff" selected="yes"' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0125_upload_file( self ):
|
|
"""Test uploading 1.fasta, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '1.fasta' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '1.fasta', hid=str( hda.hid ) )
|
|
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( id=self.security.encode_id( history.id ) )
|
|
def test_0130_upload_file( self ):
|
|
"""Test uploading 1.customtrack, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '1.customtrack' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '1.customtrack', hid=str( hda.hid ) )
|
|
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( id=self.security.encode_id( history.id ) )
|
|
def test_0135_upload_file( self ):
|
|
"""Test uploading shrimp_cs_test1.csfasta, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( 'shrimp_cs_test1.csfasta' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta', hid=str( hda.hid ) )
|
|
self.check_history_for_string( '2,500 sequences, format: <span class="csfasta">csfasta</span>, <td>>2_14_26_F3,-1282216.0</td>' )
|
|
self.check_metadata_for_string( 'value="shrimp_cs_test1.csfasta" value="\?" Change data type value="csfasta" selected="yes"' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0140_upload_file( self ):
|
|
"""Test uploading megablast_xml_parser_test1.gz, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( 'megablast_xml_parser_test1.gz' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.check_history_for_string( 'NCBI Blast XML data format: <span class="blastxml">blastxml</span>' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0145_upload_file( self ):
|
|
"""Test uploading 1.axt, NOT setting the file format"""
|
|
# Logged in as admin_user
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '1.axt' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '1.axt', hid=str( hda.hid ) )
|
|
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( id=self.security.encode_id( history.id ) )
|
|
def test_0150_upload_file( self ):
|
|
"""Test uploading 1.bam, NOT setting the file format"""
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_file( '1.bam' )
|
|
hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
assert hda is not None, "Problem retrieving hda from database"
|
|
self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ) )
|
|
self.check_history_for_string( '<span class="bam">bam</span>' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_0155_url_paste( self ):
|
|
"""Test url paste behavior"""
|
|
# Logged in as admin_user
|
|
# Deleting the current history should have created a new history
|
|
self.check_history_for_string( 'Your history is empty' )
|
|
history = sa_session.query( galaxy.model.History ) \
|
|
.filter( and_( galaxy.model.History.table.c.deleted==False,
|
|
galaxy.model.History.table.c.user_id==admin_user.id ) ) \
|
|
.order_by( desc( galaxy.model.History.table.c.create_time ) ) \
|
|
.first()
|
|
self.upload_url_paste( 'hello world' )
|
|
self.check_history_for_string( 'Pasted Entry' )
|
|
self.check_history_for_string( 'hello world' )
|
|
self.upload_url_paste( u'hello world' )
|
|
self.check_history_for_string( 'Pasted Entry' )
|
|
self.check_history_for_string( 'hello world' )
|
|
self.delete_history( id=self.security.encode_id( history.id ) )
|
|
def test_9999_clean_up( self ):
|
|
self.logout() |