def test_0095_upload_file(self):
"""Test uploading 3.maf, 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('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_0060_upload_file(self):
"""Test uploading pbed composite datatype file, manually 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()
# pbed data types include a bim_file, a bed_file and a fam_file
self.upload_composite_datatype_file('pbed',
bim_file='tinywga.bim',
bed_file='tinywga.bed',
fam_file='tinywga.fam',
base_name='rgenetics')
# Get the latest hid for testing
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"
# We'll test against the resulting ped file and map file for correctness
self.verify_composite_datatype_file_content('rgenetics.bim',
str(hda.id))
self.verify_composite_datatype_file_content('rgenetics.bed',
str(hda.id))
self.verify_composite_datatype_file_content('rgenetics.fam',
str(hda.id))
self.check_history_for_string("Uploaded Composite Dataset (pbed)")
self.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_070_history_show_and_hide_deleted_datasets(self):
"""Testing displaying deleted history items"""
# Logged in as admin_user
self.new_history(name=urllib.quote("show hide deleted datasets"))
latest_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()
)
assert latest_history is not None, "Problem retrieving latest_history from database"
self.upload_file("1.bed", dbkey="hg18")
latest_hda = (
sa_session.query(galaxy.model.HistoryDatasetAssociation)
.order_by(desc(galaxy.model.HistoryDatasetAssociation.table.c.create_time))
.first()
)
self.home()
self.visit_url("%s/root/delete?show_deleted_on_refresh=False&id=%s" % (self.url, str(latest_hda.id)))
self.check_history_for_string("Your history is empty")
self.home()
self.visit_url("%s/history/?show_deleted=True" % self.url)
self.check_page_for_string("This dataset has been deleted.")
self.check_page_for_string("1.bed")
self.home()
self.visit_url("%s/history/?show_deleted=False" % self.url)
self.check_page_for_string("Your history is empty")
self.delete_history(self.security.encode_id(latest_history.id))
def get_all_installed_repositories( actually_installed=False ):
if actually_installed:
return ga_session.query( galaxy.model.ToolShedRepository ) \
.filter( and_( galaxy.model.ToolShedRepository.table.c.deleted == False,
galaxy.model.ToolShedRepository.table.c.uninstalled == False,
galaxy.model.ToolShedRepository.table.c.status == galaxy.model.ToolShedRepository.installation_status.INSTALLED ) ) \
.all()
else:
return ga_session.query( galaxy.model.ToolShedRepository ).all()
def do_it( self, testdef ):
# If the test generation had an error, raise
if testdef.error:
if testdef.exception:
raise testdef.exception
else:
raise Exception( "Test parse failure" )
# Start with a new history
self.logout()
self.login( email='*****@*****.**' )
admin_user = sa_session.query( galaxy.model.User ).filter( galaxy.model.User.table.c.email=='*****@*****.**' ).one()
self.new_history()
latest_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()
assert latest_history is not None, "Problem retrieving latest_history from database"
if len( self.get_history_as_data_list() ) > 0:
raise AssertionError("ToolTestCase.do_it failed")
# Upload any needed files
for fname, extra in testdef.required_files:
self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ) )
print "Uploaded file: ", fname, ", ftype: ", extra.get( 'ftype', 'auto' ), ", extra: ", extra
# We need to handle the case where we've uploaded a valid compressed file since the upload
# tool will have uncompressed it on the fly.
all_inputs = {}
for name, value, _ in testdef.inputs:
if value:
for end in [ '.zip', '.gz' ]:
if value.endswith( end ):
value = value.rstrip( end )
break
all_inputs[ name ] = value
# See if we have a grouping.Repeat element
repeat_name = None
for input_name, input_value in testdef.tool.inputs_by_page[0].items():
if isinstance( input_value, grouping.Repeat ):
repeat_name = input_name
break
# Do the first page
page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs)
# Run the tool
self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs )
print "page_inputs (0)", page_inputs
# Do other pages if they exist
for i in range( 1, testdef.tool.npages ):
page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[i], all_inputs)
self.submit_form( **page_inputs )
print "page_inputs (%i)" % i, page_inputs
# Check the result
assert len( testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet."
for name, file in testdef.outputs:
self.verify_dataset_correctness( file, maxseconds=testdef.maxseconds )
self.delete_history( id=self.security.encode_id( latest_history.id ) )
def test_00_metadata_edit(self):
"""test_metadata_edit: Testing metadata editing"""
self.logout()
self.login(email='*****@*****.**', username='******')
admin_user = sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.email=='*****@*****.**' ) \
.one()
self.new_history(name='Test Metadata Edit')
history1 = 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.bed')
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
.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:
sa_session.delete(dp)
sa_session.flush()
sa_session.refresh(latest_hda.dataset)
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=str(latest_hda.hid))
"""test editing attributes"""
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=str(latest_hda.hid))
"""test Auto-detecting attributes"""
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=str(latest_hda.hid))
"""test converting formats"""
self.convert_format(hda_id=str(latest_hda.id), target_type='gff')
self.check_metadata_for_string('"gff" selected="yes"',
hid=str(latest_hda.hid))
"""test changing data type"""
self.change_datatype(hda_id=str(latest_hda.id), datatype='gff3')
self.check_metadata_for_string('gff3', hid=str(latest_hda.hid))
self.delete_history(id=self.security.encode_id(history1.id))
self.logout()
def test_0050_upload_file( self ):
"""Test uploading 454Score.png, 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( '454Score.png' )
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" )
def test_0050_upload_file(self):
"""Test uploading 454Score.png, 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('454Score.png')
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")
def test_0030_upload_file( self ):
"""Test uploading 1.scf.zip, 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.scf.zip' )
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( "'File Format' for archive consisting of binary files - use 'Binseq.zip'" )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_075_deleting_and_undeleting_history_items(self):
"""Testing deleting and un-deleting history items"""
# logged in as admin_user
# Deleting the current history in the last method created a new history
latest_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()
)
assert latest_history is not None, "Problem retrieving latest_history from database"
self.rename_history(
self.security.encode_id(latest_history.id),
latest_history.name,
new_name=urllib.quote("delete undelete history items"),
)
# Add a new history item
self.upload_file("1.bed", dbkey="hg15")
latest_hda = (
sa_session.query(galaxy.model.HistoryDatasetAssociation)
.order_by(desc(galaxy.model.HistoryDatasetAssociation.table.c.create_time))
.first()
)
self.home()
self.visit_url("%s/history/?show_deleted=False" % self.url)
self.check_page_for_string("1.bed")
self.check_page_for_string("hg15")
self.assertEqual(len(self.get_history_as_data_list()), 1)
# Delete the history item
self.delete_history_item(str(latest_hda.id), check_str="Your history is empty")
self.assertEqual(len(self.get_history_as_data_list()), 0)
# Try deleting an invalid hid
try:
self.delete_history_item("XXX")
raise AssertionError, "Inproperly able to delete hda_id 'XXX' which is not an integer"
except:
pass
# Undelete the history item
self.undelete_history_item(str(latest_hda.id))
self.home()
self.visit_url("%s/history/?show_deleted=False" % self.url)
self.check_page_for_string("1.bed")
self.check_page_for_string("hg15")
self.delete_history(self.security.encode_id(latest_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_0010_upload_file( self ):
"""Test uploading 4.bed.gz, manually 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( '4.bed.gz', dbkey='hg17', ftype='bed' )
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( '4.bed', hid=str( hda.hid ) )
self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0040_upload_file( self ):
"""Test uploading 1.sff, 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.sff' )
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.sff', hid=str( hda.hid ) )
self.check_history_for_string( 'format: <span class="sff">sff' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0025_upload_file( self ):
"""Test uploading 1.scf.zip, manually 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.scf.zip', ftype='binseq.zip' )
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.scf.zip', hid=str( hda.hid ) )
self.check_history_for_string( "Archive of 1 binary sequence files</pre>" )
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 get_library( name, description, synopsis ):
return sa_session.query( galaxy.model.Library ) \
.filter( and_( galaxy.model.Library.table.c.name==name,
galaxy.model.Library.table.c.description==description,
galaxy.model.Library.table.c.synopsis==synopsis,
galaxy.model.Library.table.c.deleted==False ) ) \
.first()
def get_installed_repository_by_name_owner_changeset_revision(
name, owner, changeset_revision):
return sa_session.query( model.ToolShedRepository ) \
.filter( and_( model.ToolShedRepository.table.c.name == name,
model.ToolShedRepository.table.c.owner == owner,
model.ToolShedRepository.table.c.installed_changeset_revision == changeset_revision ) ) \
.one()
def test_0015_upload_file(self):
"""Test uploading 1.scf, manually 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.scf', ftype='scf')
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.scf', hid=str(hda.hid))
self.check_history_for_string("Binary scf sequence file</pre>")
self.delete_history(id=self.security.encode_id(history.id))
def delete_request_type_permissions( id ):
rtps = sa_session.query( galaxy.model.RequestTypePermissions ) \
.filter( and_( galaxy.model.RequestTypePermissions.table.c.request_type_id==id ) ) \
.order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) )
for rtp in rtps:
sa_session.delete( rtp )
sa_session.flush()
def test_020_create_user_as_admin( self ):
''' Testing creating users as an admin '''
self.logout()
self.login( '*****@*****.**' )
form_one = get_latest_form(form_one_name)
user_info_values=['Educational', 'Penn State', True]
self.create_user_with_info( '*****@*****.**', 'testuser', 'test13',
user_info_forms='single',
user_info_form_id=form_one.id,
user_info_values=user_info_values )
self.logout()
self.login( '*****@*****.**' )
user = sa_session.query( galaxy.model.User ) \
.filter( and_( galaxy.model.User.table.c.email=='*****@*****.**' ) ).first()
self.home()
page = "admin/users?id=%s&operation=information&f-deleted=False" % self.security.encode_id( user.id )
self.visit_page( page )
self.check_page_for_string( 'Manage User Information' )
self.check_page_for_string( '*****@*****.**' )
self.check_page_for_string( user_info_values[0] )
self.check_page_for_string( user_info_values[1] )
self.check_page_for_string( '<input type="checkbox" name="field_2" value="true" checked>' )
# lets delete the 'Student' user info form
self.login( '*****@*****.**' )
form_one_latest = get_latest_form(form_one_name)
form_one_latest.current.deleted = True
sa_session.add( form_one_latest.current )
sa_session.flush()
self.home()
self.visit_page('forms/manage?sort=create_time&f-deleted=True')
self.check_page_for_string(form_one_latest.name)
self.logout()
def get_user_address( user, short_desc ):
return sa_session.query( galaxy.model.UserAddress ) \
.filter( and_( galaxy.model.UserAddress.table.c.user_id==user.id,
galaxy.model.UserAddress.table.c.desc==short_desc,
galaxy.model.UserAddress.table.c.deleted==False ) ) \
.order_by( desc( galaxy.model.UserAddress.table.c.create_time ) ) \
.first()
def test_030_clone_shared_history(self):
"""Testing cloning a shared history"""
# logged in as admin user
self.logout()
self.login(email=regular_user1.email)
# Shared history3 affects history options
self.history_options(user=True, histories_shared_by_others=True)
# Shared history3 should be in regular_user1's list of shared histories
self.view_shared_histories(check_str=history3.name, check_str2=admin_user.email)
self.clone_history(
self.security.encode_id(history3.id),
"activatable",
check_str_after_submit="is now included in your previously stored histories.",
)
global history3_clone1
history3_clone1 = (
sa_session.query(galaxy.model.History)
.filter(
and_(
galaxy.model.History.table.c.deleted == False,
galaxy.model.History.table.c.user_id == regular_user1.id,
)
)
.order_by(desc(galaxy.model.History.table.c.create_time))
.first()
)
assert history3_clone1 is not None, "Problem retrieving history3_clone1 from database"
# Check list of histories to make sure shared history3 was cloned
check_str = "Clone of '%s' shared by '%s'" % (history3.name, admin_user.email)
self.view_stored_active_histories(check_str=check_str)
def test_0020_upload_file(self):
"""Test uploading 1.scf, 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.scf')
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(
"File Format' to 'Scf' when uploading scf files")
self.delete_history(id=self.security.encode_id(history.id))
def test_045_change_permissions_on_current_history(self):
"""Testing changing permissions on the current history"""
# Logged in as regular_user3
self.logout()
self.login(email=admin_user.email)
# Current history is history4
self.new_history()
global history5
history5 = (
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()
)
assert history5 is not None, "Problem retrieving history5 from database"
self.rename_history(self.security.encode_id(history5.id), history5.name, new_name=urllib.quote("history 5"))
# Current history is hostory5
sa_session.refresh(history5)
# 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)
sa_session.add(dhp)
sa_session.flush()
sa_session.refresh(history5)
global history5_default_permissions
history5_default_permissions = [dhp.action for dhp in history5.default_permissions]
# Sort for later comparison
history5_default_permissions.sort()
self.upload_file("1.bed", dbkey="hg18")
history5_dataset1 = None
for hda in history5.datasets:
if hda.name == "1.bed":
history5_dataset1 = hda.dataset
break
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
dataset_permissions = [a.action for a in history5_dataset1.actions]
dataset_permissions.sort()
if dataset_permissions != history5_default_permissions:
err_msg = (
"Dataset permissions for history5_dataset1 (%s) were not correctly inherited from history permissions (%s)"
% (str(dataset_permissions), str(history5_default_permissions))
)
raise AssertionError, err_msg
# Make sure when we logout and login, the history default permissions are preserved
self.logout()
self.login(email=admin_user.email)
sa_session.refresh(history5)
current_history_permissions = [dhp.action for dhp in history5.default_permissions]
current_history_permissions.sort()
if current_history_permissions != history5_default_permissions:
raise AssertionError, "With logout and login, the history default permissions are not preserved"
def get_user_address(user, short_desc):
return sa_session.query( galaxy.model.UserAddress ) \
.filter( and_( galaxy.model.UserAddress.table.c.user_id==user.id,
galaxy.model.UserAddress.table.c.desc==short_desc,
galaxy.model.UserAddress.table.c.deleted==False ) ) \
.order_by( desc( galaxy.model.UserAddress.table.c.create_time ) ) \
.first()
def get_galaxy_repository_by_name_owner_changeset_revision(
repository_name, owner, changeset_revision):
return ga_session.query( galaxy.model.ToolShedRepository ) \
.filter( and_( galaxy.model.ToolShedRepository.table.c.name == repository_name,
galaxy.model.ToolShedRepository.table.c.owner == owner,
galaxy.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
.first()
def get_library(name, description, synopsis):
return sa_session.query( galaxy.model.Library ) \
.filter( and_( galaxy.model.Library.table.c.name==name,
galaxy.model.Library.table.c.description==description,
galaxy.model.Library.table.c.synopsis==synopsis,
galaxy.model.Library.table.c.deleted==False ) ) \
.first()
def delete_request_type_permissions(id):
rtps = sa_session.query( galaxy.model.RequestTypePermissions ) \
.filter( and_( galaxy.model.RequestTypePermissions.table.c.request_type_id==id ) ) \
.order_by( desc( galaxy.model.RequestTypePermissions.table.c.create_time ) )
for rtp in rtps:
sa_session.delete(rtp)
sa_session.flush()
def test_040_sharing_mulitple_histories_with_multiple_users(self):
"""Testing sharing multiple histories containing only public datasets with multiple users"""
# Logged in as admin_user
self.new_history()
global history4
history4 = (
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()
)
assert history4 is not None, "Problem retrieving history4 from database"
self.rename_history(self.security.encode_id(history4.id), history4.name, new_name=urllib.quote("history 4"))
sa_session.refresh(history4)
self.upload_file("2.bed", dbkey="hg18")
ids = "%s,%s" % (self.security.encode_id(history3.id), self.security.encode_id(history4.id))
emails = "%s,%s" % (regular_user2.email, regular_user3.email)
self.share_histories_with_users(ids, emails, check_str1="Share 2 histories", check_str2=history4.name)
self.logout()
self.login(email=regular_user2.email)
# Shared history3 should be in regular_user2's list of shared histories
self.view_shared_histories(check_str=history3.name, check_str2=admin_user.email)
self.logout()
self.login(email=regular_user3.email)
# Shared history3 should be in regular_user3's list of shared histories
self.view_shared_histories(check_str=history3.name, check_str2=admin_user.email)
def test_0065_upload_file(self):
"""Test uploading asian_chars_1.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('asian_chars_1.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.verify_dataset_correctness('asian_chars_1.txt', hid=str(hda.hid))
self.check_history_for_string('uploaded multi-byte char file')
self.delete_history(id=self.security.encode_id(history.id))
def test_0065_upload_file( self ):
"""Test uploading asian_chars_1.txt, NOT setting the file format"""
# 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( 'asian_chars_1.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.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda.hid ) )
self.check_history_for_string( 'uploaded multi-byte char file' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0035_upload_file(self):
"""Test uploading 1.sam 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.sam')
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.sam', hid=str(hda.hid))
self.check_history_for_string(
"<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>")
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_0010_upload_file(self):
"""Test uploading 4.bed.gz, manually 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('4.bed.gz', dbkey='hg17', ftype='bed')
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('4.bed', hid=str(hda.hid))
self.check_history_for_string(
"<th>1.Chrom</th><th>2.Start</th><th>3.End</th>")
self.delete_history(id=self.security.encode_id(history.id))
def test_00_metadata_edit( self ):
"""test_metadata_edit: Testing metadata editing"""
self.logout()
self.login( email='*****@*****.**' )
admin_user = sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.email=='*****@*****.**' ) \
.one()
self.new_history( name='Test Metadata Edit' )
history1 = 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.bed' )
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
.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:
sa_session.delete( dp )
sa_session.flush()
sa_session.refresh( latest_hda.dataset )
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=str( latest_hda.hid ) )
"""test editing attributes"""
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=str( latest_hda.hid ) )
"""test Auto-detecting attributes"""
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=str( latest_hda.hid ) )
"""test converting formats"""
self.convert_format( hda_id=str( latest_hda.id ), target_type='gff' )
self.check_metadata_for_string( '"gff" selected="yes"', hid=str( latest_hda.hid ) )
"""test changing data type"""
self.change_datatype( hda_id=str( latest_hda.id ), datatype='gff3' )
self.check_metadata_for_string( 'gff3', hid=str( latest_hda.hid ) )
self.delete_history( id=self.security.encode_id( history1.id ) )
self.logout()
def test_0150_upload_file(self):
"""Test uploading 1.bam, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, 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>')
# Make sure the Bam index was created
assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam"
self.delete_history(id=self.security.encode_id(history.id))
def test_015_edit_user_info( self ):
"""Testing editing user info as a regular user"""
self.logout()
self.login( '*****@*****.**' )
user = sa_session.query( galaxy.model.User ) \
.filter( and_( galaxy.model.User.table.c.email=='*****@*****.**' ) ).first()
self.edit_login_info( new_email='*****@*****.**', new_username='******' )
self.change_password('testuser', 'new_testuser')
self.edit_user_info( ['Research', 'PSU'] )
def test_0090_upload_file( self ):
"""Test uploading qualscores.qual454, 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( 'qualscores.qual454' )
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( 'qualscores.qual454', hid=str( hda.hid ) )
self.check_history_for_string( '49 lines, format: <span class="qual454">qual454</span>, database: \?' )
self.check_metadata_for_string( 'Change data type value="qual454" selected="yes">qual454' )
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_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_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_0150_upload_file( self ):
"""Test uploading 1.bam, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, 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>' )
# Make sure the Bam index was created
assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 1.bam"
self.delete_history( id=self.security.encode_id( history.id ) )
def get_form( name ):
fdc_list = sa_session.query( galaxy.model.FormDefinitionCurrent ) \
.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted == False ) \
.order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() )
for fdc in fdc_list:
sa_session.refresh( fdc )
sa_session.refresh( fdc.latest_form )
if fdc.latest_form.name == name:
return fdc.latest_form
return None
def test_015_edit_user_info(self):
"""Testing editing user info as a regular user"""
self.logout()
self.login('*****@*****.**')
user = sa_session.query( galaxy.model.User ) \
.filter( and_( galaxy.model.User.table.c.email=='*****@*****.**' ) ).first()
self.edit_login_info(new_email='*****@*****.**',
new_username='******')
self.change_password('testuser', 'new_testuser')
self.edit_user_info(['Research', 'PSU'])
def test_0070_upload_file(self):
"""Test uploading 2gen.fastq, 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('2gen.fastq')
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('2gen.fastq', hid=str(hda.hid))
self.check_history_for_string(
'2gen.fastq format: <span class="fastq">fastq</span>, database: \? Info: uploaded fastq file'
)
self.delete_history(id=self.security.encode_id(history.id))
def get_latest_form(form_name):
fdc_list = sa_session.query( galaxy.model.FormDefinitionCurrent ) \
.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \
.order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() )
for fdc in fdc_list:
sa_session.refresh(fdc)
sa_session.refresh(fdc.latest_form)
if form_name == fdc.latest_form.name:
return fdc.latest_form
return None
def test_0155_upload_file( self ):
"""Test uploading 3.bam, which is an unsorted Bam file, 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( '3.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"
# Since 3.bam is not sorted, we cannot verify dataset correctness since the uploaded
# dataset will be sorted. However, the check below to see if the index was created is
# sufficient.
self.check_history_for_string( '<span class="bam">bam</span>' )
# Make sure the Bam index was created
assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3.bam"
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0095_upload_file( self ):
"""Test uploading 3.maf, 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( '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_0155_upload_file(self):
"""Test uploading 3.bam, which is an unsorted Bam file, 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('3.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"
# Since 3.bam is not sorted, we cannot verify dataset correctness since the uploaded
# dataset will be sorted. However, the check below to see if the index was created is
# sufficient.
self.check_history_for_string('<span class="bam">bam</span>')
# Make sure the Bam index was created
assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3.bam"
self.delete_history(id=self.security.encode_id(history.id))
def test_0005_upload_file( self ):
"""Test uploading 1.bed, NOT setting the file format"""
self.logout()
self.login( email='*****@*****.**' )
global admin_user
admin_user = sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.email=='*****@*****.**' ) \
.one()
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.bed' )
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.bed', hid=str( hda.hid ) )
self.check_history_for_string( "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>" )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_020_create_request_type( self ):
"""Testing creating a new requestype"""
request_form = get_latest_form(form_one_name)
sample_form = get_latest_form(form_two_name)
self.create_request_type(request_type_name, "test request type",
str(request_form.id), str(sample_form.id), sample_states )
global request_type
request_type = sa_session.query( galaxy.model.RequestType ) \
.filter( and_( galaxy.model.RequestType.table.c.name==request_type_name ) ) \
.order_by( desc( galaxy.model.RequestType.table.c.create_time ) ) \
.first()
assert request_type is not None, 'Problem retrieving request type named "%s" from the database' % request_type_name
def test_0090_upload_file(self):
"""Test uploading qualscores.qual454, 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('qualscores.qual454')
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('qualscores.qual454', hid=str(hda.hid))
self.check_history_for_string(
'49 lines, format: <span class="qual454">qual454</span>, database: \?'
)
self.check_metadata_for_string(
'Change data type value="qual454" selected="yes">qual454')
self.delete_history(id=self.security.encode_id(history.id))
def test_020_create_request_type(self):
"""Testing creating a new requestype"""
request_form = get_latest_form(form_one_name)
sample_form = get_latest_form(form_two_name)
self.create_request_type(request_type_name, "test request type",
str(request_form.id), str(sample_form.id),
sample_states)
global request_type
request_type = sa_session.query( galaxy.model.RequestType ) \
.filter( and_( galaxy.model.RequestType.table.c.name==request_type_name ) ) \
.order_by( desc( galaxy.model.RequestType.table.c.create_time ) ) \
.first()
assert request_type is not None, 'Problem retrieving request type named "%s" from the database' % request_type_name
def test_0005_upload_file(self):
"""Test uploading 1.bed, NOT setting the file format"""
self.logout()
self.login(email='*****@*****.**')
global admin_user
admin_user = sa_session.query( galaxy.model.User ) \
.filter( galaxy.model.User.table.c.email=='*****@*****.**' ) \
.one()
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.bed')
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.bed', hid=str(hda.hid))
self.check_history_for_string(
"<th>1.Chrom</th><th>2.Start</th><th>3.End</th>")
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_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_0160_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_030_create_request(self):
"""Testing creating, editing and submitting a request as a regular user"""
# login as a regular user
self.logout()
self.login(email='*****@*****.**')
# set field values
fields = ['option1', str(user_address.id), 'field three value']
# create the request
request_name, request_desc = 'Request One', 'Request One Description'
self.create_request(request_type.id, request_name, request_desc,
library_one.id, 'none', fields)
global request_one
request_one = sa_session.query( galaxy.model.Request ) \
.filter( and_( galaxy.model.Request.table.c.name==request_name,
galaxy.model.Request.table.c.deleted==False ) ) \
.first()
# check if the request's state is now set to 'new'
assert request_one.state is not request_one.states.NEW, "The state of the request '%s' should be set to '%s'" \
% ( request_one.name, request_one.states.NEW )
# sample fields
samples = [('Sample One', ['S1 Field 0 Value']),
('Sample Two', ['S2 Field 0 Value'])]
# add samples to this request
self.add_samples(request_one.id, request_one.name, samples)
# edit this request
fields = [
'option2',
str(user_address.id), 'field three value (edited)'
]
self.edit_request(request_one.id, request_one.name,
request_one.name + ' (Renamed)',
request_one.desc + ' (Re-described)', library_one.id,
folder_one.id, fields)
sa_session.refresh(request_one)
# check if the request is showing in the 'new' filter
self.check_request_grid(state='New', request_name=request_one.name)
# submit the request
self.submit_request(request_one.id, request_one.name)
sa_session.refresh(request_one)
# check if the request is showing in the 'submitted' filter
self.check_request_grid(state='Submitted',
request_name=request_one.name)
# check if the request's state is now set to 'submitted'
assert request_one.state is not request_one.states.SUBMITTED, "The state of the request '%s' should be set to '%s'" \
% ( request_one.name, request_one.states.SUBMITTED )