mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-28 02:58:18 +08:00
100 lines
4.6 KiB
Python
100 lines
4.6 KiB
Python
import galaxy.model
|
|
from galaxy.model.orm import *
|
|
from galaxy.model.mapping import context as sa_session
|
|
from base.twilltestcase import TwillTestCase
|
|
|
|
""" A sample analysis"""
|
|
|
|
class AnalysisDNAseHSSFlankedGenes( TwillTestCase ):
|
|
def test_get_DNAseHSS_flanked_genes( self ):
|
|
self.logout()
|
|
self.login( email='test@bx.psu.edu' )
|
|
admin_user = sa_session.query( galaxy.model.User ) \
|
|
.filter( galaxy.model.User.table.c.email=='test@bx.psu.edu' ) \
|
|
.one()
|
|
self.new_history( name='DNAseHSS_flanked_genes' )
|
|
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()
|
|
track_params = dict(
|
|
db="hg17",
|
|
hgta_group="regulation",
|
|
hgta_table="dukeDnaseCd4Sites",
|
|
hgta_track="dukeDnaseCd4Sites",
|
|
hgta_regionType="range",
|
|
position="chr22",
|
|
hgta_outputType="bed",
|
|
sendToGalaxy="1"
|
|
)
|
|
output_params = dict(
|
|
fbQual="whole",
|
|
)
|
|
# Test 1
|
|
self.run_ucsc_main( track_params, output_params )
|
|
self.wait()
|
|
self.verify_dataset_correctness('DNAseHSS.dat')
|
|
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
# Due to twill not being able to handle the permissions forms, we'll eliminate
|
|
# DefaultHistoryPermissions prior to uploading a dataset so that the permission
|
|
# form will not be displayed on ted edit attributes page.
|
|
for dp in latest_hda.dataset.actions:
|
|
sa_session.delete( dp )
|
|
sa_session.flush()
|
|
sa_session.refresh( latest_hda.dataset )
|
|
self.edit_hda_attribute_info( str( latest_hda.id ), new_name="DNAse HS" )
|
|
self.check_metadata_for_string( "DNAse HS" )
|
|
track_params = dict(
|
|
db="hg17",
|
|
hgta_group="genes",
|
|
hgta_table="knownGene",
|
|
hgta_track="knownGene",
|
|
hgta_regionType="range",
|
|
position="chr22",
|
|
hgta_outputType="bed",
|
|
sendToGalaxy="1"
|
|
)
|
|
output_params = dict(
|
|
fbQual="whole",
|
|
)
|
|
# Test 2
|
|
self.run_ucsc_main( track_params, output_params )
|
|
self.wait()
|
|
self.verify_dataset_correctness('hg17chr22KnownGenes.dat')
|
|
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
for dp in latest_hda.dataset.actions:
|
|
sa_session.delete( dp )
|
|
sa_session.flush()
|
|
sa_session.refresh( latest_hda.dataset )
|
|
self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Genes" )
|
|
self.check_metadata_for_string( "Genes" )
|
|
# Test 3
|
|
self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" )
|
|
self.wait()
|
|
self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' )
|
|
latest_hda = sa_session.query( galaxy.model.HistoryDatasetAssociation ) \
|
|
.order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ) \
|
|
.first()
|
|
for dp in latest_hda.dataset.actions:
|
|
sa_session.delete( dp )
|
|
sa_session.flush()
|
|
sa_session.refresh( latest_hda.dataset )
|
|
self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Flanks" )
|
|
self.check_metadata_for_string( "Flanks" )
|
|
# Test 4
|
|
self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none" )
|
|
self.wait()
|
|
# We cannot verify this dataset, because this tool spits out data in a non-deterministic order
|
|
#self.verify_dataset_correctness( 'joinFlanksDNAse.dat' )
|
|
# Test 5
|
|
self.run_tool( 'Filter1', input="4", cond="c17==1000" )
|
|
self.wait()
|
|
self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' )
|
|
self.delete_history( self.security.encode_id( history1.id ) )
|
|
self.logout()
|