details:
http://www.bx.psu.edu/hg/galaxy/rev/004cd81cff72
changeset: 2444:004cd81cff72
user: Greg Von Kuster <greg(a)bx.psu.edu>
date: Wed Jun 10 15:46:26 2009 -0400
description:
Fixes for test_get_data functional test script.
1 file(s) affected in this change:
test/functional/test_get_data.py
diffs (152 lines):
diff -r 08194c60c290 -r 004cd81cff72 test/functional/test_get_data.py
--- a/test/functional/test_get_data.py Wed Jun 10 12:22:49 2009 -0400
+++ b/test/functional/test_get_data.py Wed Jun 10 15:46:26 2009 -0400
@@ -1,87 +1,74 @@
+import galaxy.model
+from galaxy.model.orm import *
from base.twilltestcase import TwillTestCase
-""" Tests are executed in order, sorted by name"""
-
class UploadData( TwillTestCase ):
- def test_00_multi_upload( self ):
- """test_get_data.test_multi_upload: Testing multiple
uploads"""
- self.login()
- self.upload_file('1.bed')
- self.verify_dataset_correctness('1.bed')
- self.upload_file('2.bed', dbkey='hg17')
- self.verify_dataset_correctness('2.bed')
- self.upload_file('3.bed', dbkey='hg17', ftype='bed')
- self.verify_dataset_correctness('3.bed')
- self.upload_file('4.bed.gz', dbkey='hg17', ftype='bed')
- self.verify_dataset_correctness('4.bed')
- self.upload_file('1.scf', ftype='scf')
- self.verify_dataset_correctness('1.scf')
- self.upload_file('1.scf.zip', ftype='binseq.zip')
- self.verify_dataset_correctness('1.scf.zip')
+ def test_000_upload_files_from_disk( self ):
+ """Test uploading data files from disk"""
+ self.logout()
+ self.login( email='tst(a)bx.psu.edu' )
+ history1 = galaxy.model.History.query().order_by( desc(
galaxy.model.History.table.c.create_time ) ).first()
+ self.upload_file( '1.bed' )
+ hda1 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda1 is not None, "Problem retrieving hda1 from database"
+ self.verify_dataset_correctness( '1.bed', hid=str( hda1.hid ) )
+ self.upload_file( '2.bed', dbkey='hg17' )
+ hda2 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda2 is not None, "Problem retrieving hda2 from database"
+ self.verify_dataset_correctness( '2.bed', hid=str( hda2.hid ) )
+ self.upload_file( '3.bed', dbkey='hg17', ftype='bed' )
+ hda3 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda3 is not None, "Problem retrieving hda3 from database"
+ self.verify_dataset_correctness( '3.bed', hid=str( hda3.hid ) )
+ self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed'
)
+ hda4 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda4 is not None, "Problem retrieving hda4 from database"
+ self.verify_dataset_correctness( '4.bed', hid=str( hda4.hid ) )
+ self.upload_file( '1.scf', ftype='scf' )
+ hda5 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda5 is not None, "Problem retrieving hda5 from database"
+ self.verify_dataset_correctness( '1.scf', hid=str( hda5.hid ) )
+ self.upload_file( '1.scf.zip', ftype='binseq.zip' )
+ hda6 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda6 is not None, "Problem retrieving hda6 from database"
+ self.verify_dataset_correctness( '1.scf.zip', hid=str( hda6.hid ) )
+ self.delete_history( id=str( history1.id ) )
+ def test_005_url_paste( self ):
+ """Test url paste behavior"""
+ # Deleting the current history should have created a new history
+ self.check_history_for_string( 'Your history is empty' )
+ history2 = galaxy.model.History.query().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.delete_history_item( 1 )
- self.delete_history_item( 2 )
- self.delete_history_item( 3 )
- self.delete_history_item( 4 )
- self.delete_history_item( 5 )
- self.delete_history_item( 6 )
- self.delete_history_item( 7 )
self.upload_url_paste( u'hello world' )
self.check_history_for_string( 'Pasted Entry' )
self.check_history_for_string( 'hello world' )
- self.delete_history_item( 8 )
- def test_9999_clean_up( self ):
- self.delete_history()
- self.logout()
-
-class GetEncodeData( TwillTestCase ):
-
- def test_00_get_encode_data( self ):
- """test_get_data.test_get_encode_data"""
- self.login()
- self.run_tool('encode_import_chromatin_and_chromosomes1',
hg17=['cc.EarlyRepSeg.20051216.bed'] )
- #hg17=[ "cc.EarlyRepSeg.20051216.bed",
"cc.EarlyRepSeg.20051216.gencode_partitioned.bed",
"cc.LateRepSeg.20051216.bed",
"cc.LateRepSeg.20051216.gencode_partitioned.bed",
"cc.MidRepSeg.20051216.bed",
"cc.MidRepSeg.20051216.gencode_partitioned.bed" ] )
+ self.delete_history( id=str( history2.id ) )
+ def test_010_upload_encode_data( self ):
+ """Test uploading encode data"""
+ # Deleting the current history should have created a new history
+ self.check_history_for_string( 'Your history is empty' )
+ history3 = galaxy.model.History.query().order_by( desc(
galaxy.model.History.table.c.create_time ) ).first()
+ self.run_tool( 'encode_import_chromatin_and_chromosomes1',
hg17=['cc.EarlyRepSeg.20051216.bed'] )
self.wait()
- self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.bed', hid=1)
-
#self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.gencode_partitioned.bed',
hid=2)
- #self.verify_dataset_correctness('cc.LateRepSeg.20051216.bed', hid=3)
-
#self.verify_dataset_correctness('cc.LateRepSeg.20051216.gencode_partitioned.bed',
hid=4)
- #self.verify_dataset_correctness('cc.MidRepSeg.20051216.bed', hid=5)
-
#self.verify_dataset_correctness('cc.MidRepSeg.20051216.gencode_partitioned.bed',
hid=6)
+ hda7 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda7 is not None, "Problem retrieving hda7 from database"
+ self.verify_dataset_correctness( 'cc.EarlyRepSeg.20051216.bed', hid=str(
hda7.hid ) )
self.run_tool('encode_import_gencode1',
hg17=['gencode.CDS.20051206.bed'])
self.wait()
- self.verify_dataset_correctness('sc_3D_cds.bed', hid=2)
- self.delete_history_item( 1 )
- self.delete_history_item( 2 )
- def test_9999_clean_up( self ):
- self.delete_history()
+ hda8 = galaxy.model.HistoryDatasetAssociation.query() \
+ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time )
).first()
+ assert hda8 is not None, "Problem retrieving hda8 from database"
+ self.verify_dataset_correctness( 'sc_3D_cds.bed', hid=str( hda8.hid ) )
+ self.delete_history( id=str( history3.id ) )
+ def test_015_reset_data_for_later_test_runs( self ):
+ """Reseting data to enable later test runs to
pass"""
self.logout()
-
-class DataSources( TwillTestCase ):
-
- #def test_hbvar(self):
- # """Getting hybrid gene mutations from HbVar"""
- # #self.load_cookies("hbvar_cookie.txt")
- # self.clear_history()
- # self.run_tool('hbvar')
- # params = dict(
- # htyp="any hybrid gene",
- # )
- # self.submit_form(form=1, button="Submit Query", **params)
- # params = dict(
- # display_format="galaxy",
- # )
- # self.submit_form(form=1, button="Go", **params)
- # params = dict(
- # build="hg17",
- # )
- # self.submit_form(form=1, button="ok", **params);
- # """
- # TODO: Currently fails when using sqlite, although successful when
- # using Postgres. Upgrading our version of sqlite may fix this, but
- # confirmation is required.
- # """
- # self.verify_dataset_correctness('hbvar_hybrid_genes.dat')
- pass