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galaxy/test/functional/test_get_data.py
T
John Chilton 79c8f59341 Models: Introduce real class for app.model (ModelMapping). 
Shared across Tool Shed and Galaxy to reduce code duplication. Previously this was just a bunch, making it a real class allows placing some shared logic in there.

This refactoring also eliminates some global variables galaxy.model.mapping.Session, galaxy.model.mapping.context, and same for tool shed. This may break things, but these are things that should probably be fixed anyway.

In particular small changes to db_shell.py and a unit test that depended on these global variables have been updated. The functional test frameworks likewise needed to be updated to not depend on these - these changes were more substantial.

To fix these functional tests, I essentially replace old references to global variables in Galaxy with references to global variables just defined in the test framework in test/functional/database_contexts.py (a slight improvement).
2013-12-05 00:20:54 -06:00

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import galaxy.model
from galaxy.model.orm import *
from base.twilltestcase import TwillTestCase
from base.test_db_util import *
class UploadData( TwillTestCase ):
def test_0000_setup_upload_tests( self ):
"""
Configuring upload tests, setting admin_user
"""
self.logout()
self.login( email='test@bx.psu.edu' )
global admin_user
admin_user = get_user( email='test@bx.psu.edu' )
def create_fresh_history( self, user ):
"""
Deletes latest history for the given user, checks for an empty history,
and returns that new, empty history
"""
# in order to remove a lot of boiler plate - and not have cascading errors
history = get_latest_history_for_user( user )
self.delete_history( id=self.security.encode_id( history.id ) )
self.is_history_empty()
return get_latest_history_for_user( user )
def test_0005_upload_file( self ):
"""
Test uploading 1.bed, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.bed' )
hda = get_latest_hda()
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_0006_upload_file( self ):
"""
Test uploading 1.bed.spaces, with space to tab selected, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.bed.spaces', space_to_tab = True )
hda = get_latest_hda()
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_0010_upload_file( self ):
"""
Test uploading 4.bed.gz, manually setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0012_upload_file( self ):
"""
Test uploading 4.bed.bz2, manually setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '4.bed.bz2', dbkey='hg17', ftype='bed' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0015_upload_file( self ):
"""
Test uploading 1.scf, manually setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.scf', ftype='scf' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.scf', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"peek", "Binary scf sequence file", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0020_upload_file( self ):
"""
Test uploading 1.scf, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.scf' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"misc_info", "File Format' to 'Scf' when uploading scf files", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0025_upload_file( self ):
"""
Test uploading 4.bed.zip, manually setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '4.bed.zip', ftype='bed' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0030_upload_file( self ):
"""
Test uploading 4.bed.zip, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '4.bed.zip' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '4.bed', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"peek", "<th>1.Chrom</th><th>2.Start</th><th>3.End</th>", use_string_contains=True )
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
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.sam' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.sam', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"peek", "<th>1.QNAME</th><th>2.FLAG</th><th>3.RNAME</th><th>4.POS</th>", use_string_contains=True )
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
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.sff' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.sff', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"misc_info", "sff", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0045_upload_file( self ):
"""
Test uploading 454Score.pdf, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '454Score.pdf' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"name", "454Score.pdf" )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0050_upload_file( self ):
"""
Test uploading 454Score.png, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '454Score.png' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"name", "454Score.png" )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0055_upload_file( self ):
"""
Test uploading lped composite datatype file, manually setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
# lped data types include a ped_file and a map_file ( which is binary )
self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped' }, { 'name':'map_file', 'value':'tinywga.map'} ] )
# Get the latest hid for testing
hda = get_latest_hda()
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( 'tinywga.ped', str( hda.id ), base_name = 'rgenetics.ped' )
self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"metadata_base_name", "rgenetics", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0056_upload_file( self ):
"""
Test uploading lped composite datatype file, manually setting the file format, and using space to tab on one file (tinywga.ped)
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
# lped data types include a ped_file and a map_file ( which is binary )
self.upload_file( None, ftype='lped', metadata = [ { 'name':'base_name', 'value':'rgenetics' } ], composite_data = [ { 'name':'ped_file', 'value':'tinywga.ped', 'space_to_tab':True }, { 'name':'map_file', 'value':'tinywga.map'} ] )
# Get the latest hid for testing
hda = get_latest_hda()
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( 'tinywga.ped.space_to_tab', str( hda.id ), base_name = 'rgenetics.ped' )
self.verify_composite_datatype_file_content( 'tinywga.map', str( hda.id ), base_name = 'rgenetics.map' )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"metadata_base_name", "rgenetics", use_string_contains=True )
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
history = self.create_fresh_history( admin_user )
# pbed data types include a bim_file, a bed_file and a fam_file
self.upload_file( None, ftype='pbed',
metadata = [ { 'name':'base_name', 'value':'rgenetics' } ],
composite_data = [
{ 'name':'bim_file', 'value':'tinywga.bim' },
{ 'name':'bed_file', 'value':'tinywga.bed' },
{ 'name':'fam_file', 'value':'tinywga.fam' } ])
# Get the latest hid for testing
hda = get_latest_hda()
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( 'tinywga.bim', str( hda.id ), base_name = 'rgenetics.bim' )
self.verify_composite_datatype_file_content( 'tinywga.bed', str( hda.id ), base_name = 'rgenetics.bed' )
self.verify_composite_datatype_file_content( 'tinywga.fam', str( hda.id ), base_name = 'rgenetics.fam' )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"metadata_base_name", "rgenetics", use_string_contains=True )
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
history = self.create_fresh_history( admin_user )
self.upload_file( 'asian_chars_1.txt' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( 'asian_chars_1.txt', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"misc_info", "uploaded multi-byte char file", use_string_contains=True )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0070_upload_file( self ):
"""
Test uploading 2gen.fastq, NOT setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
self.upload_file( '2gen.fastq' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '2gen.fastq', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "fastq" )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0075_upload_file( self ):
"""
Test uploading 1.wig, NOT setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
self.upload_file( '1.wig' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.wig', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "wig" )
self.check_metadata_for_string( 'value="1.wig" value="\?"' )
self.check_metadata_for_string( 'Change data type selected value="wig" selected="yes"' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0080_upload_file( self ):
"""
Test uploading 1.tabular, NOT setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
self.upload_file( '1.tabular' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.tabular', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "tabular" )
self.check_metadata_for_string( 'value="1.tabular" value="\?"' )
self.check_metadata_for_string( 'Change data type selected value="tabular" selected="yes"' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0085_upload_file( self ):
"""
Test uploading qualscores.qualsolid, NOT setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
self.upload_file( 'qualscores.qualsolid' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( 'qualscores.qualsolid', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "qualsolid" )
self.check_metadata_for_string( 'Change data type value="qualsolid" selected="yes">qualsolid' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0090_upload_file( self ):
"""
Test uploading qualscores.qual454, NOT setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
self.upload_file( 'qualscores.qual454' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( 'qualscores.qual454', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "qual454" )
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_0095_upload_file( self ):
"""
Test uploading 3.maf, NOT setting the file format
"""
# Logged in as admin_user
history = self.create_fresh_history( admin_user )
self.upload_file( '3.maf' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '3.maf', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "maf" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( '1.lav' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.lav', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "lav" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( '1.interval' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.interval', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "interval" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( '5.gff3' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '5.gff3', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "gff3" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( 'html_file.txt' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ),
"misc_info", "The uploaded file contains inappropriate HTML content", use_string_contains=True )
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
Test sniffer for gff.
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '5.gff' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '5.gff', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "gff" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( '1.fasta' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.fasta', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "fasta" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( '1.customtrack' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.customtrack', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "customtrack" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( 'shrimp_cs_test1.csfasta' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( 'shrimp_cs_test1.csfasta', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "csfasta" )
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
history = self.create_fresh_history( admin_user )
self.upload_file( '1.axt' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.axt', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "axt" )
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, which is a sorted Bam file creaed by the Galaxy sam_to_bam tool, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.bam' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.bam', hid=str( hda.hid ), attributes={ 'ftype' : 'bam' } )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bam" )
# 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_0155_upload_file( self ):
"""
Test uploading 3unsorted.bam, which is an unsorted Bam file, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '3unsorted.bam' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
# Since 3unsorted.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_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bam" )
# Make sure the Bam index was created
assert hda.metadata.bam_index is not None, "Bam index was not correctly created for 3unsorted.bam"
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
history = self.create_fresh_history( admin_user )
self.upload_url_paste( 'hello world' )
self.check_history_for_exact_string( 'Pasted Entry' )
self.check_history_for_exact_string( 'hello world' )
self.upload_url_paste( u'hello world' )
self.check_history_for_exact_string( 'Pasted Entry' )
self.check_history_for_exact_string( 'hello world' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0165_upload_file( self ):
"""
Test uploading 1.pileup, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.pileup' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.pileup', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "pileup" )
self.check_metadata_for_string( 'value="1.pileup" value="\?" Change data type selected value="pileup" selected="yes"' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0170_upload_file( self ):
"""
Test uploading 1.bigbed, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.bigbed' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.bigbed', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bigbed" )
self.check_metadata_for_string( 'value="1.bigbed" value="\?" Change data type selected value="bigbed" selected="yes"' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_0175_upload_file( self ):
"""
Test uploading 1.bigwig, NOT setting the file format
"""
history = self.create_fresh_history( admin_user )
self.upload_file( '1.bigwig' )
hda = get_latest_hda()
assert hda is not None, "Problem retrieving hda from database"
self.verify_dataset_correctness( '1.bigwig', hid=str( hda.hid ) )
self.check_hda_json_for_key_value( self.security.encode_id( hda.id ), "data_type", "bigwig" )
self.check_metadata_for_string( 'value="1.bigwig" value="\?" Change data type selected value="bigwig" selected="yes"' )
self.delete_history( id=self.security.encode_id( history.id ) )
def test_9999_clean_up( self ):
self.logout()
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