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Fixes, cleanup and new functional tests for data types and upload:

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- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types
This commit is contained in:
Greg Von Kuster
2009-11-13 14:13:03 -05:00
parent 531e8043ad
commit e38e78f5e4
10 changed files with 748 additions and 648 deletions
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tools/data_source/upload.py
+23 -22
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@@ -9,6 +9,7 @@ from galaxy import eggs
# need to import model before sniff to resolve a circular import dependency
import galaxy.model
from galaxy.datatypes import sniff
from galaxy.datatypes.binary import sniffable_binary_formats, unsniffable_binary_formats
from galaxy import util
from galaxy.util.json import *
@@ -200,25 +201,29 @@ def add_file( dataset, json_file, output_path ):
ext = dataset.file_type
if not data_type:
if check_binary( dataset.path ):
if dataset.is_binary is not None:
data_type = 'binary'
ext = dataset.file_type
else:
parts = dataset.name.split( "." )
if len( parts ) > 1:
ext = parts[1].strip().lower()
if not( ext == 'ab1' or ext == 'scf' ):
file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
data_type = 'binary'
binary_ok = False
parts = dataset.name.split( "." )
if len( parts ) > 1:
ext = parts[1].strip().lower()
if ext in unsniffable_binary_formats and dataset.file_type == ext:
binary_ok = True
elif ext in unsniffable_binary_formats and dataset.file_type != ext:
err_msg = "You must manually set the 'File Format' to '%s' when uploading %s files." % ( ext.capitalize(), ext )
file_err( err_msg, dataset, json_file )
return
if not binary_ok and ext in sniffable_binary_formats:
# Sniff the file to confirm it's data type
tmp_ext = sniff.guess_ext( dataset.path )
if tmp_ext == ext:
binary_ok = True
else:
err_msg = "The content of the file does not match its type (%s)." % ext.capitalize()
file_err( err_msg, dataset, json_file )
return
if ext == 'ab1' and dataset.file_type != 'ab1':
file_err( "You must manually set the 'File Format' to 'Ab1' when uploading ab1 files.", dataset, json_file )
return
elif ext == 'scf' and dataset.file_type != 'scf':
file_err( "You must manually set the 'File Format' to 'Scf' when uploading scf files.", dataset, json_file )
return
else:
ext = 'binary'
data_type = 'binary'
if not binary_ok:
file_err( 'The uploaded file contains inappropriate content', dataset, json_file )
return
if not data_type:
# We must have a text file
if check_html( dataset.path ):
@@ -234,10 +239,6 @@ def add_file( dataset, json_file, output_path ):
else:
ext = dataset.file_type
data_type = ext
elif data_type == 'binary' and ext == 'auto':
# currently we are only sniffing sff binary files
ext = sniff.guess_ext( dataset.path )
data_type = ext
# Save job info for the framework
if ext == 'auto' and dataset.ext:
ext = dataset.ext