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Merge pull request 171.

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This commit is contained in:
John Chilton
2014-01-16 23:57:43 -06:00
parent 2752bc74de fb01c3cc96
commit 658ea5966c
5 changed files with 26 additions and 6 deletions
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lib/galaxy/datatypes/data.py
+2 -1
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@@ -512,13 +512,14 @@ class Data( object ):
def before_setting_metadata( self, dataset ):
"""This function is called on the dataset before metadata is set."""
dataset.clear_associated_files( metadata_safe = True )
def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, space_to_tab = False, **kwds ):
def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, to_posix_lines = True, space_to_tab = False, **kwds ):
kwds[ 'name' ] = name
kwds[ 'optional' ] = optional
kwds[ 'mimetype' ] = mimetype
kwds[ 'description' ] = description
kwds[ 'substitute_name_with_metadata' ] = substitute_name_with_metadata
kwds[ 'is_binary' ] = is_binary
kwds[ 'to_posix_lines' ] = to_posix_lines
kwds[ 'space_to_tab' ] = space_to_tab
return Bunch( **kwds )
def add_composite_file( self, name, **kwds ):
lib/galaxy/tools/actions/upload_common.py
+1
View File
@@ -332,6 +332,7 @@ def create_paramfile( trans, uploaded_datasets ):
is_binary=is_binary,
link_data_only=link_data_only,
uuid=uuid_str,
to_posix_lines=uploaded_dataset.to_posix_lines,
space_to_tab=uploaded_dataset.space_to_tab,
in_place=trans.app.config.external_chown_script is None,
path=uploaded_dataset.path )
lib/galaxy/tools/parameters/grouping.py
+11
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@@ -266,6 +266,9 @@ class UploadDataset( Group ):
name = context.get( 'NAME', None )
info = context.get( 'INFO', None )
warnings = []
to_posix_lines = False
if context.get( 'to_posix_lines', None ) not in [ "None", None, False ]:
to_posix_lines = True
space_to_tab = False
if context.get( 'space_to_tab', None ) not in [ "None", None, False ]:
space_to_tab = True
@@ -298,6 +301,7 @@ class UploadDataset( Group ):
break
if file_bunch.path:
break
file_bunch.to_posix_lines = to_posix_lines
file_bunch.space_to_tab = space_to_tab
return file_bunch, warnings
def get_filenames( context ):
@@ -307,16 +311,21 @@ class UploadDataset( Group ):
ftp_files = context['ftp_files']
name = context.get( 'NAME', None )
info = context.get( 'INFO', None )
to_posix_lines = False
if context.get( 'to_posix_lines', None ) not in [ "None", None, False ]:
to_posix_lines = True
space_to_tab = False
if context.get( 'space_to_tab', None ) not in [ "None", None, False ]:
space_to_tab = True
warnings = []
file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info )
if file_bunch.path:
file_bunch.to_posix_lines = to_posix_lines
file_bunch.space_to_tab = space_to_tab
rval.append( file_bunch )
for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ):
if file_bunch.path:
file_bunch.to_posix_lines = to_posix_lines
file_bunch.space_to_tab = space_to_tab
rval.append( file_bunch )
# look for files uploaded via FTP
@@ -390,11 +399,13 @@ class UploadDataset( Group ):
#replace sniff here with just creating an empty file
temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file( dataset ) ), prefix='upload_auto_primary_file' )
dataset.primary_file = temp_name
dataset.to_posix_lines = True
dataset.space_to_tab = False
else:
file_bunch, warnings = get_one_filename( groups_incoming[ 0 ] )
writable_files_offset = 1
dataset.primary_file = file_bunch.path
dataset.to_posix_lines = file_bunch.to_posix_lines
dataset.space_to_tab = file_bunch.space_to_tab
dataset.warnings.extend( warnings )
if dataset.primary_file is None:#remove this before finish, this should create an empty dataset
tools/data_source/upload.py
+8 -4
View File
@@ -264,10 +264,14 @@ def add_file( dataset, registry, json_file, output_path ):
if link_data_only == 'copy_files':
if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]:
in_place = False
if dataset.space_to_tab:
line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place )
else:
line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place )
# Convert universal line endings to Posix line endings, but allow the user to turn it off,
# so that is becomes possible to upload gzip, bz2 or zip files with binary data without
# corrupting the content of those files.
if dataset.to_posix_lines:
if dataset.space_to_tab:
line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place )
else:
line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place )
if dataset.file_type == 'auto':
ext = sniff.guess_ext( dataset.path, registry.sniff_order )
else:
tools/data_source/upload.xml
+4 -1
View File
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<tool name="Upload File" id="upload1" version="1.1.3" workflow_compatible="false">
<tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false">
<description>
from your computer
</description>
@@ -38,6 +38,9 @@
</param>
<param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/>
<param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>
<param name="to_posix_lines" type="select" display="checkboxes" multiple="True" label="Convert universal line endings to Posix line endings" help="Turn this option off if you upload a gzip, bz2 or zip archive which contains a binary file.">
<option value="Yes" selected="true">Yes</option>
</param>
<param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand.">
<option value="Yes">Yes</option>
</param>