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Merge pull request #2819 from SANBI-SA/upload_admin_line_endings

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Functionality to allow admins to switch on/off the line endings conversion on import
This commit is contained in:
Martin Cech
2016-09-27 15:37:45 -04:00
committed by GitHub
parent 8ff8af7b24 e85cd284d0
commit aa70a97e1e
2 changed files with 34 additions and 0 deletions
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lib/galaxy/webapps/galaxy/controllers/library_common.py
+11
View File
@@ -799,6 +799,10 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
replace_id = kwd.get( 'replace_id', None )
replace_dataset = None
upload_option = kwd.get( 'upload_option', 'upload_file' )
if kwd.get( 'files_0|uni_to_posix', False ):
to_posix_lines = kwd.get( 'files_0|to_posix_lines', '' )
else:
to_posix_lines = kwd.get( 'to_posix_lines', '' )
if kwd.get( 'files_0|space_to_tab', False ):
space_to_tab = kwd.get( 'files_0|space_to_tab', '' )
else:
@@ -1027,6 +1031,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
history=history,
widgets=widgets,
template_id=template_id,
to_posix_lines=to_posix_lines,
space_to_tab=space_to_tab,
link_data_only=link_data_only,
show_deleted=show_deleted,
@@ -1143,6 +1148,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
uploaded_dataset.ext = None
uploaded_dataset.file_type = file_type
uploaded_dataset.dbkey = params.get( 'dbkey', None )
uploaded_dataset.to_posix_lines = params.get('to_posix_lines', None)
uploaded_dataset.space_to_tab = params.get( 'space_to_tab', None )
if in_folder:
uploaded_dataset.in_folder = in_folder
@@ -1269,6 +1275,10 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
replace_id = kwd.get( 'replace_id', None )
replace_dataset = None
upload_option = kwd.get( 'upload_option', 'import_from_history' )
if kwd.get( 'files_0|to_posix_lines', False ):
to_posix_lines = kwd.get( 'files_0|to_posix_lines', '' )
else:
to_posix_lines = kwd.get( 'to_posix_lines', '' )
if kwd.get( 'files_0|space_to_tab', False ):
space_to_tab = kwd.get( 'files_0|space_to_tab', '' )
else:
@@ -1442,6 +1452,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
history=history,
widgets=[],
template_id=template_id,
to_posix_lines=to_posix_lines,
space_to_tab=space_to_tab,
link_data_only=link_data_only,
show_deleted=show_deleted,
templates/webapps/galaxy/library/common/common.mako
+23
View File
@@ -267,6 +267,29 @@
</div>
</div>
<div style="clear: both"></div>
<!-- Convert from universal line endings to Posix line endings. -->
<div class="form-row">
<label>
Convert universal line endings to Posix line endings:
</label>
<div class="form-row-input">
<%
if to_posix_lines == 'true':
checked = ' checked'
else:
checked = ''
if upload_option == 'upload_file':
name = 'files_0|to_posix_lines'
else:
name = 'to_posix_lines'
uni2posix = '<input type="checkbox" name="%s" value="true"%s/>Yes' % ( name, checked )
%>
${uni2posix}
</div>
<div class="toolParamHelp" style="clear: both;">
Use this option if you need your datasets to be converted from uni to posix line endings.
</div>
</div>
<div class="form-row">
<label>Genome:</label>
<div class="form-row-input">