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changes to the version

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Zipho Mashologu
2017-06-13 14:51:23 +02:00
parent 8731ec7646
commit 40edf26ceb
3 changed files with 44 additions and 38 deletions
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lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
+4 -1
View File
@@ -1,5 +1,8 @@
<tool id="CONVERTER_neostorezip_to_neostore" name="Convert neostore.zip files to neostore" version="1.0.0" hidden="true">
<command>unzip '$input1' -d '$output1.files_path' > $output1</command>
<command><![CDATA[
unzip '${input1.extra_files_path}/neostore_file.zip' -d '${output1.files_path}' > $output1
]]>
</command>
<inputs>
<param format="neostore.zip" name="input1" type="data" label="Choose neostore database file"/>
</inputs>
lib/galaxy/datatypes/neo4j.py
+5 -4
View File
@@ -73,7 +73,7 @@ class Neo4j(Html):
trans.log_event("Display dataset id: %s" % str(data.id))
# the target directory name
neo4j_dir_name = '/dataset_{}_files/neo4jdb'.format(
neo4j_dir_name = '/dataset_{}_files'.format(
data.dataset.id)
dir_name = str(os.path.dirname(
trans.app.object_store.get_filename(data.dataset))) + neo4j_dir_name
@@ -160,12 +160,13 @@ class Neo4jDB(Neo4j, Data):
class Neo4jDBzip(Neo4j, Data):
"""Class for neo4jDB database files."""
MetadataElement(name='reference_name', default='neostore', desc='Reference Name',
MetadataElement(name='reference_name', default='neostore_file', desc='Reference Name',
readonly=True, visible=True, set_in_upload=True, no_value='neostore')
MetadataElement(name="neostore_zip", default=None, desc="Neostore zip",
readonly=True, visible=True, set_in_upload=True, no_value=None, optional=True)
file_ext = "noestore.zip"
file_ext = "neostore.zip"
composite_type = 'auto_primary_file'
allow_datatype_change = False
def __init__(self, **kwd):
@@ -179,4 +180,4 @@ Binary.register_sniffable_binary_format(
if __name__ == '__main__':
import doctest
doctest.testmod(sys.modules[__name__])
doctest.testmod(sys.modules[__name__])
tools/data_source/upload.py
+35 -33
View File
@@ -5,6 +5,7 @@
# to be reflected in galaxy.web.controllers.tool_runner and galaxy.tools
from __future__ import print_function
import logging
import codecs
import gzip
import os
@@ -24,6 +25,7 @@ from galaxy.util import multi_byte
from galaxy.util.checkers import check_binary, check_bz2, check_gzip, check_html, check_zip
from galaxy.util.image_util import get_image_ext
log = logging.getLogger( __name__ )
try:
import bz2
@@ -343,39 +345,39 @@ def add_file( dataset, registry, json_file, output_path ):
def add_composite_file( dataset, json_file, output_path, files_path ):
if dataset.composite_files:
os.mkdir( files_path )
for name, value in dataset.composite_files.items():
value = util.bunch.Bunch( **value )
if dataset.composite_file_paths[ value.name ] is None and not value.optional:
file_err( 'A required composite data file was not provided (%s)' % name, dataset, json_file )
break
elif dataset.composite_file_paths[value.name] is not None:
dp = dataset.composite_file_paths[value.name][ 'path' ]
isurl = dp.find('://') != -1 # todo fixme
if isurl:
try:
temp_name, dataset.is_multi_byte = sniff.stream_to_file( urlopen( dp ), prefix='url_paste' )
except Exception as e:
file_err( 'Unable to fetch %s\n%s' % ( dp, str( e ) ), dataset, json_file )
return
dataset.path = temp_name
dp = temp_name
if not value.is_binary:
tmpdir = output_adjacent_tmpdir( output_path )
tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ):
sniff.convert_newlines_sep2tabs( dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
else:
sniff.convert_newlines( dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
shutil.move( dp, os.path.join( files_path, name ) )
# Move the dataset to its "real" path
shutil.move( dataset.primary_file, output_path )
# Write the job info
info = dict( type='dataset',
dataset_id=dataset.dataset_id,
stdout='uploaded %s file' % dataset.file_type )
json_file.write( dumps( info ) + "\n" )
if dataset.composite_files:
os.mkdir( files_path )
for name, value in dataset.composite_files.items():
value = util.bunch.Bunch( **value )
if dataset.composite_file_paths[ value.name ] is None and not value.optional:
file_err( 'A required composite data file was not provided (%s)' % name, dataset, json_file )
break
elif dataset.composite_file_paths[value.name] is not None:
dp = dataset.composite_file_paths[value.name][ 'path' ]
isurl = dp.find('://') != -1 # todo fixme
if isurl:
try:
temp_name, dataset.is_multi_byte = sniff.stream_to_file( urlopen( dp ), prefix='url_paste' )
except Exception as e:
file_err( 'Unable to fetch %s\n%s' % ( dp, str( e ) ), dataset, json_file )
return
dataset.path = temp_name
dp = temp_name
if not value.is_binary:
tmpdir = output_adjacent_tmpdir( output_path )
tmp_prefix = 'data_id_%s_convert_' % dataset.dataset_id
if dataset.composite_file_paths[ value.name ].get( 'space_to_tab', value.space_to_tab ):
sniff.convert_newlines_sep2tabs( dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
else:
sniff.convert_newlines( dp, tmp_dir=tmpdir, tmp_prefix=tmp_prefix )
shutil.move( dp, os.path.join( files_path, name ) )
# Move the dataset to its "real" path
shutil.move( dataset.primary_file, output_path )
# Write the job info
info = dict( type='dataset',
dataset_id=dataset.dataset_id,
stdout='uploaded %s file' % dataset.file_type )
json_file.write( dumps( info ) + "\n" )
def output_adjacent_tmpdir( output_path ):