From 40edf26ceba2e6484e3b856cfd0487b9b728a8c4 Mon Sep 17 00:00:00 2001
From: Zipho Mashologu <zipho.m@gmail.com>
Date: Tue, 13 Jun 2017 14:51:23 +0200
Subject: [PATCH] changes to the version

---
 .../neostorezip_to_neostore_converter.xml     |  5 +-
 lib/galaxy/datatypes/neo4j.py                 |  9 +--
 tools/data_source/upload.py                   | 68 ++++++++++---------
 3 files changed, 44 insertions(+), 38 deletions(-)

diff --git a/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml b/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
index e2eb598bca9..74486fe30d4 100644
--- a/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
+++ b/lib/galaxy/datatypes/converters/neostorezip_to_neostore_converter.xml
@@ -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>
diff --git a/lib/galaxy/datatypes/neo4j.py b/lib/galaxy/datatypes/neo4j.py
index 35440ba835a..3566f2fc845 100644
--- a/lib/galaxy/datatypes/neo4j.py
+++ b/lib/galaxy/datatypes/neo4j.py
@@ -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__])
\ No newline at end of file
diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py
index 972d62c5686..f05b77df119 100644
--- a/tools/data_source/upload.py
+++ b/tools/data_source/upload.py
@@ -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 ):