Merge pull request #9500 from mvdbeek/keep_status_code_on_message_exception

[20.01] Keep status code on message exception and history import/export fixes

lib/galaxy/jobs/__init__.py

@@ -1939,7 +1939,7 @@ class JobWrapper(HasResourceParameters):
         self.output_paths = [t[2] for t in results]
         self.output_hdas_and_paths = dict([(t[0], t[1:]) for t in results])
         if special:
-            false_path = dataset_path_rewriter.rewrite_dataset_path(special.dataset, 'output')
+            false_path = dataset_path_rewriter.rewrite_dataset_path(special, 'output')
             dsp = DatasetPath(special.dataset.id, special.dataset.file_name, false_path)
             self.output_paths.append(dsp)
         return self.output_paths

lib/galaxy/tools/imp_exp/imp_history_from_archive.xml

@@ -1,6 +1,9 @@
-<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history">
+<tool id="__IMPORT_HISTORY__" name="Import History" version="0.1" tool_type="import_history" profile="16.04">
   <type class="ImportHistoryTool" module="galaxy.tools"/>
   <action module="galaxy.tools.actions.history_imp_exp" class="ImportHistoryToolAction"/>
+  <requirements>
+    <requirement type="package" version="2.23.0">requests</requirement>
+  </requirements>
   <command>#from base64 import b64encode#
 python '$__tool_directory__/unpack_tar_gz_archive.py'
 '${ b64encode(str($__ARCHIVE_SOURCE__).encode('utf-8')).decode('utf-8')}'

lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py

@@ -10,7 +10,6 @@ from __future__ import print_function
 import math
 import optparse
 import os
-import sys
 import tarfile
 import tempfile
 from base64 import b64decode
@@ -26,22 +25,18 @@ def url_to_file(url, dest_file):
     """
     Transfer a file from a remote URL to a temporary file.
     """
-    try:
-        url_reader = requests.get(url, stream=True)
-        CHUNK = 10 * 1024  # 10k
-        total = 0
-        fp = open(dest_file, 'wb')
+    url_reader = requests.get(url, stream=True)
+    assert url_reader.ok, "History import failed, server returned '%s'" % url_reader.reason
+    CHUNK = 10 * 1024  # 10k
+    total = 0
+    with open(dest_file, 'wb') as fp:
         for chunk in url_reader.iter_content(chunk_size=CHUNK):
             if chunk:
                 fp.write(chunk)
                 total += CHUNK
                 if total > MAX_SIZE:
                     break
-        fp.close()
-        return dest_file
-    except Exception as e:
-        print("Exception getting file from URL: %s" % e, file=sys.stderr)
-        return None
+    return dest_file
 
 
 def check_archive(archive_file, dest_dir):
@@ -96,7 +91,4 @@ if __name__ == "__main__":
     parser.add_option('-F', '--file', dest='is_file', action="store_true", help='Source is a file.')
     parser.add_option('-e', '--encoded', dest='is_b64encoded', action="store_true", default=False, help='Source and destination dir values are base64 encoded.')
     (options, args) = parser.parse_args()
-    try:
-        main(options, args)
-    except Exception as e:
-        print("Error unpacking tar/gz archive: %s" % e, file=sys.stderr)
+    main(options, args)

lib/galaxy/web/framework/webapp.py

@@ -106,6 +106,7 @@ class WebApplication(base.WebApplication):
         if isinstance(e, MessageException):
             # In the case of a controller exception, sanitize to make sure
             # unsafe html input isn't reflected back to the user
+            trans.response.status = e.status_code
             return trans.show_message(sanitize_html(e.err_msg), e.type)
 
     def make_body_iterable(self, trans, body):