From 8536ca4315fdf09afb546f818ab09b1e6eb23282 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 15 Dec 2014 00:20:35 -0500
Subject: [PATCH] Allow downloading index files via tool data API. This
 provides direct access to the files to admins - probably still wise to
 provide some mechanism to download a copressed archive of these files.

---
 lib/galaxy/webapps/galaxy/api/tool_data.py | 13 +++++++++++++
 lib/galaxy/webapps/galaxy/buildapp.py      |  1 +
 test/api/test_tool_data.py                 |  6 ++++++
 3 files changed, 20 insertions(+)

diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py
index 24945481dbf..7646502e624 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -1,6 +1,9 @@
+import os
+
 from galaxy import exceptions
 from galaxy import web
 from galaxy.web import _future_expose_api as expose_api
+from galaxy.web import _future_expose_api_raw as expose_api_raw
 from galaxy.web.base.controller import BaseAPIController
 
 
@@ -74,6 +77,16 @@ class ToolData( BaseAPIController ):
         """
         return self._data_table_field( id, value ).to_dict()
 
+    @web.require_admin
+    @expose_api_raw
+    def download_field_file( self, trans, id, value, path, **kwds ):
+        field_value = self._data_table_field( id, value )
+        base_dir = field_value.get_base_dir()
+        full_path = os.path.join( base_dir, path )
+        if full_path not in field_value.get_files():
+            raise exceptions.ObjectNotFound("No such path in data table field.")
+        return open(full_path, "r")
+
     def _data_table_field( self, id, value ):
         out = self._data_table(id).get_field(value)
         if out is None:
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index afae14b7d27..7015b23627a 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -171,6 +171,7 @@ def populate_api_routes( webapp, app ):
 
     webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' )
     webapp.mapper.resource( 'tool_data', 'tool_data', path_prefix='/api' )
+    webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}/files/{path:.+?}', action='download_field_file', controller="tool_data" )
     webapp.mapper.connect( '/api/tool_data/{id:.+?}/fields/{value:.+?}', action='show_field', controller="tool_data" )
     webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/')
     webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' )
diff --git a/test/api/test_tool_data.py b/test/api/test_tool_data.py
index f30d354dabc..f1f154a2eff 100644
--- a/test/api/test_tool_data.py
+++ b/test/api/test_tool_data.py
@@ -36,3 +36,9 @@ class ToolDataApiTestCase( api.ApiTestCase ):
         self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" )
         files = field[ "files" ]
         assert len( files ) == 2
+
+    def test_download_field_file(self):
+        show_field_response = self._get( "tool_data/testalpha/fields/data1/files/entry.txt", admin=True )
+        self._assert_status_code_is( show_field_response, 200 )
+        content = show_field_response.content
+        assert content == "This is data 1.", content