From 4262ff7673bfcd1ff68c01aa09e2ea3484a6c11a Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 15 Dec 2014 00:20:35 -0500
Subject: [PATCH] Implement a detailed break down of data table fields via API.
 Originally this approach was laid out by Kyle Ellrott in this pull request
 (https://bitbucket.org/galaxy/galaxy-central/pull-request/531/add-downloads-to-tool-data-api/diff).
 The changes to galaxy.tools.data are entirely his contribution, I only
 reworked the API and endpoint slightly and did some stylistic fixes and
 refactoring.

---
 lib/galaxy/tools/data/__init__.py          | 63 ++++++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/tool_data.py | 16 ++++++
 lib/galaxy/webapps/galaxy/buildapp.py      |  1 +
 test/api/test_tool_data.py                 |  8 +++
 4 files changed, 88 insertions(+)

diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py
index edb471dbadc..4cfc408211f 100644
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -9,7 +9,11 @@ to modify the tool configurations.
 import logging
 import os
 import os.path
+import re
 import string
+import hashlib
+
+from glob import glob
 
 from galaxy import util
 from galaxy.util.odict import odict
@@ -340,6 +344,13 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
     def get_fields( self ):
         return self.data
 
+    def get_field(self, value):
+        rval = None
+        for i in self.get_named_fields_list():
+            if i['value'] == value:
+                rval = TabularToolDataField(i)
+        return rval
+
     def get_named_fields_list( self ):
         rval = []
         named_colums = self.get_column_name_list()
@@ -580,6 +591,58 @@ class TabularToolDataTable( ToolDataTable, Dictifiable ):
         return rval
 
 
+class TabularToolDataField(Dictifiable, object):
+
+    dict_collection_visible_keys = []
+
+    def __init__(self, data):
+        self.data = data
+
+    def __getitem__(self, key):
+        return self.data[key]
+
+    def get_base_path(self):
+        return os.path.normpath(os.path.abspath( self.data['path'] ))
+
+    def get_base_dir(self):
+        path = self.get_base_path()
+        if not os.path.isdir(path):
+            path = os.path.dirname(path)
+        return path
+
+    def clean_base_dir(self, path):
+        return re.sub( "^" + self.get_base_dir() + r"/*", "", path )
+
+    def get_files(self):
+        return glob( self.get_base_path() + "*" )
+
+    def get_filesize_map(self, rm_base_dir=False):
+        out = {}
+        for path in self.get_files():
+            if rm_base_dir:
+                out[self.clean_base_dir(path)] = os.path.getsize(path)
+            else:
+                out[path] = os.path.getsize(path)
+        return out
+
+    def get_fingerprint(self):
+        sha1 = hashlib.sha1()
+        fmap = self.get_filesize_map(True)
+        for k in sorted(fmap.keys()):
+            sha1.update(k)
+            sha1.update(str(fmap[k]))
+        return sha1.hexdigest()
+
+    def to_dict(self):
+        rval = super(TabularToolDataField, self).to_dict()
+        rval['name'] = self.data['value']
+        rval['fields'] = self.data
+        rval['base_dir'] = self.get_base_dir(),
+        rval['files'] = self.get_filesize_map(True)
+        rval['fingerprint'] = self.get_fingerprint()
+        return rval
+
+
 def expand_here_template(content, here=None):
     if here and content:
         content = string.Template(content).safe_substitute( { "__HERE__": here })
diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py
index 585b9878c37..24945481dbf 100644
--- a/lib/galaxy/webapps/galaxy/api/tool_data.py
+++ b/lib/galaxy/webapps/galaxy/api/tool_data.py
@@ -64,6 +64,22 @@ class ToolData( BaseAPIController ):
 
         return data_table.remove_entry(split_values)
 
+    @web.require_admin
+    @expose_api
+    def show_field( self, trans, id, value, **kwds ):
+        """
+        GET /api/tool_data/<id>/fields/<value>
+
+        Get information about a partiular field in a tool_data table
+        """
+        return self._data_table_field( id, value ).to_dict()
+
+    def _data_table_field( self, id, value ):
+        out = self._data_table(id).get_field(value)
+        if out is None:
+            raise exceptions.ObjectNotFound("No such field %s in data table %s." % (value, id))
+        return out
+
     def _data_table( self, id ):
         try:
             return self._data_tables[id]
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 661c338be42..afae14b7d27 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:.+?}', action='show_field', controller="tool_data" )
     webapp.mapper.resource( 'dataset_collection', 'dataset_collections', path_prefix='/api/')
     webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' )
     webapp.mapper.resource( 'request', 'requests', path_prefix='/api' )
diff --git a/test/api/test_tool_data.py b/test/api/test_tool_data.py
index 60cca5dd9e8..f30d354dabc 100644
--- a/test/api/test_tool_data.py
+++ b/test/api/test_tool_data.py
@@ -28,3 +28,11 @@ class ToolDataApiTestCase( api.ApiTestCase ):
         assert first_entry[0] == "data1"
         assert first_entry[1] == "data1name"
         assert first_entry[2].endswith("test/functional/tool-data/data1/entry.txt")
+
+    def test_show_field(self):
+        show_field_response = self._get( "tool_data/testalpha/fields/data1", admin=True )
+        self._assert_status_code_is( show_field_response, 200 )
+        field = show_field_response.json()
+        self._assert_has_keys( field, "files", "name", "fields", "fingerprint", "base_dir" )
+        files = field[ "files" ]
+        assert len( files ) == 2