Added tool test for recursive subset of h5 keys

lib/galaxy/tools/verify/asserts/hdf5.py

@@ -31,3 +31,21 @@ def assert_has_h5_keys(output_bytes, keys):
     output_temp = io.BytesIO(output_bytes)
     local_keys = sorted(list(h5py.File(output_temp, 'r').keys()))
     assert local_keys == h5_keys, "Not a HDF5 file or H5 keys do not match:\n\t%s\n\t%s" % (local_keys, h5_keys)
+
+
+def assert_contains_h5_keys(output_bytes, keys):
+    """ Asserts the specified HDF5 output contains the given keys, including recursive group paths."""
+    _assert_h5py()
+    keys = [k.strip() for k in keys.strip().split(',')]
+    h5_keys = sorted(keys)
+    output_temp = io.BytesIO(output_bytes)
+    local_keys = []
+    def append_keys(key):
+        local_keys.append(key)
+        return None
+    h5py.File(output_temp, 'r').visit(append_keys)
+    missing = 0
+    for key in h5_keys:
+        if key not in local_keys:
+            missing += 1
+    assert missing == 0, "Not a HDF5 file or H5 keys missing:\n\t%s\n\t%s" % (local_keys, h5_keys)

lib/galaxy/tools/xsd/galaxy.xsd

@@ -1652,6 +1652,8 @@ module.
       </xs:element>
       <xs:element name="has_h5_keys" type="AssertHasH5Keys">
       </xs:element>
+      <xs:element name="contains_h5_keys" type="AssertContainsH5Keys">
+      </xs:element>
       <xs:element name="has_h5_attribute" type="AssertHasH5Attribute">
       </xs:element>
       <xs:element name="has_archive_member" type="AssertHasArchiveMember">
@@ -1668,6 +1670,16 @@ module.
       </xs:annotation>
     </xs:attribute>
   </xs:complexType>
+  <xs:complexType name="AssertContainsH5Keys">
+    <xs:annotation>
+      <xs:documentation xml:lang="en"><![CDATA[Asserts HDF5 output includes a set of attributes (``keys``) including nested attributes, specified as a comma-separated list (e.g. ``<contains_h5_keys keys="bins,resolution/chroms,indexes,pixels" />``).]]></xs:documentation>
+    </xs:annotation>
+    <xs:attribute name="keys" type="xs:string">
+      <xs:annotation>
+        <xs:documentation xml:lang="en">Comma-separated list of HDF5 attributes to check for.</xs:documentation>
+      </xs:annotation>
+    </xs:attribute>
+  </xs:complexType>
   <xs:complexType name="AssertHasH5Attribute">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[Asserts HDF5 output contains the specified ``value`` for an attribute (``key``) (e.g. ``<has_attr key="nchroms" value="15" />``).]]></xs:documentation>

lib/galaxy/web/proxy/js/lib/proxy.js

@@ -60,6 +60,7 @@ DynamicProxy.prototype.rewriteRequest = function(request) {
 DynamicProxy.prototype.targetForRequest = function(request) {
     // return proxy target for a given url
     var session = this.findSession(request);
+    console.log('Session: ', session);
     for (var mappedSession in this.sessionMap) {
         if(session == mappedSession) {
             return this.sessionMap[session].target;
@@ -70,8 +71,10 @@ DynamicProxy.prototype.targetForRequest = function(request) {
 };
 
 DynamicProxy.prototype.findSession = function(request) {
+    console.log("SessionCookie: ", this.sessionCookie);
     var sessionCookie = this.sessionCookie,
         rc = request.headers.cookie;
+    console.log('RequestCookie: ', rc);
     if(!rc) {
         return null;
     }
@@ -91,6 +94,10 @@ DynamicProxy.prototype.findSession = function(request) {
 DynamicProxy.prototype.handleProxyRequest = function(req, res) {
     var othis = this;
     var target = this.targetForRequest(req);
+    console.log(req.method);
+    console.log(req.url);
+    console.log(target.host);
+    console.log(target.port);
     if(this.debug) {
         console.log("PROXY " + req.method + " " + req.url + " to " + target.host + ':' + target.port);
     }

test/functional/tools/validation_hdf5.xml

@@ -13,7 +13,8 @@
             <param name="input" value="matrix.cool" />
             <output name="output">
                 <assert_contents>
-                    <has_h5_keys keys="bins, chroms,indexes,pixels" />
+                    <has_h5_keys keys="bins,chroms,indexes,pixels" />
+                    <contains_h5_keys keys="bins,chroms/length,chroms,name" />
                     <has_h5_attribute key="nbins" value="33754" />
                     <has_h5_attribute key="nchroms" value="15" />
                 </assert_contents>