Merge pull request ome#2398 from bpindelski/rebased/develop/12146_all…

…_groups

CLI download looks for resources in all user groups (fix #12146). (rebased onto develop)

components/tools/OmeroPy/src/omero/clients.py

@@ -120,7 +120,7 @@ def __init__(self, args = None, id = None, \
         if id.properties == None:
             id.properties = Ice.createProperties(args)
 
-        id.properties.parseCommandLineOptions("omero", args);
+        id.properties.parseCommandLineOptions("omero", args)
         if host:
             id.properties.setProperty("omero.host", str(host))
         if not port:
@@ -175,7 +175,7 @@ def _initData(self, id):
         """
 
         if not id:
-            raise omero.ClientError("No initialization data provided.");
+            raise omero.ClientError("No initialization data provided.")
 
         # Strictly necessary for this class to work
         id.properties.setProperty("Ice.ImplicitContext", "Shared")
@@ -408,6 +408,18 @@ def getImplicitContext(self):
         """
         return self.getCommunicator().getImplicitContext()
 
+    def getContext(self, group=None):
+        """
+        Returns a copy of the implicit context's context, i.e.
+        dict(getImplicitContext().getContext()) for use as the
+        last argument to any remote method.
+        """
+        ctx = self.getImplicitContext().getContext()
+        ctx = dict(ctx)
+        if group is not None:
+            ctx["omero.group"] = str(group)
+        return ctx
+
     def getProperties(self):
         """
         Returns the active properties for this instance
@@ -504,7 +516,7 @@ def createSession(self, username=None, password=None):
                     self.__logger.warning(\
                     "%s - createSession retry: %s"% (reason, retries) )
                 try:
-                    ctx = dict(self.getImplicitContext().getContext())
+                    ctx = self.getContext()
                     ctx[omero.constants.AGENT] = self.__agent
                     if self.__ip is not None:
                         ctx[omero.constants.IP] = self.__ip
@@ -761,16 +773,23 @@ def upload(self, filename, name = None, path = None,
         return ofile
 
     def download(self, ofile, filename = None, block_size = 1024*1024, filehandle = None):
+        if not self.__sf:
+            raise omero.ClientError("No session. Use createSession first.")
+
+        # Search for objects in all groups. See #12146
+        ctx = self.getContext(group=-1)
         prx = self.__sf.createRawFileStore()
+
         try:
             if not ofile or not ofile.id:
                 raise omero.ClientError("No file to download")
-            ofile = self.__sf.getQueryService().get("OriginalFile", ofile.id.val)
+            ofile = self.__sf.getQueryService().get("OriginalFile", ofile.id.val,
+                                                    ctx)
 
             if block_size > ofile.size.val:
                 block_size = ofile.size.val
 
-            prx.setFileId(ofile.id.val)
+            prx.setFileId(ofile.id.val, ctx)
 
             size = ofile.size.val
             offset = 0
@@ -888,7 +907,7 @@ def killSession(self):
         except:
             self.__logger.warning("Cannot get session service for killSession. Using closeSession")
             self.closeSession()
-            return -1;
+            return -1
 
         count = 0
         try:
@@ -1025,7 +1044,7 @@ def _noop(self):
             pass
         def _closeSession(self):
             try:
-                self.oa.deactivate();
+                self.oa.deactivate()
             except Exception, e:
                 sys.err.write("On session closed: " + str(e))
 

components/tools/OmeroPy/src/omero/plugins/download.py

@@ -71,7 +71,8 @@ def get_file_id(self, session, value):
         query = session.getQueryService()
         if ':' not in value:
             try:
-                ofile = query.get("OriginalFile", long(value))
+                ofile = query.get("OriginalFile", long(value),
+                                  {'omero.group': '-1'})
                 return ofile.id.val
             except ValueError:
                 self.ctx.die(601, 'Invalid OriginalFile ID input')
@@ -82,7 +83,8 @@ def get_file_id(self, session, value):
         file_id = self.parse_object_id("OriginalFile", value)
         if file_id:
             try:
-                ofile = query.get("OriginalFile", file_id)
+                ofile = query.get("OriginalFile", file_id,
+                                  {'omero.group': '-1'})
             except omero.ValidationException:
                 self.ctx.die(601, 'No OriginalFile with input ID')
             return ofile.id.val
@@ -91,7 +93,7 @@ def get_file_id(self, session, value):
         fa_id = self.parse_object_id("FileAnnotation", value)
         if fa_id:
             try:
-                fa = query.get("FileAnnotation", fa_id)
+                fa = query.get("FileAnnotation", fa_id, {'omero.group': '-1'})
             except omero.ValidationException:
                 self.ctx.die(601, 'No FileAnnotation with input ID')
             return fa.getFile().id.val
@@ -106,7 +108,7 @@ def get_file_id(self, session, value):
                 " join fs.usedFiles as uf" \
                 " join uf.originalFile as f" \
                 " where i.id = :iid"
-            query_out = query.projection(sql, params)
+            query_out = query.projection(sql, params, {'omero.group': '-1'})
             if not query_out:
                 self.ctx.die(602, 'Input image has no associated Fileset')
             if len(query_out) > 1:

components/tools/OmeroPy/test/integration/clitest/test_download.py

@@ -53,6 +53,13 @@ def create_original_file(self, content):
         finally:
             rfs.close()
 
+    def setup_user_and_two_groups(self):
+        group1 = self.new_group(perms='rw----')
+        group2 = self.new_group(perms='rw----')
+        user = self.new_user()
+        self.add_groups(user, [group1, group2], owner=True)
+        return user, group1, group2
+
     @py.test.mark.parametrize(
         'bad_input',
         ['-1', 'OriginalFile:-1', 'FileAnnotation:-1', 'Image:-1'])
@@ -87,6 +94,17 @@ def testOriginalFileStdout(self, prefix, capsys):
         out, err = capsys.readouterr()
         assert out == "test"
 
+    @py.test.mark.parametrize('prefix', ['', 'OriginalFile:'])
+    def testOriginalFileMultipleGroups(self, prefix, capsys):
+        user, group1, group2 = self.setup_user_and_two_groups()
+        client = self.new_client(user=user, password="ome")
+        ofile = self.create_original_file("test")
+        self.set_context(client, group2.id.val)
+        self.args += ['%s%s' % (prefix, str(ofile.id.val)), '-']
+        self.cli.invoke(self.args, strict=True)
+        out, err = capsys.readouterr()
+        assert out == "test"
+
     # FileAnnotation tests
     # ========================================================================
     def testNonExistingFileAnnotation(self, tmpdir):
@@ -119,6 +137,19 @@ def testFileAnnotationStdout(self, capsys):
         out, err = capsys.readouterr()
         assert out == "test"
 
+    def testFileAnnotationMultipleGroups(self, capsys):
+        user, group1, group2 = self.setup_user_and_two_groups()
+        client = self.new_client(user=user, password="ome")
+        ofile = self.create_original_file("test")
+        fa = omero.model.FileAnnotationI()
+        fa.setFile(ofile)
+        fa = self.update.saveAndReturnObject(fa)
+        self.set_context(client, group2.id.val)
+        self.args += ['FileAnnotation:%s' % str(fa.id.val), '-']
+        self.cli.invoke(self.args, strict=True)
+        out, err = capsys.readouterr()
+        assert out == "test"
+
     # Image tests
     # ========================================================================
     def testNonExistingImage(self, tmpdir):
@@ -163,3 +194,20 @@ def testImageNoFileset(self, tmpdir):
         self.args += ["Image:%s" % pixels.getImage().id.val, str(tmpfile)]
         with py.test.raises(NonZeroReturnCode):
             self.cli.invoke(self.args, strict=True)
+
+    def testImageMultipleGroups(self, tmpdir):
+        user, group1, group2 = self.setup_user_and_two_groups()
+        client = self.new_client(user=user, password="ome")
+        filename = self.OmeroPy / ".." / ".." / ".." / \
+            "components" / "common" / "test" / "tinyTest.d3d.dv"
+        with open(filename) as f:
+            bytes1 = f.read()
+        pix_ids = self.import_image(filename)
+        pixels = self.query.get("Pixels", long(pix_ids[0]))
+        tmpfile = tmpdir.join('test')
+        self.set_context(client, group2.id.val)
+        self.args += ["Image:%s" % pixels.getImage().id.val, str(tmpfile)]
+        self.cli.invoke(self.args, strict=True)
+        with open(str(tmpfile)) as f:
+            bytes2 = f.read()
+        assert bytes1 == bytes2