refactor to allow use with console entry points

cellxgene_gateway/subprocess_backend.py

@@ -0,0 +1,71 @@
+# Copyright 2019 Novartis Institutes for BioMedical Research Inc. Licensed
+# under the Apache License, Version 2.0 (the "License"); you may not use
+# this file except in compliance with the License. You may obtain a copy
+# of the License at http://www.apache.org/licenses/LICENSE-2.0. Unless
+# required by applicable law or agreed to in writing, software distributed
+# under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES
+# OR CONDITIONS OF ANY KIND, either express or implied. See the License for
+# the specific language governing permissions and limitations under the License.
+
+import logging
+import subprocess
+
+from flask_api import status
+
+from cellxgene_gateway.process_exception import ProcessException
+
+
+class SubprocessBackend:
+    def __init__(self):
+        pass
+
+    def create_cmd(self, cellxgene_loc, file_path, port, scripts):
+
+        cmd = (
+            f"yes | {cellxgene_loc} launch {file_path}"
+            + " --port "
+            + str(port)
+            + " --host 127.0.0.1"
+        )
+
+        for s in scripts:
+            cmd += f" --scripts {s}"
+
+        return cmd
+
+    def launch(self, cellxgene_loc, scripts, cache_entry):
+
+        cmd = self.create_cmd(
+            cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
+        )
+        logging.getLogger("werkzeug").info(f"launching {cmd}")
+        process = subprocess.Popen(
+            [cmd], stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True
+        )
+
+        while True:
+            output = process.stdout.readline().decode()
+            if output == "[cellxgene] Type CTRL-C at any time to exit.\n":
+                break
+            elif output == "":
+                stderr = process.stderr.read().decode()
+                if (
+                    "Error while loading file" in stderr
+                    or "Could not open file" in stderr
+                ):
+                    message = "File was invalid."
+                    http_status = status.HTTP_400_BAD_REQUEST
+                else:
+                    message = "Cellxgene failed to launch dataset."
+                    http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
+
+                cache_entry.status = "error"
+                cache_entry.set_error(message, stderr, http_status)
+
+                raise ProcessException.from_pid_object(cache_entry)
+            else:
+                cache_entry.all_output += output
+
+        cache_entry.set_loaded(process.pid)
+
+        return