removed trailing slash from render_annotations

.pre-commit-config.yaml

@@ -7,12 +7,6 @@ repos:
       language: system
       types: [python]
       stages: [commit]
-    - id: flake8
-      name: flake8
-      language: system
-      entry: flake8
-      types: [python]
-      stages: [commit]
     - id: black
       language_version: python3.6+
       name: black

cellxgene_gateway/cache_entry.py

@@ -8,14 +8,14 @@
 # the specific language governing permissions and limitations under the License.
 import datetime
 import logging
-from flask.helpers import url_for
+import re
-from flask.wrappers import Response
+from enum import Enum
 
 import psutil
-from enum import Enum
 from flask import make_response, render_template, request
+from flask.helpers import url_for
+from flask.wrappers import Response
 from requests import get, post, put
-import re
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
@@ -103,9 +103,7 @@ class CacheEntry:
             terminated.append(p.pid)
             p.terminate()
             psutil.wait_procs([p], callback=on_terminate)
-            logging.getLogger("cellxgene_gateway").info(
+            logging.getLogger("cellxgene_gateway").info(f"terminated {terminated}")
-                f"terminated {terminated}"
-            )
         self.status = CacheEntryStatus.terminated
 
     def rewrite_text_content(self, cellxgene_content):
@@ -182,9 +180,7 @@ class CacheEntry:
                 data=request.data,
             )
         else:
-            raise CellxgeneException(
+            raise CellxgeneException(f"Unexpected method {request.method}", 400)
-                f"Unexpected method {request.method}", 400
-            )
         content_type = cellxgene_response.headers["content-type"]
         if "text" in content_type:
             gateway_content = self.rewrite_text_content(

cellxgene_gateway/env.py

@@ -29,15 +29,11 @@ enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in [
     "true",
     "1",
 ]
-enable_annotations = os.environ.get(
+enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in [
-    "GATEWAY_ENABLE_ANNOTATIONS", ""
-).lower() in [
     "true",
     "1",
 ]
-enable_backed_mode = os.environ.get(
+enable_backed_mode = os.environ.get("GATEWAY_ENABLE_BACKED_MODE", "").lower() in [
-    "GATEWAY_ENABLE_BACKED_MODE", ""
-).lower() in [
     "true",
     "1",
 ]

cellxgene_gateway/filecrawl.py

@@ -8,14 +8,12 @@
 # the specific language governing permissions and limitations under the License.
 
 import os
-from cellxgene_gateway import env
+
-from cellxgene_gateway.dir_util import (
-    make_h5ad,
-    make_annotations,
-    annotations_suffix,
-)
 from flask import url_for
 
+from cellxgene_gateway import env
+from cellxgene_gateway.dir_util import annotations_suffix, make_annotations, make_h5ad
+
 
 def recurse_dir(path):
     if not os.path.exists(path):
@@ -45,19 +43,18 @@ def recurse_dir(path):
                     "name": x[:-13]
                     if (len(x) > 13 and x[-13] in ["-", "_"])
                     else (x[:-4] if x.endswith(".csv") else x),
-                    "path": os.path.join(full_path, x).replace(
+                    "path": os.path.join(full_path, x + "/").replace(
                         env.cellxgene_data, ""
                     ),
                 }
                 for x in sorted(os.listdir(full_path))
-                if x.endswith(".csv")
+                if x.endswith(".csv") and os.path.isfile(os.path.join(full_path, x))
-                and os.path.isfile(os.path.join(full_path, x))
             ]
         return [
             {
                 "name": "new",
                 "class": "new",
-                "path": full_path.replace(env.cellxgene_data, ""),
+                "path": full_path.replace(env.cellxgene_data, "").rstrip("/"),
             }
         ] + entries
 
@@ -92,7 +89,7 @@ def render_entries(entries):
 
 
 def get_url(entry):
-    return url_for("do_view", path=entry["path"].lstrip("/") + "/")
+    return url_for("do_view", path=entry["path"].lstrip("/"))
 
 
 def get_class(entry):
@@ -113,7 +110,7 @@ def render_annotations(entry):
 
 def render_entry(entry):
     if entry["type"] == "file":
-        return f"<li> <a href='{ get_url(entry) }'>{entry['name']}</a> {render_annotations(entry)}</li>"
+        return f"<li> <a href='{ get_url(entry) }/'>{entry['name']}</a> {render_annotations(entry)}</li>"
     elif entry["type"] == "directory":
         url = f"/filecrawl/{entry['path'].lstrip('/')}"
         return f"<li><a href='{url}'>{entry['name']}</a>{render_entries(entry['children'])}</li>"

cellxgene_gateway/gateway.py

@@ -9,8 +9,6 @@
 
 import json
 import logging
-
-# import BaseHTTPServer
 import os
 from threading import Lock, Thread
 
@@ -24,8 +22,9 @@ from flask import (
     url_for,
 )
 from flask_api import status
-from werkzeug.utils import secure_filename
 from werkzeug.middleware.proxy_fix import ProxyFix
+from werkzeug.utils import secure_filename
+
 from cellxgene_gateway import env
 from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cache_entry import CacheEntryStatus
@@ -163,11 +162,7 @@ def upload_file():
             if "file" in request.files:
                 f = request.files["file"]
                 if f and f.filename.endswith(".h5ad"):
-                    f.save(
+                    f.save(os.path.join(full_upload_path, secure_filename(f.filename)))
-                        os.path.join(
-                            full_upload_path, secure_filename(f.filename)
-                        )
-                    )
                     return redirect(url_for("filecrawl"), code=302)
                 else:
                     raise CellxgeneException(
@@ -180,21 +175,15 @@ def upload_file():
                     status.HTTP_400_BAD_REQUEST,
                 )
     else:
-        raise CellxgeneException(
+        raise CellxgeneException("Invalid directory.", status.HTTP_400_BAD_REQUEST)
-            "Invalid directory.", status.HTTP_400_BAD_REQUEST
-        )
 
     return redirect(url_for("index"), code=302)
 
 
 if env.enable_upload:
     app.add_url_rule("/make_user", "make_user", make_user, methods=["POST"])
-    app.add_url_rule(
+    app.add_url_rule("/make_subdir", "make_subdir", make_subdir, methods=["POST"])
-        "/make_subdir", "make_subdir", make_subdir, methods=["POST"]
+    app.add_url_rule("/upload_file", "upload_file", upload_file, methods=["POST"])
-    )
-    app.add_url_rule(
-        "/upload_file", "upload_file", upload_file, methods=["POST"]
-    )
 
 
 def set_no_cache(resp):

cellxgene_gateway/prune_process_cache.py

@@ -10,8 +10,7 @@
 import logging
 import time
 
-from cellxgene_gateway import env
+from cellxgene_gateway import env, util
-from cellxgene_gateway import util
 
 logger = logging.getLogger(__name__)
 
@@ -29,9 +28,7 @@ class PruneProcessCache:
     def prune(self):
         timestamp = util.current_time_stamp()
         cutoff = timestamp - self.expire_seconds
-        processes_to_delete = [
+        processes_to_delete = [p for p in self.cache.entry_list if p.timestamp < cutoff]
-            p for p in self.cache.entry_list if p.timestamp < cutoff
-        ]
         processes_to_keep = [
             p for p in self.cache.entry_list if not p.timestamp < cutoff
         ]
@@ -42,9 +39,7 @@ class PruneProcessCache:
 
         for process in processes_to_delete:
             try:
-                logger.info(
+                logger.info(f"pruning process {process.pid} ({process.key.dataset})")
-                    f"pruning process {process.pid} ({process.key.dataset})"
-                )
                 self.cache.prune(process)
             except Exception:
                 logger.exception(

cellxgene_gateway/subprocess_backend.py

@@ -11,14 +11,11 @@ import logging
 import subprocess
 
 from flask_api import status
+
 from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.dir_util import make_annotations
+from cellxgene_gateway.env import cellxgene_args, enable_annotations, enable_backed_mode
 from cellxgene_gateway.path_util import get_annotation_file_path, get_file_path
-from cellxgene_gateway.env import (
-    enable_annotations,
-    enable_backed_mode,
-    cellxgene_args,
-)
 from cellxgene_gateway.process_exception import ProcessException
 
 
@@ -26,14 +23,10 @@ class SubprocessBackend:
     def __init__(self):
         pass
 
-    def create_cmd(
+    def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
-        self, cellxgene_loc, file_path, port, scripts, annotation_file_path
-    ):
         if enable_annotations and not annotation_file_path is None:
             if annotation_file_path == "":
-                extra_args = (
+                extra_args = f" --annotations-dir {make_annotations(file_path)}"
-                    f" --annotations-dir {make_annotations(file_path)}"
-                )
             else:
                 extra_args = f" --annotations-file {annotation_file_path}"
         else: