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removed trailing slash from render_annotations

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This commit is contained in:
Alok Saldanha
2021-03-28 21:59:03 -04:00
parent 6f2b372d32
commit 5404a8b0f3
7 changed files with 30 additions and 70 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.pre-commit-config.yaml
-6
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@@ -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
+6 -10
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@@ -8,14 +8,14 @@
# the specific language governing permissions and limitations under the License.
import datetime
import logging
from flask.helpers import url_for
from flask.wrappers import Response
import re
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(
f"terminated {terminated}"
)
logging.getLogger("cellxgene_gateway").info(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(
f"Unexpected method {request.method}", 400
)
raise CellxgeneException(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
+2 -6
View File
@@ -29,15 +29,11 @@ enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in [
"true",
"1",
]
enable_annotations = os.environ.get(
"GATEWAY_ENABLE_ANNOTATIONS", ""
).lower() in [
enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in [
"true",
"1",
]
enable_backed_mode = os.environ.get(
"GATEWAY_ENABLE_BACKED_MODE", ""
).lower() in [
enable_backed_mode = os.environ.get("GATEWAY_ENABLE_BACKED_MODE", "").lower() in [
"true",
"1",
]
cellxgene_gateway/filecrawl.py
+9 -12
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@@ -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")
and os.path.isfile(os.path.join(full_path, x))
if x.endswith(".csv") 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
+6 -17
View File
@@ -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(
os.path.join(
full_upload_path, secure_filename(f.filename)
)
)
f.save(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(
"Invalid directory.", status.HTTP_400_BAD_REQUEST
)
raise CellxgeneException("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(
"/make_subdir", "make_subdir", make_subdir, methods=["POST"]
)
app.add_url_rule(
"/upload_file", "upload_file", upload_file, methods=["POST"]
)
app.add_url_rule("/make_subdir", "make_subdir", make_subdir, 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
+3 -8
View File
@@ -10,8 +10,7 @@
import logging
import time
from cellxgene_gateway import env
from cellxgene_gateway import util
from cellxgene_gateway import env, 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 = [
p for p in self.cache.entry_list if p.timestamp < cutoff
]
processes_to_delete = [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(
f"pruning process {process.pid} ({process.key.dataset})"
)
logger.info(f"pruning process {process.pid} ({process.key.dataset})")
self.cache.prune(process)
except Exception:
logger.exception(
cellxgene_gateway/subprocess_backend.py
+4 -11
View File
@@ -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(
self, cellxgene_loc, file_path, port, scripts, annotation_file_path
):
def create_cmd(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 = (
f" --annotations-dir {make_annotations(file_path)}"
)
extra_args = f" --annotations-dir {make_annotations(file_path)}"
else:
extra_args = f" --annotations-file {annotation_file_path}"
else: