fork/cellxgene-gateway
1
0
Fork 0
mirror of https://github.com/Novartis/cellxgene-gateway.git synced 2026-10-08 16:58:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

#22 blackened code

Browse Source
This commit is contained in:
Alok Saldanha
2020-08-10 17:56:32 -04:00
parent 63cdfe1953
commit bfa80f7ef8
15 changed files with 295 additions and 151 deletions
Download Patch File Download Diff File Expand all files Collapse all files
cellxgene_gateway/filecrawl.py
+49 -13
View File
@@ -9,7 +9,12 @@
import os
from cellxgene_gateway import env
from cellxgene_gateway.dir_util import make_h5ad, make_annotations, annotations_suffix
from cellxgene_gateway.dir_util import (
make_h5ad,
make_annotations,
annotations_suffix,
)
def recurse_dir(path):
if not os.path.exists(path):
@@ -18,21 +23,42 @@ def recurse_dir(path):
)
all_entries = sorted(os.listdir(path))
def is_h5ad(el):
return el.endswith('.h5ad') and os.path.isfile(os.path.join(path, el))
return el.endswith(".h5ad") and os.path.isfile(os.path.join(path, el))
h5ad_entries = [x for x in all_entries if is_h5ad(x)]
annotation_dir_entries = [x for x in all_entries if x.endswith(annotations_suffix) and make_h5ad(x) in h5ad_entries]
annotation_dir_entries = [
x
for x in all_entries
if x.endswith(annotations_suffix) and make_h5ad(x) in h5ad_entries
]
def list_annotations(el):
full_path = os.path.join(path, el)
if not os.path.isdir(full_path):
entries = []
else:
entries = [{
"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(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))]
return [{"name":'new', "class":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
entries = [
{
"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(
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))
]
return [
{
"name": "new",
"class": "new",
"path": full_path.replace(env.cellxgene_data, ""),
}
] + entries
def make_entry(el):
full_path = os.path.join(path, el)
@@ -63,16 +89,26 @@ def recurse_dir(path):
def render_entries(entries):
return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
def get_url(entry):
return f"/view/{ entry['path'].lstrip('/') }"
def get_class(entry):
return f" class='{entry['class']}'" if 'class' in entry else ''
return f" class='{entry['class']}'" if "class" in entry else ""
def render_annotations(entry):
if len(entry['annotations']) > 0:
return ' | annotations: ' + ", ".join([f"<a href='{get_url(a)}'{get_class(a)}>{a['name']}</a>" for a in entry['annotations']])
if len(entry["annotations"]) > 0:
return " | annotations: " + ", ".join(
[
f"<a href='{get_url(a)}'{get_class(a)}>{a['name']}</a>"
for a in entry["annotations"]
]
)
else:
return ''
return ""
def render_entry(entry):
if entry["type"] == "file":