diff --git a/cellxgene_gateway/filecrawl.py b/cellxgene_gateway/filecrawl.py
index 3b0234c..8ce66b7 100644
--- a/cellxgene_gateway/filecrawl.py
+++ b/cellxgene_gateway/filecrawl.py
@@ -23,7 +23,7 @@ def recurse_dir(path):
x[:-4] if x.endwith('.csv') else x),
"path": os.path.join(full_path, x).replace(env.cellxgene_data, ""),
} for x in os.listdir(full_path) if x.endswith('.csv') and os.path.isfile(os.path.join(full_path, x))]
- return [{"name":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
+ return [{"name":'new', "class":'new', "path":full_path.replace(env.cellxgene_data, "")}] + entries
def make_entry(el):
full_path = os.path.join(path, el)
@@ -56,12 +56,14 @@ def render_entries(entries):
def get_url(entry):
return f"view/{ entry['path'].lstrip('/') }"
+def get_class(entry):
+ return f" class='{entry['class']}'" if 'class' in entry else ''
def render_annotations(entry):
if len(entry['annotations']) > 0:
- return ' | annotations: ' + ", ".join([f"{a['name']}" for a in entry['annotations']])
+ return ' | annotations: ' + ", ".join([f"{a['name']}" for a in entry['annotations']])
else:
- return '';
+ return ''
def render_entry(entry):
if entry["type"] == "file":
diff --git a/cellxgene_gateway/gateway.py b/cellxgene_gateway/gateway.py
index 441cdd9..b3d34ec 100644
--- a/cellxgene_gateway/gateway.py
+++ b/cellxgene_gateway/gateway.py
@@ -17,6 +17,7 @@ import json
from flask import (
Flask,
redirect,
+ make_response,
render_template,
request,
send_from_directory,
@@ -163,11 +164,16 @@ if env.enable_upload:
def filecrawl():
entries = recurse_dir(env.cellxgene_data)
rendered_html = render_entries(entries)
- return render_template(
+ resp = make_response(render_template(
"filecrawl.html",
extra_scripts=get_extra_scripts(),
rendered_html=rendered_html,
- )
+ ))
+ resp.headers["Cache-Control"] = "no-cache, no-store, must-revalidate"
+ resp.headers["Pragma"] = "no-cache"
+ resp.headers["Expires"] = "0"
+ resp.headers['Cache-Control'] = 'public, max-age=0'
+ return resp
@app.route("/filecrawl/")
def do_filecrawl(path):
diff --git a/cellxgene_gateway/path_util.py b/cellxgene_gateway/path_util.py
index cf93d1c..08e5ccf 100644
--- a/cellxgene_gateway/path_util.py
+++ b/cellxgene_gateway/path_util.py
@@ -28,12 +28,13 @@ def get_key(path):
if trimmed.endswith('.h5ad') and data_file_exists(trimmed):
# 1) somedir/dataset.h5ad: a dataset
return CacheKey(trimmed, trimmed, None)
- elif trimmed.endswith('.csv') and data_file_exists(trimmed):
+ elif trimmed.endswith('.csv'):
- # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
+ # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotations file.
annotations_dir = os.path.split(trimmed)[0]
dataset = make_h5ad(annotations_dir)
if data_file_exists(dataset):
+ data_dir_ensure(annotations_dir)
return CacheKey(trimmed, dataset, trimmed)
elif trimmed.endswith('_annotations') and data_dir_exists(trimmed):
# 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
@@ -74,6 +75,10 @@ def data_dir_exists(dataset):
file_path = os.path.join(env.cellxgene_data, dataset)
validate_is_dir(file_path)
return True
+def data_dir_ensure(dataset):
+ file_path = os.path.join(env.cellxgene_data, dataset)
+ if not os.path.exists(file_path):
+ os.makedirs(file_path)
def get_file_path(key):
dataset = key.dataset
@@ -82,12 +87,9 @@ def get_file_path(key):
return file_path
def get_annotation_file_path(key):
- print(f"getting annotaiton_file_path for {key.annotation_file}")
if key.annotation_file is None:
return None
if key.annotation_file == '':
return ''
file_path = os.path.join(env.cellxgene_data, key.annotation_file)
- print(f"getting annotaiton_file_path for {key}, file_path {file_path}")
- validate_is_file(file_path)
return file_path
diff --git a/cellxgene_gateway/static/js/annotation.js b/cellxgene_gateway/static/js/annotation.js
new file mode 100644
index 0000000..9698a13
--- /dev/null
+++ b/cellxgene_gateway/static/js/annotation.js
@@ -0,0 +1,21 @@
+// neandertal javascript
+const new_annotation_callback = (() =>{
+ const chars = "ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789";
+ const pickn = (c, n) => n==0?'':c.substr(Math.random()*c.length,1) + pickn(c,n-1);
+ const suffix = `_${pickn(chars,8)}.csv`;
+ return (e) => {
+ e.preventDefault();
+ const el = $(e.target);
+ const href = el.attr('href');
+ const base = prompt(`Name your annotations collection\nnote: the suffix "${suffix}" will be appended`);
+ if (base !== null && base.length > 0) {
+ if (/^[0-9a-zA-Z_]+$/.test(base)) {
+ window.location = `${href}/${base}${suffix}`;
+ } else {
+ alert("Error: name must match ^[0-9a-zA-Z_]+$\nthat is, only numbers, letters and underscore are allowed")
+ }
+ }
+ return false;
+ }
+})()
+
diff --git a/cellxgene_gateway/templates/filecrawl.html b/cellxgene_gateway/templates/filecrawl.html
index a6a5948..7d59e34 100644
--- a/cellxgene_gateway/templates/filecrawl.html
+++ b/cellxgene_gateway/templates/filecrawl.html
@@ -16,7 +16,8 @@
{% for script in extra_scripts %}
- {% endfor %}
+ {% endfor %}
+
@@ -41,5 +42,10 @@
homepage
+