#14 enabled new annotations

Due to issue with opening annotation files with "-" in the name, this doesn't quite work.

cellxgene_gateway/backend_cache.py

@@ -33,12 +33,12 @@ class BackendCache:
         contents = self.entry_list
         return [c.port for c in contents]
 
-    def check_entry(self, dataset):
+    def check_entry(self, key):
         contents = self.entry_list
         matches = [
             c
             for c in contents
-            if c.dataset == dataset and c.status != "terminated"
+            if c.key.dataset == key.dataset and c.key.annotation_file == key.annotation_file and c.status != "terminated"
         ]
 
         if len(matches) == 0:
@@ -51,13 +51,14 @@ class BackendCache:
                 "Found " + str(len(matches)) + " for " + dataset,
             )
 
-    def create_entry(self, dataset, file_path, scripts):
+    def create_entry(self, key, scripts):
         port = 8000
         existing_ports = self.get_ports()
+
         while (port in existing_ports) or is_port_in_use(port):
             port += 1
 
-        entry = CacheEntry.for_dataset(dataset, file_path, port)
+        entry = CacheEntry.for_key(key, port)
 
         background_thread = Thread(
             target=process_backend.launch,

cellxgene_gateway/cache_entry.py

@@ -15,13 +15,13 @@ from requests import get, post, put
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 from cellxgene_gateway.util import current_time_stamp
+from cellxgene_gateway.flask_util import querystring
 
 class CacheEntry:
     def __init__(
         self,
         pid,
-        dataset,
-        file_path,
+        key,
         port,
         launchtime,
         timestamp,
@@ -32,8 +32,7 @@ class CacheEntry:
         http_status,
     ):
         self.pid = pid
-        self.dataset = dataset
-        self.file_path = file_path
+        self.key = key
         self.port = port
         self.launchtime = launchtime
         self.timestamp = timestamp
@@ -44,11 +43,11 @@ class CacheEntry:
         self.http_status = http_status
 
     @classmethod
-    def for_dataset(cls, dataset, file_path, port):
+    def for_key(cls, key, port):
+
         return cls(
             None,
-            dataset,
-            file_path,
+            key,
             port,
             current_time_stamp(),
             current_time_stamp(),
@@ -93,45 +92,59 @@ class CacheEntry:
         self.status = "terminated"
 
     def serve_content(self, path):
-        dataset = self.dataset
+        dataset = self.key.dataset
 
         gateway_basepath = (
-            f"{env.external_protocol}://{env.external_host}/view/{dataset}/"
+            f"{env.external_protocol}://{env.external_host}/view/{self.key.pathpart}/"
         )
-        subpath = path[len(dataset) :]  # noqa: E203
+        subpath = path[len(self.key.pathpart) :]  # noqa: E203
 
         if len(subpath) == 0:
             r = make_response(f"Redirect to {gateway_basepath}\n", 301)
-            r.headers["location"] = gateway_basepath
+            r.headers["location"] = gateway_basepath+querystring()
             return r
 
         port = self.port
         cellxgene_basepath = f"http://127.0.0.1:{port}"
-
         headers = {}
-
-        if "accept" in request.headers:
-            headers["accept"] = request.headers["accept"]
-        if "user-agent" in request.headers:
-            headers["user-agent"] = request.headers["user-agent"]
-        if "content-type" in request.headers:
-            headers["content-type"] = request.headers["content-type"]
+        copy_headers = [
+            'accept',
+            'accept-encoding',
+            'accept-language',
+            'cache-control',
+            'connection',
+            'content-length',
+            'content-type',
+            'cookie',
+            'host',
+            'origin',
+            'pragma',
+            'referer',
+            'sec-fetch-mode',
+            'sec-fetch-site',
+            'user-agent'
+        ]
+        for h in copy_headers:
+            if h in request.headers:
+                headers[h] = request.headers[h]
+
+        full_path = cellxgene_basepath + subpath + querystring()
 
         if request.method in ["GET", "HEAD", "OPTIONS"]:
             cellxgene_response = get(
-                cellxgene_basepath + subpath, headers=headers
+                full_path, headers=headers
             )
         elif request.method == "PUT":
             cellxgene_response = put(
-                cellxgene_basepath + subpath,
+                full_path,
                 headers=headers,
-                data=request.data.decode(),
+                data=request.data,
             )
         elif request.method == "POST":
             cellxgene_response = post(
-                cellxgene_basepath + subpath,
+                full_path,
                 headers=headers,
-                data=request.data.decode(),
+                data=request.data,
             )
         else:
             raise CellxgeneException(
@@ -146,10 +159,15 @@ class CacheEntry:
         else:
             gateway_content = cellxgene_response.content
 
+        resp_headers = {}
+        for h in copy_headers:
+            if h in cellxgene_response.headers:
+                resp_headers[h] = cellxgene_response.headers[h]
+
         gateway_response = make_response(
             gateway_content,
             cellxgene_response.status_code,
-            {"Content-Type": content_type},
+            resp_headers,
         )
 
         return gateway_response

cellxgene_gateway/cache_key.py

+# 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 os
+
+from flask_api import status
+
+from cellxgene_gateway import env
+from cellxgene_gateway.cellxgene_exception import CellxgeneException
+
+# There are three kinds of CacheKey:
+# 1) somedir/dataset.h5ad: a dataset
+#    in this case, pathpart == dataset == 'somedir/dataset.h5ad'
+# 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
+#    in this case, pathpart == 'dataset_annotations/saldaal1-T5HMVBNV.csv', dataset == 'somedir/dataset.h5ad'
+# 3) somedir/dataset_annotations: an annotation directory. The corresponding h5ad must exist, but the directory may not.
+#    in this case, pathpart == 'dataset_annotations', dataset == 'somedir/dataset.h5ad'
+
+class CacheKey:
+    def __init__(self, pathpart, dataset, annotation_file):
+        self.pathpart = pathpart
+        self.dataset = dataset
+        self.annotation_file = annotation_file

cellxgene_gateway/dir_util.py

@@ -51,45 +51,8 @@ def create_dir(parent_path, dir_name):
     else:
         os.mkdir(full_path)
 
-
-def recurse_dir(path):
-    if not os.path.exists(path):
-        raise CellxgeneException(
-            "The given path does not exist.", status.HTTP_400_BAD_REQUEST
-        )
-
-    def make_entry(el):
-        full_path = os.path.join(path, el)
-        if os.path.isfile(full_path):
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "file",
-            }
-        elif os.path.isdir(full_path):
-            return {
-                "path": full_path.replace(env.cellxgene_data, ""),
-                "name": el,
-                "type": "directory",
-                "children": recurse_dir(full_path),
-            }
-        else:
-            raise CellxgeneException(
-                "Given path is neither file nor directory.",
-                status.HTTP_400_BAD_REQUEST,
-            )
-
-    return [make_entry(x) for x in os.listdir(path)]
-
-
-def render_entries(entries):
-    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
-
-
-def render_entry(entry):
-    if entry["type"] == "file":
-        url = f"/view/{entry['path'].lstrip('/')}"
-        return f"<li> <a href='{ url}'>{entry['name']}</a></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>"
+annotations_suffix = '_annotations'
+def make_h5ad(el):
+    return el[:-len(annotations_suffix)]+'.h5ad'
+def make_annotations(el):
+    return el[:-5]+annotations_suffix

cellxgene_gateway/env.py

@@ -20,6 +20,7 @@ ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 ttl = os.environ.get("GATEWAY_TTL")
 enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
+enable_annotations = os.environ.get("GATEWAY_ENABLE_ANNOTATIONS", "").lower() in ['true', '1']
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
@@ -34,6 +35,7 @@ optional_env_vars = {
     "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
     "GATEWAY_TTL": ttl,
     "GATEWAY_ENABLE_UPLOAD": enable_upload,
+    "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
 }
 
 def validate():

cellxgene_gateway/filecrawl.py

+import os
+from cellxgene_gateway import env
+from cellxgene_gateway.dir_util import make_h5ad, make_annotations, annotations_suffix
+
+def recurse_dir(path):
+    if not os.path.exists(path):
+        raise CellxgeneException(
+            "The given path does not exist.", status.HTTP_400_BAD_REQUEST
+        )
+
+    all_entries = os.listdir(path)
+    def is_h5ad(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]
+    def list_annotations(el):
+        full_path = os.path.join(path, el)
+        if not os.path.isdir(full_path):
+            entries = []
+        else:
+            entries = [{
+                "name": x[:x.index('-')] if '-' in x 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
+
+    def make_entry(el):
+        full_path = os.path.join(path, el)
+        if el in h5ad_entries:
+            return {
+                "path": full_path.replace(env.cellxgene_data, ""),
+                "name": el,
+                "type": "file",
+                "annotations": list_annotations(make_annotations(el)),
+            }
+        elif os.path.isdir(full_path) and el not in annotation_dir_entries:
+            return {
+                "path": full_path.replace(env.cellxgene_data, ""),
+                "name": el,
+                "type": "directory",
+                "children": recurse_dir(full_path),
+            }
+        else:
+            return {
+                "path": full_path,
+                "name": el,
+                "type": "neither",
+            }
+
+    return [make_entry(x) for x in os.listdir(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 render_annotations(entry):
+    if len(entry['annotations']) > 0:
+        return ' | annotations: ' + ", ".join([f"<a href='{get_url(a)}'>{a['name']}</a>" for a in entry['annotations']])
+    else:
+        return '';
+
+def render_entry(entry):
+    if entry["type"] == "file":
+        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>"
+    else:
+        return ""

cellxgene_gateway/flask_util.py

+from flask import request
+
+def querystring():
+    qs = request.query_string.decode()
+    return f'?{qs}' if len(qs) > 0 else ''

cellxgene_gateway/gateway.py

@@ -28,12 +28,13 @@ from werkzeug import secure_filename
 from cellxgene_gateway import env
 from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import create_dir, recurse_dir, render_entries, is_subdir
+from cellxgene_gateway.dir_util import create_dir, is_subdir
+from cellxgene_gateway.filecrawl import recurse_dir, render_entries
 from cellxgene_gateway.extra_scripts import get_extra_scripts
-from cellxgene_gateway.path_util import get_dataset, get_file_path
 from cellxgene_gateway.process_exception import ProcessException
 from cellxgene_gateway.prune_process_cache import PruneProcessCache
 from cellxgene_gateway.util import current_time_stamp
+from cellxgene_gateway.path_util import get_key
 
 app = Flask(__name__)
 cache = BackendCache()
@@ -73,7 +74,8 @@ def handle_invalid_process(error):
             http_status=error.http_status,
             stdout=error.stdout,
             stderr=error.stderr,
-            dataset=error.dataset,
+            dataset=error.key.dataset,
+            annotation_file=error.key.annotation_file,
         ),
         error.http_status,
     )
@@ -159,7 +161,6 @@ if env.enable_upload:
 
 @app.route("/filecrawl.html")
 def filecrawl():
-
     entries = recurse_dir(env.cellxgene_data)
     rendered_html = render_entries(entries)
     return render_template(
@@ -187,13 +188,13 @@ def do_filecrawl(path):
 entry_lock = Lock()
 @app.route("/view/<path:path>", methods=["GET", "PUT", "POST"])
 def do_view(path):
-    dataset = get_dataset(path)
-    file_path = get_file_path(dataset)
+    key = get_key(path)
+    print(f"view path={path}, dataset={key.dataset}, annotation_file= {key.annotation_file}, key={key.pathpart}")
     with entry_lock:
-        match = cache.check_entry(dataset)
+        match = cache.check_entry(key)
         if match is None:
             uascripts = get_extra_scripts()
-            match = cache.create_entry(dataset, file_path, uascripts)
+            match = cache.create_entry(key, uascripts)
 
     match.timestamp = current_time_stamp()
 
@@ -216,7 +217,8 @@ def do_GET_status():
 def do_GET_status_json():
     return json.dumps({'launchtime':app.launchtime,
     'entry_list':[{
-        'dataset': entry.dataset,
+        'dataset': entry.key.dataset,
+        'annotation_file': entry.key.annotation_file,
         'launchtime': entry.launchtime,
         'last_access': entry.timestamp,
         'status': entry.status
@@ -224,16 +226,17 @@ def do_GET_status_json():
 
 @app.route("/relaunch/<path:path>", methods=["GET"])
 def do_relaunch(path):
-    dataset = get_dataset(path)
-    match = cache.check_entry(dataset)
+    key = get_key(path)
+    match = cache.check_entry(key)
     if not match is None:
         match.terminate()
-    return redirect(url_for("do_view", path=path), code=302)
+    qs = request.query_string.decode()
+    return redirect(url_for("do_view", path=path) + (f'?{qs}' if len(qs) > 0 else ''), code=302)
 
 @app.route("/terminate/<path:path>", methods=["GET"])
 def do_terminate(path):
-    dataset = get_dataset(path)
-    match = cache.check_entry(dataset)
+    key = get_key(path)
+    match = cache.check_entry(key)
     if not match is None:
         match.terminate()
     return redirect(url_for("do_GET_status"), code=302)

cellxgene_gateway/path_util.py

@@ -13,37 +13,81 @@ from flask_api import status
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
+from cellxgene_gateway.dir_util import make_h5ad
+from cellxgene_gateway.cache_key import CacheKey
 
-
-def get_dataset(path):
+def get_key(path):
     if path == "/" or path == "":
         raise CellxgeneException(
             "No matching dataset found.", status.HTTP_404_NOT_FOUND
         )
 
     trimmed = path[:-1] if path[-1] == "/" else path
-
     try:
-        get_file_path(trimmed)
-        return trimmed
-    except CellxgeneException:
-        split = os.path.split(trimmed)
-        return get_dataset(split[0])
+        # valid paths come in three forms:
+        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):
 
+            # 2) somedir/dataset_annotations/saldaal1-T5HMVBNV.csv : an actual annotaitons file.
+            annotations_dir = os.path.split(trimmed)[0]
+            dataset = make_h5ad(annotations_dir)
+            if data_file_exists(dataset):
+                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.
+            dataset = make_h5ad(trimmed)
+            if data_file_exists(dataset):
+                return CacheKey(trimmed, dataset, '')
+    except CellxgeneException:
+        pass
+    split = os.path.split(trimmed)
+    return get_key(split[0])
 
-def validate_path(file_path):
+def validate_exists(file_path):
     if not os.path.exists(file_path):
         raise CellxgeneException(
             "File does not exist: " + file_path, status.HTTP_400_BAD_REQUEST
         )
+
+def validate_is_file(file_path):
+    validate_exists(file_path)
     if not os.path.isfile(file_path):
         raise CellxgeneException(
             "Path is not file: " + file_path, status.HTTP_400_BAD_REQUEST
         )
     return
+def validate_is_dir(file_path):
+    validate_exists(file_path)
+    if not os.path.isdir(file_path):
+        raise CellxgeneException(
+            "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
+        )
+    return
 
+def data_file_exists(dataset):
+    file_path = os.path.join(env.cellxgene_data, dataset)
+    validate_is_file(file_path)
+    return True
+def data_dir_exists(dataset):
+    file_path = os.path.join(env.cellxgene_data, dataset)
+    validate_is_dir(file_path)
+    return True
 
-def get_file_path(dataset):
+def get_file_path(key):
+    dataset = key.dataset
     file_path = os.path.join(env.cellxgene_data, dataset)
-    validate_path(file_path)
+    validate_is_file(file_path)
+    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

cellxgene_gateway/process_exception.py

@@ -15,7 +15,7 @@ class ProcessException(Exception):
         self.stdout = stdout
         self.stderr = stderr
         self.http_status = http_status
-        self.dataset = dataset
+        self.key = key
 
     @classmethod
     def from_cache_entry(cls, cache_entry):
@@ -24,5 +24,5 @@ class ProcessException(Exception):
             cache_entry.all_output,
             cache_entry.stderr,
             cache_entry.http_status,
-            cache_entry.dataset,
+            cache_entry.key,
         )

cellxgene_gateway/subprocess_backend.py

@@ -11,21 +11,30 @@ import logging
 import subprocess
 
 from flask_api import status
-
+from cellxgene_gateway.env import enable_annotations
 from cellxgene_gateway.process_exception import ProcessException
-
+from cellxgene_gateway.dir_util import make_annotations
+from cellxgene_gateway.path_util import get_file_path, get_annotation_file_path
 
 class SubprocessBackend:
     def __init__(self):
         pass
 
-    def create_cmd(self, cellxgene_loc, file_path, port, scripts):
-
+    def create_cmd(self, cellxgene_loc, file_path, port, scripts, annotation_file_path):
+        if enable_annotations and not annotation_file_path is None:
+            annotation_args_prefix = " --experimental-annotations"
+            if annotation_file_path == "":
+                annotation_args = f"{annotation_args_prefix} --experimental-annotations-output-dir {make_annotations(file_path)}"
+            else:
+                annotation_args = f"{annotation_args_prefix} --experimental-annotations-file {annotation_file_path}"
+        else:
+            annotation_args = ""
         cmd = (
             f"yes | {cellxgene_loc} launch {file_path}"
             + " --port "
             + str(port)
             + " --host 127.0.0.1"
+            + annotation_args
         )
 
         for s in scripts:
@@ -36,7 +45,7 @@ class SubprocessBackend:
     def launch(self, cellxgene_loc, scripts, cache_entry):
 
         cmd = self.create_cmd(
-            cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
+            cellxgene_loc, get_file_path(cache_entry.key), cache_entry.port, scripts, get_annotation_file_path(cache_entry.key)
         )
         logging.getLogger("cellxgene_gateway").info(f"launching {cmd}")
         process = subprocess.Popen(

cellxgene_gateway/templates/cache_status.html

@@ -29,6 +29,7 @@
           <tr>
                <th>PID</th>
                <th>dataset</th>
+               <th>annotation_file</th>
                <th>port</th>
                <th>launchtime</th>
                <th>last access</th>
@@ -42,7 +43,8 @@
 	{% for entry in entry_list %}
           <tr>
                <td>{{ entry.pid }}</td>
-               <td><a href="{{ url_for('do_view', path=entry.dataset) }}">{{ entry.dataset }}</a></td>
+               <td><a href="{{ url_for('do_view', path=entry.dataset) }}">{{ entry.key.dataset }}</a></td>
+               <td>{{ entry.key.annotation_file }}</td>