#9 only prune entries that have a pid

.gitignore

@@ -136,6 +136,3 @@ dmypy.json
 .pyre/
 
 # End of https://www.gitignore.io/api/python
-
-*.patch
-.vscode

.travis.yml

@@ -1,41 +0,0 @@
-# This is necessary for nxviz as matplotlib is involved.
-# before_script:
-#   - "export DISPLAY=:99.0"
-#   - "sh -e /etc/init.d/xvfb start"
-#   - sleep 5 # give xvfb some time to start
-
-language: python
-matrix:
-  include:
-    - python: 3.5 # we don't actually use this
-      env: PYTHON_VERSION=3.7
-
-install:
-  # We do this conditionally because it saves us some downloading if the
-  # version is the same.
-  - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-  - bash miniconda.sh -b -p $HOME/miniconda
-  - export PATH="$HOME/miniconda/bin:$PATH"
-  - hash -r
-  - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
-  - conda config --add channels conda-forge
-
-  # Useful for debugging any issues with conda
-  - conda info -a
-
-  # Install Python, py.test, and required packages.
-  - conda env create -f environment.yml
-  - source activate cellxgene-gateway
-  - python setup.py install
-
-script:
-  # Your test script goes here
-  - black -l 79 . --check
-  - python -m unittest discover tests
-
-after_success:
-  - bash <(curl -s https://codecov.io/bash)
-
-notifications:
-  email: true

Changelog.md

@@ -1,17 +0,0 @@
-# 0.2.2
-
-  * Fixed bug with annotations (missing annotation.js asset)
-
-# 0.2.1
-
-  * Minor fixes to enable cellxgene 0.16.0
-  * Added CELLXGENE_ARGS to enable passing additional arguments to cellxgene
-  * added metadata/ip_address endpoint
-
-# 0.2.0
-
-Incrementing minor version since the changes for 0.15 are breaking, and we may want to release bugfixes from 0.1.0 branch.
-
-# 0.1.1
-
-Added support for cellxgene 0.15

Readme.md

@@ -30,7 +30,7 @@ Note: you may need to downgrade h5py with `pip install h5py==2.9.0` due to an [i
 ### Option 2: Install from PyPI
 
 ```bash
-pip install cellxgene-gateway
+# NOT YET DONE, COMING! STAY TUNED
 ```
 
 ## Running cellxgene gateway
@@ -39,7 +39,7 @@ pip install cellxgene-gateway
 
 ```bash
 mkdir ../cellxgene_data
-wget https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
+wget https://github.com/chanzuckerberg/cellxgene/raw/master/example-dataset/pbmc3k.h5ad -O ../cellxgene_data/pbmc3k.h5ad
 ```
 
 
@@ -48,6 +48,9 @@ wget https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-d
 ```bash
 export CELLXGENE_DATA=../cellxgene_data  # change this directory if you put data in a different place.
 export CELLXGENE_LOCATION=`which cellxgene`
+export GATEWAY_HOST=localhost:5005
+export GATEWAY_PROTOCOL=http
+export GATEWAY_IP=127.0.0.1
 ```
 
 3. Now, execute the cellxgene gateway:
@@ -59,21 +62,13 @@ cellxgene-gateway
 Here's what the environment variables mean:
 
 * `CELLXGENE_LOCATION` - the location of the cellxgene executable, e.g. `~/anaconda2/envs/cellxgene/bin/cellxgene`
-
-At least one of the following is required:
 * `CELLXGENE_DATA` - a directory that can contain subdirectories with `.h5ad` data files, *without* trailing slash, e.g. `/mnt/cellxgene_data`
-* `CELLXGENE_BUCKET` - an s3 bucket that can contain keys with `.h5ad` data files, e.g. `my-cellxgene-data-bucket`
+* `GATEWAY_HOST` - the hostname and port that the gateway will run on, typically `localhost:5005` if running locally
-Cellxgene Gateway is designed to make it easy to add additional data sources, please see the source code for gateway.py and the ItemSource interface in items/item_source.py
+* `GATEWAY_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy.
-
+* `GATEWAY_IP` - ip addess of instance gateway is running on, mostly used to display SSH instructions
 Optional environment variables:
-* `CELLXGENE_ARGS` - catch-all variable that can be used to pass additional command line args to cellxgene server
-* `EXTERNAL_HOST` - the hostname and port from the perspective of the web browser, typically `localhost:5005` if running locally. Defaults to "localhost:{GATEWAY_PORT}"
-* `EXTERNAL_PROTOCOL` - typically http when running locally, can be https when deployed if the gateway is behind a load balancer or reverse proxy that performs https termination. Default value "http"
-* `GATEWAY_IP` - ip addess of instance gateway is running on, mostly used to display SSH instructions. Defaults to `socket.gethostbyname(socket.gethostname())`
-* `GATEWAY_PORT` - local port that the gateway should bind to, defaults to 5005
 * `GATEWAY_EXTRA_SCRIPTS` - JSON array of script paths, will be embedded into each page and forwarded with `--scripts` to cellxgene server
-* `GATEWAY_ENABLE_ANNOTATIONS` - Set to `true` or to `1` to enable cellxgene annotations. 
+* `GATEWAY_ENABLE_UPLOAD` - Set to `true` or `1` to enable HTTP uploads. This is not recommended for a public server.
-* `GATEWAY_ENABLE_BACKED_MODE` - Set to `true` or to `1` to load AnnData in file-backed mode. This saves memory and speeds up launch time but may reduce overall performance.  
 
 The defaults should be fine if you set up a venv and cellxgene_data folder as above.
 
@@ -119,8 +114,6 @@ For convenience, the code repo includes a `run.sh.example` shell script to run t
 
 ## Running Tests
 
-[![Build Status](https://travis-ci.org/Novartis/cellxgene-gateway.svg?branch=master)](https://travis-ci.org/Novartis/cellxgene-gateway)
-
 ```bash
     python -m unittest discover tests
 ```
@@ -130,8 +123,9 @@ For convenience, the code repo includes a `run.sh.example` shell script to run t
 pip install isort flake8 black
 
 ```bash
-isort -rc . # rc means recursive, and was deprecated in dev version of isort
+isort -rc .
-black .
+flake8 .
+black -l 79 .
 ```
 
 # Getting Help

cellxgene_gateway/__init__.py

@@ -6,5 +6,3 @@
 # 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.
-
-__version__ = "0.2.2"

cellxgene_gateway/backend_cache.py

@@ -13,21 +13,17 @@ from threading import Thread
 from flask_api import status
 
 from cellxgene_gateway import env
-from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
+from cellxgene_gateway.cache_entry import CacheEntry
-from cellxgene_gateway.cache_key import CacheKey
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
 from cellxgene_gateway.subprocess_backend import SubprocessBackend
-from typing import List
 
 process_backend = SubprocessBackend()
 
 
 def is_port_in_use(port):
     import socket
-
     with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
-        return s.connect_ex(("localhost", port)) == 0
+        return s.connect_ex(('localhost', port)) == 0
-
 
 class BackendCache:
     def __init__(self):
@@ -37,14 +33,12 @@ class BackendCache:
         contents = self.entry_list
         return [c.port for c in contents]
 
-    def check_path(self, source, path):
+    def check_entry(self, dataset):
         contents = self.entry_list
         matches = [
             c
             for c in contents
-            if c.key.source.name == source.name
+            if c.dataset == dataset and c.status != "terminated"
-            and path.startswith(c.key.descriptor)
-            and c.status != CacheEntryStatus.terminated
         ]
 
         if len(matches) == 0:
@@ -54,35 +48,16 @@ class BackendCache:
         else:
             raise CellxgeneException(
                 status.HTTP_500_INTERNAL_SERVER_ERROR,
-                "Found " + str(len(matches)) + " for " + path,
+                "Found " + str(len(matches)) + " for " + dataset,
             )
 
-    def check_entry(self, key):
+    def create_entry(self, dataset, file_path, scripts):
-        contents = self.entry_list
-        matches = [
-            c
-            for c in contents
-            if c.key.equals(key) and c.status != CacheEntryStatus.terminated
-        ]
-
-        if len(matches) == 0:
-            return None
-        elif len(matches) == 1:
-            return matches[0]
-        else:
-            raise CellxgeneException(
-                status.HTTP_500_INTERNAL_SERVER_ERROR,
-                "Found " + str(len(matches)) + " for " + key.dataset,
-            )
-
-    def create_entry(self, key: CacheKey, scripts: List[str]):
         port = 8000
         existing_ports = self.get_ports()
-
         while (port in existing_ports) or is_port_in_use(port):
             port += 1
 
-        entry = CacheEntry.for_key(key, port)
+        entry = CacheEntry.for_dataset(dataset, file_path, port)
 
         background_thread = Thread(
             target=process_backend.launch,

cellxgene_gateway/cache_entry.py

@@ -6,45 +6,34 @@
 # 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 datetime
-import logging
-import urllib.parse
-from enum import Enum
-
 import psutil
-from flask import make_response, render_template, request
+import logging
+
+from flask import make_response, request
 from requests import get, post, put
-import re
 
 from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.flask_util import querystring
 from cellxgene_gateway.util import current_time_stamp
 
-
-class CacheEntryStatus(Enum):
-    loaded = "loaded"
-    loading = "loading"
-    error = "error"
-    terminated = "terminated"
-
-
 class CacheEntry:
     def __init__(
         self,
         pid,
-        key,
+        dataset,
+        file_path,
         port,
         launchtime,
         timestamp,
-        status: CacheEntryStatus,
+        status,
         message,
         all_output,
         stderr,
         http_status,
     ):
         self.pid = pid
-        self.key = key
+        self.dataset = dataset
+        self.file_path = file_path
         self.port = port
         self.launchtime = launchtime
         self.timestamp = timestamp
@@ -55,34 +44,30 @@ class CacheEntry:
         self.http_status = http_status
 
     @classmethod
-    def for_key(cls, key, port):
+    def for_dataset(cls, dataset, file_path, port):
-
         return cls(
             None,
-            key,
+            dataset,
+            file_path,
             port,
             current_time_stamp(),
             current_time_stamp(),
-            CacheEntryStatus.loading,
+            "loading",
             None,
             None,
             None,
             None,
         )
 
-    @property
-    def source_name(self):
-        return self.key.source_name
-
     def set_loaded(self, pid):
         self.pid = pid
-        self.status = CacheEntryStatus.loaded
+        self.status = "loaded"
 
     def set_error(self, message, stderr, http_status):
         self.message = message
         self.stderr = stderr
         self.http_status = http_status
-        self.status = CacheEntryStatus.error
+        self.status = "error"
 
     def append_output(self, output):
         if self.all_output == None:
@@ -92,105 +77,61 @@ class CacheEntry:
 
     def terminate(self):
         pid = self.pid
-        if pid != None and self.status != CacheEntryStatus.terminated:
+        if pid != None and self.status != "terminated":
             terminated = []
-
             def on_terminate(p):
                 terminated.append(p.pid)
-
             p = psutil.Process(pid)
             children = p.children()
             for child in children:
                 child.terminate()
             psutil.wait_procs(children, callback=on_terminate)
-            # the parent process may automatically die once its children have --
+            terminated.append(p.pid)
-            try:
+            p.terminate()
-                p.terminate()
+            psutil.wait_procs([p], callback=on_terminate)
-                psutil.wait_procs([p], callback=on_terminate)
+            logging.getLogger("cellxgene_gateway").info(f"terminated {terminated}")
-            except psutil.NoSuchProcess:
+        self.status = "terminated"
-                pass
-
-            logging.getLogger("cellxgene_gateway").info(
-                f"terminated {terminated}"
-            )
-        self.status = CacheEntryStatus.terminated
-
-    def rewrite_text_content(self, cellxgene_content):
-        # for v0.16.0 compatibility, see issue #24
-        gateway_content = (
-            re.sub(
-                '(="|\()/static/',
-                f"\\1{self.gateway_basepath()}static/",
-                cellxgene_content,
-            )
-            .replace("http://fonts.gstatic.com", "https://fonts.gstatic.com")
-            .replace(self.cellxgene_basepath(), self.gateway_basepath())
-        )
-        return gateway_content
-
-    def gateway_basepath(self):
-        source_path = (
-            f"/source/{urllib.parse.quote_plus(self.source_name)}"
-            if self.source_name
-            else ""
-        )
-        return f"{env.external_protocol}://{env.external_host}{source_path}/view/{self.key.descriptor}/"
-
-    def cellxgene_basepath(self):
-        return f"http://127.0.0.1:{self.port}"
 
     def serve_content(self, path):
-        gateway_basepath = self.gateway_basepath()
+        dataset = self.dataset
-        subpath = path[len(self.key.descriptor) :]  # noqa: E203
+
+        gateway_basepath = (
+            f"{env.gateway_protocol}://{env.gateway_host}/view/{dataset}/"
+        )
+        subpath = path[len(dataset) :]  # noqa: E203
+
         if len(subpath) == 0:
             r = make_response(f"Redirect to {gateway_basepath}\n", 301)
-            r.headers["location"] = gateway_basepath + querystring()
+            r.headers["location"] = gateway_basepath
             return r
-        elif self.status == CacheEntryStatus.loading:
+
-            launch_time = datetime.datetime.fromtimestamp(self.launchtime)
+        port = self.port
-            return render_template(
+        cellxgene_basepath = f"http://127.0.0.1:{port}"
-                "loading.html",
-                launchtime=launch_time,
-                all_output=self.all_output,
-            )
 
         headers = {}
-        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 = self.cellxgene_basepath() + subpath + querystring()
+        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"]
 
         if request.method in ["GET", "HEAD", "OPTIONS"]:
-            cellxgene_response = get(full_path, headers=headers)
+            cellxgene_response = get(
+                cellxgene_basepath + subpath, headers=headers
+            )
         elif request.method == "PUT":
             cellxgene_response = put(
-                full_path,
+                cellxgene_basepath + subpath,
                 headers=headers,
-                data=request.data,
+                data=request.data.decode(),
             )
         elif request.method == "POST":
             cellxgene_response = post(
-                full_path,
+                cellxgene_basepath + subpath,
                 headers=headers,
-                data=request.data,
+                data=request.data.decode(),
             )
         else:
             raise CellxgeneException(
@@ -198,20 +139,17 @@ class CacheEntry:
             )
         content_type = cellxgene_response.headers["content-type"]
         if "text" in content_type:
-            gateway_content = self.rewrite_text_content(
+            cellxgene_content = cellxgene_response.content.decode()
-                cellxgene_response.content.decode()
+            gateway_content = cellxgene_content.replace(
-            )
+                "http://fonts.gstatic.com", "https://fonts.gstatic.com"
+            ).replace(cellxgene_basepath, gateway_basepath)
         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,
-            resp_headers,
+            {"Content-Type": content_type},
         )
+
         return gateway_response

cellxgene_gateway/cache_key.py

@@ -1,70 +0,0 @@
-# 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.
-
-# There are three kinds of CacheKey:
-# 1) somedir/dataset.h5ad: a dataset
-#    in this case, descriptor == dataset == 'somedir/dataset.h5ad'
-# 2) somedir/dataset_annotations/my_annotations.csv : an actual annotations file.
-#    in this case, descriptor == 'somedir/dataset_annotations/my_annotations.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, descriptor == 'somedir/dataset_annotations', dataset == 'somedir/dataset.h5ad'
-
-from cellxgene_gateway.items.item import Item
-from cellxgene_gateway.items.item_source import ItemSource, LookupResult
-
-
-class CacheKey:
-    @property
-    def descriptor(self):
-        if self.annotation_item is None:
-            return self.h5ad_item.descriptor
-        else:
-            return self.annotation_item.descriptor
-
-    @property
-    def file_path(self):
-        return self.source.get_local_path(self.h5ad_item)
-
-    @property
-    def annotation_file_path(self):
-        if self.annotation_item is None:
-            return None
-        else:
-            return self.source.get_local_path(self.annotation_item)
-
-    @property
-    def source_name(self):
-        return self.source.name
-
-    @property
-    def annotation_descriptor(self):
-        if self.annotation_item is None:
-            return None
-        else:
-            return self.annotation_item.descriptor
-
-    def equals(self, other):
-        return (
-            (self.source.name == other.source.name)
-            and (self.h5ad_item.descriptor == other.h5ad_item.descriptor)
-            and (self.annotation_descriptor == other.annotation_descriptor)
-        )
-
-    def __init__(
-        self, h5ad_item: Item, source: ItemSource, annotation_item: Item = None
-    ):
-        assert h5ad_item is not None
-        assert source is not None
-        self.h5ad_item = h5ad_item
-        self.annotation_item = annotation_item
-        self.source = source
-
-    @classmethod
-    def for_lookup(cls, source: ItemSource, lookup: LookupResult):
-        return CacheKey(lookup.h5ad_item, source, lookup.annotation_item)

cellxgene_gateway/dir_util.py

@@ -52,13 +52,43 @@ def create_dir(parent_path, dir_name):
         os.mkdir(full_path)
 
 
-annotations_suffix = "_annotations"
+def recurse_dir(path):
-h5ad_suffix = ".h5ad"
+    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,
+                "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 make_h5ad(el):
+def render_entries(entries):
-    return el[: -len(annotations_suffix)] + h5ad_suffix
+    return "<ul>" + "\n".join([render_entry(e) for e in entries]) + "</ul>"
 
 
-def make_annotations(el):
+def render_entry(entry):
-    return el[:-5] + annotations_suffix
+    if entry["type"] == "file":
+        url = 'view' + '/' + entry['path'].lstrip("/")
+        return f"<li> <a href='{ url}'>{entry['name']}</a></li>"
+    elif entry["type"] == "directory":
+        return f"<li>{entry['name']}{render_entries(entry['children'])}</li>"

cellxgene_gateway/env.py

@@ -7,55 +7,32 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-import logging
 import os
-import socket
+import logging
 
 cellxgene_location = os.environ.get("CELLXGENE_LOCATION")
 cellxgene_data = os.environ.get("CELLXGENE_DATA")
-cellxgene_args = os.environ.get("CELLXGENE_ARGS", None)
+gateway_host = os.environ.get("GATEWAY_HOST")
-gateway_port = int(os.environ.get("GATEWAY_PORT", "5005"))
+gateway_protocol = os.environ.get("GATEWAY_PROTOCOL")
-external_host = os.environ.get(
-    "EXTERNAL_HOST",
-    os.environ.get("GATEWAY_HOST", f"localhost:{gateway_port}"),
-)
-external_protocol = os.environ.get(
-    "EXTERNAL_PROTOCOL", os.environ.get("GATEWAY_PROTOCOL", "http")
-)
 ip = os.environ.get("GATEWAY_IP")
 extra_scripts = os.environ.get("GATEWAY_EXTRA_SCRIPTS")
 ttl = os.environ.get("GATEWAY_TTL")
-enable_annotations = os.environ.get(
+enable_upload = os.environ.get("GATEWAY_ENABLE_UPLOAD", "").lower() in ['true', '1']
-    "GATEWAY_ENABLE_ANNOTATIONS", ""
-).lower() in [
-    "true",
-    "1",
-]
-enable_backed_mode = os.environ.get(
-    "GATEWAY_ENABLE_BACKED_MODE", ""
-).lower() in [
-    "true",
-    "1",
-]
 
 env_vars = {
     "CELLXGENE_LOCATION": cellxgene_location,
+    "CELLXGENE_DATA": cellxgene_data,
+    "GATEWAY_HOST": gateway_host,
+    "GATEWAY_PROTOCOL": gateway_protocol,
+    "GATEWAY_IP": ip,
 }
 
 optional_env_vars = {
-    "EXTERNAL_HOST": external_host,
-    "EXTERNAL_PROTOCOL": external_protocol,
-    "GATEWAY_IP": ip,
-    "GATEWAY_PORT": gateway_port,
     "GATEWAY_EXTRA_SCRIPTS": extra_scripts,
     "GATEWAY_TTL": ttl,
-    "GATEWAY_ENABLE_ANNOTATIONS": enable_annotations,
+    "GATEWAY_ENABLE_UPLOAD": enable_upload,
-    "GATEWAY_ENABLE_BACKED_MODE": enable_backed_mode,
-    "CELLXGENE_ARGS": cellxgene_args,
-    "CELLXGENE_DATA": cellxgene_data,
 }
 
-
 def validate():
     if not all(env_vars.values()):
         raise ValueError(
@@ -70,12 +47,11 @@ def validate():
 
         export CELLXGENE_LOCATION=~/anaconda/envs/cellxgene-dev/bin/cellxgene
         export CELLXGENE_DATA=../cellxgene_data
+        export GATEWAY_HOST=localhost:5005
+        export GATEWAY_PROTOCOL=http
+        export GATEWAY_IP=127.0.0.1
     """
         )
     else:
-        logging.getLogger("cellxgene_gateway").info(
+        logging.getLogger("cellxgene_gateway").info(f"Got required env: {env_vars}", )
-            f"Got required env: {env_vars}",
+        logging.getLogger("cellxgene_gateway").info(f"Got optional env: {optional_env_vars}")
-        )
-        logging.getLogger("cellxgene_gateway").info(
-            f"Got optional env: {optional_env_vars}"
-        )

cellxgene_gateway/extra_scripts.py

@@ -7,14 +7,13 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-from json import loads
-
 from cellxgene_gateway import env
+from json import loads
 
 
 def get_extra_scripts():
     # can be array of script tags to inject on every page, e.g. for google analytics could be
     # ['https://www.googletagmanager.com/gtag/js?id=UA-123456-2',
-    #  f"{env.external_protocol}://{env.external_host}/static/js/google_ua.js"]
+    #  f"{env.gateway_protocol}://{env.gateway_host}/static/js/google_ua.js"]
     # where google_ua.js is a script you add to the static/js folder prior to deployment.
     return [] if env.extra_scripts is None else loads(env.extra_scripts)

cellxgene_gateway/filecrawl.py

@@ -1,68 +0,0 @@
-# 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
-import urllib.parse
-
-
-def render_annotations(item, item_source):
-    subpath = f"/source/{urllib.parse.quote_plus(item_source.name)}/view/"
-    new_annotation = f"<a class='new' href='{subpath}{item_source.get_annotations_subpath(item)}'>new</a>"
-    annotations = (
-        ", ".join(
-            [
-                f"<a href='{subpath}{a.descriptor}/'>{a.name}</a>"
-                for a in item.annotations
-            ]
-        )
-        + ", "
-        if item.annotations
-        else ""
-    )
-
-    return " | annotations: " + annotations + new_annotation
-
-
-def render_item(item, item_source):
-    url = f"/source/{urllib.parse.quote_plus(item_source.name)}/view/{item.descriptor}/"
-    item_string = f"<li> <a href='{ url }'>{item.name}</a> {render_annotations(item, item_source)}</li>"
-    return item_string
-
-
-def render_item_tree(item_tree, item_source):
-    items = (
-        "\n".join([render_item(i, item_source) for i in item_tree.items])
-        if item_tree.items
-        else ""
-    )
-    branches = (
-        "\n".join(
-            [render_item_tree(b, item_source) for b in item_tree.branches]
-        )
-        if item_tree.branches
-        else ""
-    )
-    html = "<ul>" + items + branches + "</ul>"
-    if item_tree.descriptor:
-        descriptor = item_tree.descriptor.lstrip("/")
-        url = f"/filecrawl/{descriptor}?source={item_source.name}"
-        name = (
-            descriptor.rsplit("/")[1]
-            if descriptor.find("/") >= 0
-            else descriptor
-        )
-        return f"<li><a href='{url}'>{name}</a>{html}</li>"
-    else:
-        return html
-
-
-def render_item_source(item_source, filter=None):
-    item_tree = item_source.list_items(filter)
-    heading = f"<h6><a href='/filecrawl.html?source={urllib.parse.quote_plus(item_source.name)}'>{item_source.name}</a></h6>"
-    return heading + render_item_tree(item_tree, item_source)

cellxgene_gateway/flask_util.py

@@ -1,15 +0,0 @@
-# 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.
-
-from flask import request
-
-
-def querystring():
-    qs = request.query_string.decode()
-    return f"?{qs}" if len(qs) > 0 else ""

cellxgene_gateway/gateway.py

@@ -6,16 +6,16 @@
 # 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 BaseHTTPServer
-import json
+import datetime
-import logging
 import os
-import urllib.parse
+import logging
-from threading import Lock, Thread
+from threading import Thread, Lock
+import json
 
 from flask import (
     Flask,
-    make_response,
     redirect,
     render_template,
     request,
@@ -23,38 +23,21 @@ from flask import (
     url_for,
 )
 from flask_api import status
-from werkzeug.utils import secure_filename
+from werkzeug import secure_filename
 
 from cellxgene_gateway import env
 from cellxgene_gateway.backend_cache import BackendCache
-from cellxgene_gateway.cache_entry import CacheEntryStatus
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import create_dir, is_subdir
+from cellxgene_gateway.dir_util import create_dir, recurse_dir, render_entries, is_subdir
 from cellxgene_gateway.extra_scripts import get_extra_scripts
-from cellxgene_gateway.filecrawl import render_item_source
+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.cache_key import CacheKey
 
 app = Flask(__name__)
-
-item_sources = []
-default_item_source = None
-
-
-def _force_https(app):
-    def wrapper(environ, start_response):
-        environ["wsgi.url_scheme"] = env.external_protocol
-        return app(environ, start_response)
-
-    return wrapper
-
-
-app.wsgi_app = _force_https(app.wsgi_app)
-
 cache = BackendCache()
-location = f"{env.external_protocol}://{env.external_host}"
+location = f"{env.gateway_protocol}://{env.gateway_host}"
 
 
 @app.errorhandler(CellxgeneException)
@@ -90,8 +73,7 @@ def handle_invalid_process(error):
             http_status=error.http_status,
             stdout=error.stdout,
             stderr=error.stderr,
-            dataset=error.key.h5ad_item.descriptor,
+            dataset=error.dataset,
-            annotation_file=error.key.annotation_descriptor,
         ),
         error.http_status,
     )
@@ -108,94 +90,105 @@ def favicon():
 
 @app.route("/")
 def index():
+    users = [
+        name
+        for name in os.listdir(env.cellxgene_data)
+        if os.path.isdir(os.path.join(env.cellxgene_data, name))
+    ]
     return render_template(
         "index.html",
         ip=env.ip,
         cellxgene_data=env.cellxgene_data,
         extra_scripts=get_extra_scripts(),
+        users=users,
+        enable_upload=env.enable_upload,
     )
 
+def make_user():
+    dir_name = request.form["directory"]
+
+    create_dir(env.cellxgene_data, dir_name)
+
+    return redirect(location, code=302)
+
+
+def make_subdir():
+    parent_path = os.path.join(env.cellxgene_data, request.form["usernames"])
+    dir_name = request.form["directory"]
+
+    create_dir(parent_path, dir_name)
+
+    return redirect(location, code=302)
+
+
+def upload_file():
+    upload_dir = request.form["path"]
+
+    full_upload_path = os.path.join(env.cellxgene_data, upload_dir)
+    if is_subdir(full_upload_path, env.cellxgene_data) and os.path.isdir(full_upload_path):
+        if request.method == "POST":
+            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))
+                    )
+                    return redirect("/filecrawl.html", code=302)
+                else:
+                    raise CellxgeneException(
+                        "Uploaded file must be in anndata (.h5ad) format.",
+                        status.HTTP_400_BAD_REQUEST,
+                    )
+            else:
+                raise CellxgeneException(
+                    "A file must be chosen to upload.",
+                    status.HTTP_400_BAD_REQUEST,
+                )
+    else:
+        raise CellxgeneException(
+            "Invalid directory.", status.HTTP_400_BAD_REQUEST
+        )
+
+    return redirect(env.location, 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.route("/filecrawl.html")
-@app.route("/filecrawl/<path:path>")
+def filecrawl():
-def filecrawl(path=None):
-    source_name = request.args.get("source")
-    sources = (
-        filter(
-            lambda x: x.name == urllib.parse.unquote_plus(source_name),
-            item_sources,
-        )
-        if source_name
-        else item_sources
-    )
-    # loop all data sources --
-    rendered_sources = [
-        render_item_source(item_source, path) for item_source in sources
-    ]  # will we need to make this async in the page???
-    rendered_html = "\n".join(rendered_sources)
 
-    resp = make_response(
+    entries = recurse_dir(env.cellxgene_data)
-        render_template(
+    rendered_html = render_entries(entries)
-            "filecrawl.html",
+    return render_template(
-            extra_scripts=get_extra_scripts(),
+        "filecrawl.html",
-            rendered_html=rendered_html,
+        extra_scripts=get_extra_scripts(),
-            path=path,
+        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
-
 
 entry_lock = Lock()
-
-
-def matching_source(source_name):
-    if source_name is None:
-        source_name = default_item_source.name
-    matching = [i for i in item_sources if i.name == source_name]
-    if len(matching) != 1:
-        raise Exception(f"Could not find matching item source {source_name}")
-    source = matching[0]
-    return source
-
-
-@app.route(
-    "/source/<path:source_name>/view/<path:path>",
-    methods=["GET", "PUT", "POST"],
-)
 @app.route("/view/<path:path>", methods=["GET", "PUT", "POST"])
-def do_view(path, source_name=None):
+def do_view(path):
-    source = matching_source(source_name)
+    dataset = get_dataset(path)
-    match = cache.check_path(source, path)
+    file_path = get_file_path(dataset)
-
+    with entry_lock:
-    if match is None:
+        match = cache.check_entry(dataset)
-        lookup = source.lookup(path)
+        if match is None:
-        if lookup is None:
+            uascripts = get_extra_scripts()
-            raise CellxgeneException(
+            match = cache.create_entry(dataset, file_path, uascripts)
-                f"Could not find item for path {path} in source {source.name}",
-                404,
-            )
-        key = CacheKey.for_lookup(source, lookup)
-        print(
-            f"view path={path}, source_name={source_name}, dataset={key.file_path}, annotation_file= {key.annotation_file_path}, key={key.descriptor}, source={key.source_name}"
-        )
-        with entry_lock:
-            match = cache.check_entry(key)
-            if match is None:
-                uascripts = get_extra_scripts()
-                match = cache.create_entry(key, uascripts)
 
     match.timestamp = current_time_stamp()
 
-    if (
+    if match.status == "loaded":
-        match.status == CacheEntryStatus.loaded
-        or match.status == CacheEntryStatus.loading
-    ):
         return match.serve_content(path)
-    elif match.status == CacheEntryStatus.error:
+    elif match.status == "loading":
+        launch_time = datetime.datetime.fromtimestamp(match.launchtime)
+        return render_template(
+            "loading.html", launchtime=launch_time, all_output=match.all_output
+        )
+    elif match.status == "error":
         raise ProcessException.from_cache_entry(match)
 
 
@@ -203,92 +196,43 @@ def do_view(path, source_name=None):
 def do_GET_status():
     return render_template("cache_status.html", entry_list=cache.entry_list)
 
-
 @app.route("/cache_status.json", methods=["GET"])
 def do_GET_status_json():
-    return json.dumps(
+    return json.dumps({'launchtime':app.launchtime,
-        {
+    'entry_list':[{
-            "launchtime": app.launchtime,
+        'dataset': entry.dataset,
-            "entry_list": [
+        'launchtime': entry.launchtime,
-                {
+        'last_access': entry.timestamp,
-                    "dataset": entry.key.dataset,
+        'status': entry.status
-                    "annotation_file": entry.key.annotation_file,
+    } for entry in cache.entry_list]})
-                    "launchtime": entry.launchtime,
-                    "last_access": entry.timestamp,
-                    "status": entry.status,
-                }
-                for entry in cache.entry_list
-            ],
-        }
-    )
-
 
 @app.route("/relaunch/<path:path>", methods=["GET"])
 def do_relaunch(path):
-    source_name = request.args.get("source") or default_item_source.name
+    dataset = get_dataset(path)
-    source = matching_source(source_name)
+    match = cache.check_entry(dataset)
-    key = CacheKey.for_lookup(source, source.lookup(path))
-    match = cache.check_entry(key)
     if not match is None:
         match.terminate()
-    qs = request.query_string.decode()
+    return redirect(url_for("do_view", path=path), code=302)
-    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):
-    source_name = request.args.get("source_name") or default_item_source.name
+    dataset = get_dataset(path)
-    source = matching_source(source_name)
+    match = cache.check_entry(dataset)
-    key = CacheKey.for_lookup(source, source.lookup(path))
-    match = cache.check_entry(key)
     if not match is None:
         match.terminate()
     return redirect(url_for("do_GET_status"), code=302)
 
 
-def launch():
+def main():
+    logging.basicConfig(level=logging.INFO, format='%(asctime)s:%(name)s:%(levelname)s:%(message)s')
     env.validate()
-    if not item_sources or not len(item_sources):
-        raise Exception("No data sources specified for Cellxgene Gateway")
-
-    global default_item_source
-    if default_item_source is None:
-        default_item_source = item_sources[0]
-
     pruner = PruneProcessCache(cache)
 
     background_thread = Thread(target=pruner)
     background_thread.start()
 
     app.launchtime = current_time_stamp()
-    app.run(host="0.0.0.0", port=env.gateway_port, debug=False)
+    app.run(host="0.0.0.0", port=5005, debug=False)
-
-
-def main():
-    logging.basicConfig(
-        level=logging.INFO,
-        format="%(asctime)s:%(name)s:%(levelname)s:%(message)s",
-    )
-    cellxgene_data = os.environ.get("CELLXGENE_DATA", None)
-    cellxgene_bucket = os.environ.get("CELLXGENE_BUCKET", None)
-
-    if cellxgene_bucket is not None:
-        from cellxgene_gateway.items.s3.s3item_source import S3ItemSource
-
-        item_sources.append(S3ItemSource(cellxgene_bucket, name="s3"))
-        default_item_source = "s3"
-    if cellxgene_data is not None:
-        from cellxgene_gateway.items.file.fileitem_source import FileItemSource
-
-        item_sources.append(FileItemSource(cellxgene_data, name="local"))
-        default_item_source = "local"
-    if len(item_sources) == 0:
-        raise Exception("Please specify CELLXGENE_DATA or CELLXGENE_BUCKET")
-
-    launch()
 
 
 if __name__ == "__main__":

cellxgene_gateway/items/file/fileitem.py

@@ -1,27 +0,0 @@
-# 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 cellxgene_gateway.items.item import Item
-
-
-class FileItem(Item):
-    """e.g. FileItem(subpath = subpath, name = filename, type = ItemType.h5ad)
-
-    The Item superclass expects a 'name' and 'type'.
-    """
-
-    def __init__(self, subpath: str, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.subpath = subpath
-
-    @property
-    def descriptor(self) -> str:
-        return os.path.join(self.subpath, self.name).strip("/")

cellxgene_gateway/items/file/fileitem_source.py

@@ -1,185 +0,0 @@
-# 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 typing import List
-
-from cellxgene_gateway import dir_util
-from cellxgene_gateway.items.file.fileitem import FileItem
-from cellxgene_gateway.items.item import ItemTree, ItemType
-from cellxgene_gateway.items.item_source import ItemSource, LookupResult
-
-
-class FileItemSource(ItemSource):
-    def __init__(
-        self,
-        base_path,
-        name=None,
-        h5ad_suffix=dir_util.h5ad_suffix,
-        annotation_dir_suffix=dir_util.annotations_suffix,
-        annotation_file_suffix=".csv",
-    ):
-        self._name = name
-        self.base_path = base_path
-        self.h5ad_suffix = h5ad_suffix
-        self.annotation_dir_suffix = annotation_dir_suffix
-        self.annotation_file_suffix = annotation_file_suffix
-
-    @property
-    def name(self):
-        return self._name or f"Files:{self.base_path}"
-
-    def is_h5ad_file(self, path: str) -> bool:
-        return path.endswith(self.h5ad_suffix) and os.path.isfile(path)
-
-    def convert_annotation_path_to_h5ad(self, path):
-        return path[: -len(self.annotation_dir_suffix)] + self.h5ad_suffix
-
-    def convert_h5ad_path_to_annotation(self, path):
-        return path[: -len(self.h5ad_suffix)] + self.annotation_dir_suffix
-
-    def get_local_path(self, item: FileItem) -> str:
-        return os.path.join(self.base_path, item.descriptor)
-
-    def get_annotations_subpath(self, item) -> str:
-        return self.convert_h5ad_path_to_annotation(item.descriptor)
-
-    def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory()
-
-        """def get_items(dir):
-            if dir.branches:
-                return [*dir.items, *[item for subdir in dir.branches for item in get_items(subdir)]]
-            else:
-                return dir.items
-
-        return get_items(self.item_tree)"""
-
-        return item_tree
-
-    def scan_directory(self, subpath="") -> dict:
-        base_path = os.path.join(self.base_path, subpath)
-
-        if not os.path.exists(base_path):
-            raise Exception(
-                f"Path for local files '{base_path}' does not exist."
-            )
-
-        filepath_map = dict(
-            (filepath, os.path.join(base_path, filepath))
-            for filepath in sorted(os.listdir(base_path))
-        )
-
-        def is_annotation_dir(dir):
-            return (
-                dir.endswith(self.annotation_dir_suffix)
-                and self.convert_annotation_path_to_h5ad(dir) in h5ad_paths
-            )
-
-        h5ad_paths = [
-            filepath
-            for filepath, full_path in filepath_map.items()
-            if self.is_h5ad_file(full_path)
-        ]
-
-        subdirs = [
-            filepath
-            for filepath, full_path in filepath_map.items()
-            if os.path.isdir(full_path) and not is_annotation_dir(filepath)
-        ]
-
-        items = [
-            self.make_fileitem_from_path(filename, subpath)
-            for filename in h5ad_paths
-        ]
-        branches = None
-        if len(subdirs) > 0:
-            branches = [
-                self.scan_directory(os.path.join(subpath, subdir))
-                for subdir in subdirs
-            ]
-
-        return ItemTree(subpath, items, branches)
-
-    def create_annotation(self, item: FileItem, name: str) -> FileItem:
-        annotation = self.make_fileitem_from_path(
-            name, self.get_annotations_subpath(item), is_annotation=True
-        )
-        item.annotations = (item.annotations or []).append(annotation)
-        return annotation
-
-    def update(self, item: FileItem) -> None:
-        pass
-
-    def full_path(self, p):
-        return os.path.join(self.base_path, p)
-
-    def lookup_item(self, descriptor):
-        full_path = self.full_path(descriptor)
-        if self.is_h5ad_file(full_path):
-            return self.shallowitem_from_descriptor(descriptor)
-
-    def lookup(self, indescriptor: str) -> LookupResult:
-        descriptor = indescriptor.strip("/")
-        if descriptor.endswith(self.annotation_file_suffix):
-            annotation_item = self.shallowitem_from_descriptor(
-                descriptor, True
-            )
-            h5ad_descriptor = self.convert_annotation_path_to_h5ad(
-                annotation_item.subpath
-            )
-            item = self.lookup_item(h5ad_descriptor)
-            if item is not None:
-                return LookupResult(item, annotation_item)
-        else:
-            item = self.lookup_item(descriptor)
-            if item is not None:
-                return LookupResult(item)
-
-    def shallowitem_from_descriptor(self, descriptor, is_annotation=False):
-        filename = os.path.basename(descriptor)
-        subpath = os.path.dirname(descriptor)
-        return self.make_fileitem_from_path(
-            filename,
-            subpath,
-            is_annotation,
-            True,
-        )
-
-    def make_fileitem_from_path(
-        self, filename, subpath, is_annotation=False, is_shallow=False
-    ) -> FileItem:
-        item = FileItem(
-            subpath=subpath,
-            name=filename,
-            type=ItemType.annotation if is_annotation else ItemType.h5ad,
-        )
-
-        if not is_annotation and not is_shallow:
-            annotations = self.make_annotations_for_fileitem(item)
-            item.annotations = annotations
-
-        return item
-
-    def make_annotations_for_fileitem(self, item: FileItem) -> List[FileItem]:
-        annotations_subpath = self.get_annotations_subpath(item)
-        annotations_fullpath = self.full_path(annotations_subpath)
-        if os.path.isdir(annotations_fullpath):
-            return [
-                self.make_fileitem_from_path(
-                    annotation, annotations_subpath, True
-                )
-                for annotation in sorted(os.listdir(annotations_fullpath))
-                if annotation.endswith(self.annotation_file_suffix)
-                and os.path.isfile(
-                    os.path.join(annotations_fullpath, annotation)
-                )
-            ]
-        else:
-            return None

cellxgene_gateway/items/item.py

@@ -1,43 +0,0 @@
-# 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.
-
-from abc import ABC, abstractmethod
-from enum import Enum
-from typing import List
-
-
-class ItemType(Enum):
-    annotation = "annotation"
-    h5ad = "h5ad"
-
-
-class Item(ABC):
-    def __init__(
-        self, name: str, type: ItemType, annotations: List["Item"] = None
-    ):
-        self.name = name
-        self.type = type
-        self.annotations = annotations
-
-    @property
-    @abstractmethod
-    def descriptor(self):
-        raise Exception('"descriptor" not implemented')
-
-
-class ItemTree:
-    def __init__(
-        self,
-        descriptor: str,
-        items: List[Item] = None,
-        branches: List["ItemTree"] = None,
-    ):
-        self.descriptor = descriptor
-        self.items = items
-        self.branches = branches

cellxgene_gateway/items/item_source.py

@@ -1,50 +0,0 @@
-# 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.
-
-from abc import ABC, abstractmethod
-from typing import List
-
-from cellxgene_gateway.items.item import Item
-
-
-class LookupResult:
-    def __init__(self, h5ad_item: Item, annotation_item: Item = None):
-        self.h5ad_item = h5ad_item
-        self.annotation_item = annotation_item
-
-
-class ItemSource(ABC):
-    @abstractmethod
-    def list_items(self, filter: str = None) -> List[Item]:
-        raise Exception('"list_items" unimplemented')
-
-    @abstractmethod
-    def get_local_path(self, item: Item) -> str:
-        raise Exception('"local_path" unimplemented')
-
-    @abstractmethod
-    def get_annotations_subpath(self, item) -> str:
-        raise Exception('"annotations_path" unimplemented')
-
-    @abstractmethod
-    def create_annotation(self, item: Item, name: str) -> Item:
-        raise Exception('"annotation" unimplemented')
-
-    @abstractmethod
-    def update(self, item: Item) -> None:
-        raise Exception('"update" unimplemented')
-
-    @abstractmethod
-    def lookup(self, descriptor: str) -> LookupResult:
-        raise Exception('"lookup" unimplemented')
-
-    @property
-    @abstractmethod
-    def name(self):
-        pass

cellxgene_gateway/items/s3/s3item.py

@@ -1,27 +0,0 @@
-# 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 cellxgene_gateway.items.item import Item
-
-
-class S3Item(Item):
-    """e.g. FileItem(subpath = subpath, name = filename, type = ItemType.h5ad)
-
-    The Item superclass expects a 'name' and 'type'.
-    """
-
-    def __init__(self, s3key: str, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.s3key = s3key
-
-    @property
-    def descriptor(self) -> str:
-        return self.s3key

cellxgene_gateway/items/s3/s3item_source.py

@@ -1,171 +0,0 @@
-# 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.
-
-from typing import List
-from os.path import join, dirname, basename
-from cellxgene_gateway import dir_util
-import s3fs
-from cellxgene_gateway.items.s3.s3item import S3Item
-from cellxgene_gateway.items.item import ItemTree, ItemType
-from cellxgene_gateway.items.item_source import ItemSource, LookupResult
-
-
-class S3ItemSource(ItemSource):
-    def __init__(
-        self,
-        bucket,
-        name=None,
-        h5ad_suffix=dir_util.h5ad_suffix,
-        annotation_dir_suffix=dir_util.annotations_suffix,
-        annotation_file_suffix=".csv",
-    ):
-        self._name = name
-        self.s3 = s3fs.S3FileSystem()
-        self.bucket = bucket
-        self.h5ad_suffix = h5ad_suffix
-        self.annotation_dir_suffix = annotation_dir_suffix
-        self.annotation_file_suffix = annotation_file_suffix
-
-    def url(self, path):
-        return "s3://" + join(self.bucket, path)
-
-    @property
-    def name(self):
-        return self._name or f"Items:{self.url('')}"
-
-    def is_h5ad_url(self, s3url: str) -> bool:
-        return s3url.endswith(self.h5ad_suffix) and self.s3.exists(s3url)
-
-    def convert_annotation_key_to_h5ad(self, s3key):
-        return s3key[: -len(self.annotation_dir_suffix)] + self.h5ad_suffix
-
-    def convert_h5ad_key_to_annotation(self, s3key):
-        return s3key[: -len(self.h5ad_suffix)] + self.annotation_dir_suffix
-
-    def get_local_path(self, item: S3Item) -> str:
-        return self.url(item.descriptor)
-
-    def get_annotations_subpath(self, item) -> str:
-        return self.convert_h5ad_key_to_annotation(item.descriptor)
-
-    def list_items(self, filter: str = None) -> ItemTree:
-        item_tree = self.scan_directory()
-        return item_tree
-
-    def scan_directory(self, subpath="") -> dict:
-        url = self.url(subpath)
-
-        if not self.s3.exists(url):
-            raise Exception(f"S3 url '{url}' does not exist.")
-
-        s3key_map = dict(
-            (filepath[len(self.bucket) :], "s3://" + filepath)
-            for filepath in sorted(self.s3.ls(url))
-        )
-
-        def is_annotation_dir(dir_s3key):
-            return (
-                dir_s3key.endswith(self.annotation_dir_suffix)
-                and self.convert_annotation_key_to_h5ad(dir_s3key)
-                in h5ad_paths
-            )
-
-        h5ad_paths = [
-            filepath
-            for filepath, item_url in s3key_map.items()
-            if self.is_h5ad_url(item_url)
-        ]
-
-        subdirs = [
-            filepath
-            for filepath, item_url in s3key_map.items()
-            if self.s3.isdir(item_url) and not is_annotation_dir(filepath)
-        ]
-
-        items = [
-            self.make_s3item_from_key(filename, join(subpath, filename))
-            for filename in h5ad_paths
-        ]
-        branches = None
-        if len(subdirs) > 0:
-            branches = [
-                self.scan_directory(join(subpath, subdir))
-                for subdir in subdirs
-            ]
-
-        return ItemTree(subpath, items, branches)
-
-    def create_annotation(self, item: S3Item, name: str) -> S3Item:
-        annotation = self.make_s3item_from_key(
-            name, self.get_annotations_subpath(item), is_annotation=True
-        )
-        item.annotations = (item.annotations or []).append(annotation)
-        return annotation
-
-    def update(self, item: S3Item) -> None:
-        pass
-
-    def lookup_item(self, descriptor):
-        full_path = self.url(descriptor)
-        if self.is_h5ad_url(full_path):
-            return self.shallowitem_from_descriptor(descriptor)
-
-    def lookup(self, indescriptor: str) -> LookupResult:
-        descriptor = indescriptor.strip("/")
-        if descriptor.endswith(self.annotation_file_suffix):
-            annotation_item = self.shallowitem_from_descriptor(
-                descriptor, True
-            )
-            if not self.s3.exists(self.url(annotation_item.s3key)):
-                with self.s3.open(self.url(annotation_item.s3key), "w") as f:
-                    f.write("")
-            h5ad_descriptor = self.convert_annotation_key_to_h5ad(
-                dirname(annotation_item.s3key)
-            )
-            item = self.shallowitem_from_descriptor(h5ad_descriptor)
-            return LookupResult(item, annotation_item)
-        else:
-            item = self.lookup_item(descriptor)
-            if item is not None:
-                return LookupResult(item)
-
-    def shallowitem_from_descriptor(self, descriptor, is_annotation=False):
-        return self.make_s3item_from_key(
-            basename(descriptor), descriptor, is_annotation, True
-        )
-
-    def make_s3item_from_key(
-        self, name, s3key, is_annotation=False, is_shallow=False
-    ) -> S3Item:
-        item = S3Item(
-            s3key=s3key,
-            name=name,
-            type=ItemType.annotation if is_annotation else ItemType.h5ad,
-        )
-
-        if not is_annotation and not is_shallow:
-            annotations = self.make_annotations_for_fileitem(item)
-            item.annotations = annotations
-
-        return item
-
-    def make_annotations_for_fileitem(self, item: S3Item) -> List[S3Item]:
-        annotations_subpath = self.get_annotations_subpath(item)
-        annotations_fullpath = self.url(annotations_subpath)
-        if self.s3.isdir(annotations_fullpath):
-            return [
-                self.make_s3item_from_key(
-                    annotation, join(annotations_subpath, annotation), True
-                )
-                for annotation in sorted(self.s3.ls(annotations_fullpath))
-                if annotation.endswith(self.annotation_file_suffix)
-                and self.s3.isfile(join(annotations_fullpath, annotation))
-            ]
-        else:
-            return None

cellxgene_gateway/path_util.py

@@ -11,20 +11,31 @@ import os
 
 from flask_api import status
 
-from cellxgene_gateway.cache_key import CacheKey
+from cellxgene_gateway import env
 from cellxgene_gateway.cellxgene_exception import CellxgeneException
-from cellxgene_gateway.dir_util import make_h5ad
 
 
-def validate_exists(file_path):
+def get_dataset(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])
+
+
+def validate_path(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
@@ -32,10 +43,7 @@ def validate_is_file(file_path):
     return
 
 
-def validate_is_dir(file_path):
+def get_file_path(dataset):
-    validate_exists(file_path)
+    file_path = os.path.join(env.cellxgene_data, dataset)
-    if not os.path.isdir(file_path):
+    validate_path(file_path)
-        raise CellxgeneException(
+    return file_path
-            "Path is not dir: " + file_path, status.HTTP_400_BAD_REQUEST
-        )
-    return

cellxgene_gateway/process_exception.py

@@ -9,13 +9,13 @@
 
 
 class ProcessException(Exception):
-    def __init__(self, message, stdout, stderr, http_status, key):
+    def __init__(self, message, stdout, stderr, http_status, dataset):
         Exception.__init__(self)
         self.message = message
         self.stdout = stdout
         self.stderr = stderr
         self.http_status = http_status
-        self.key = key
+        self.dataset = dataset
 
     @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.key,
+            cache_entry.dataset,
         )

cellxgene_gateway/prune_process_cache.py

@@ -7,17 +7,16 @@
 # OR CONDITIONS OF ANY KIND, either express or implied. See the License for
 # the specific language governing permissions and limitations under the License.
 
-import logging
 import time
+import logging
 
-from cellxgene_gateway.env import ttl
 from cellxgene_gateway.util import current_time_stamp
-
+from cellxgene_gateway.env import ttl
 
 class PruneProcessCache:
     def __init__(self, cache):
         self.cache = cache
-        self.expire_seconds = 3600 if ttl is None else int(ttl)
+        self.expire_seconds = (3600 if ttl is None else int(ttl))
 
     def __call__(self):
         while True:
@@ -27,24 +26,16 @@ class PruneProcessCache:
     def prune(self):
         timestamp = current_time_stamp()
         cutoff = timestamp - self.expire_seconds
-        processes_to_delete = [
+        def prunable(p):
-            p for p in self.cache.entry_list if p.timestamp < cutoff
+            return p.timestamp < cutoff and p.pid != None
-        ]
+        processes_to_delete = [p for p in self.cache.entry_list if  prunable(p)]
-        processes_to_keep = [
+        processes_to_keep = [p for p in self.cache.entry_list if not prunable(p)]
-            p for p in self.cache.entry_list if not p.timestamp < cutoff
-        ]
         logger = logging.getLogger("cellxgene_gateway")
-        logger.debug(
+        logger.debug(f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}")
-            f"Cutoff {cutoff} = timestamp {timestamp} - expire seconds {self.expire_seconds} , keeping {processes_to_keep}"
-        )
         
         for process in processes_to_delete:
             try:
-                logger.info(
+                logger.info(f"pruning process {process.pid} ({process.dataset})")
-                    f"pruning process {process.pid} ({process.key.dataset})"
-                )
                 self.cache.prune(process)
             except Exception:
-                logger.exception(
+                logger.exception("failed to prune process {process.pid} ({process.dataset})")
-                    "failed to prune process {process.pid} ({process.dataset})"
-                )

cellxgene_gateway/static/js/annotation.js

@@ -1,20 +0,0 @@
-// neandertal javascript
-// TODO: rewrite this --
-const new_annotation_callback = (() =>{
-    const suffix = `.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;
-    }
-})()
-

cellxgene_gateway/subprocess_backend.py

@@ -12,13 +12,6 @@ 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 (
-    enable_annotations,
-    enable_backed_mode,
-    cellxgene_args,
-)
 from cellxgene_gateway.process_exception import ProcessException
 
 
@@ -26,28 +19,13 @@ class SubprocessBackend:
     def __init__(self):
         pass
 
-    def create_cmd(
+    def create_cmd(self, cellxgene_loc, file_path, port, scripts):
-        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)}"
-                )
-            else:
-                extra_args = f" --annotations-file {annotation_file_path}"
-        else:
-            extra_args = " --disable-annotations"
-        if enable_backed_mode:
-            extra_args += " --backed"
-        if not cellxgene_args is None:
-            extra_args += f" {cellxgene_args}"
 
         cmd = (
             f"yes | {cellxgene_loc} launch {file_path}"
-            + f" --port {port}"
+            + " --port "
+            + str(port)
             + " --host 127.0.0.1"
-            + extra_args
         )
 
         for s in scripts:
@@ -56,12 +34,9 @@ class SubprocessBackend:
         return cmd
 
     def launch(self, cellxgene_loc, scripts, cache_entry):
+
         cmd = self.create_cmd(
-            cellxgene_loc,
+            cellxgene_loc, cache_entry.file_path, cache_entry.port, scripts
-            cache_entry.key.file_path,
-            cache_entry.port,
-            scripts,
-            cache_entry.key.annotation_file_path,
         )
         logging.getLogger("cellxgene_gateway").info(f"launching {cmd}")
         process = subprocess.Popen(
@@ -84,7 +59,7 @@ class SubprocessBackend:
                     message = "Cellxgene failed to launch dataset."
                     http_status = status.HTTP_500_INTERNAL_SERVER_ERROR
 
-                cache_entry.status = CacheEntryStatus.error
+                cache_entry.status = "error"
                 cache_entry.set_error(message, stderr, http_status)
 
                 raise ProcessException.from_cache_entry(cache_entry)

cellxgene_gateway/templates/cache_status.html

@@ -10,68 +10,57 @@
 -->
 
 <html>
-
 <head>
      <title>Cellxgene Gateway - FILE CRAWLER</title>
      <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
      <link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
-     {% for script in extra_scripts %}
+	{% for script in extra_scripts %}
-     <script src="{{ script }}"></script>
+	<script src="{{ script }}"></script>
-     {% endfor %}
+	{% endfor %}
-     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css"
+     <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
-          integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
 </head>
-
 <body>
      <header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
-          <h3>Cellxgene Gateway - Cache Status</h3>
+       <h3>Cellxgene Gateway - Cache Status</h3>
      </header>
      <br>
      <table class="table">
           <thead>
-               <tr>
+          <tr>
-                    <th>PID</th>
+               <th>PID</th>
-                    <th>dataset</th>
+               <th>dataset</th>
-                    <th>annotation_file</th>
+               <th>port</th>
-                    <th>source</th>
+               <th>launchtime</th>
-                    <th>port</th>
+               <th>last access</th>
-                    <th>launchtime</th>
+               <th>status</th>
-                    <th>last access</th>
+               <th>message</th>
-                    <th>status</th>
+               <th>http_status</th>
-                    <th>message</th>
+               <th>actions</th>
-                    <th>http_status</th>
+          </tr>
-                    <th>actions</th>
+     </thead>
-               </tr>
+     <tbody>
-          </thead>
+	{% for entry in entry_list %}
-          <tbody>
+          <tr>
-               {% for entry in entry_list %}
+               <td>{{ entry.pid }}</td>
-               <tr>
+               <td><a href="{{ url_for('do_view', path=entry.dataset) }}">{{ entry.dataset }}</a></td>
-                    <td>{{ entry.pid }}</td>
+               <td>{{ entry.port }}</td>
-                    <td><a
+               <td class="timestamp">{{ entry.launchtime }}</td>
-                              href="{{ url_for('do_view', path=entry.key.descriptor, source_name=entry.key.source_name) }}">{{ entry.key.h5ad_item.descriptor }}</a>
+               <td class="timestamp">{{ entry.timestamp }}</td>
-                    </td>
+               <td>{{ entry.status }}</td>
-                    <td>{{ entry.key.annotation_descriptor }}</td>
+               <td>{{ entry.message }}</td>
-                    <td>{{ entry.source_name }}</td>
+               <td>{{ entry.http_status }}</td>
-                    <td>{{ entry.port }}</td>
+               <td>
-                    <td class="timestamp">{{ entry.launchtime }}</td>
+                 {% if entry.status == 'loaded' %}
-                    <td class="timestamp">{{ entry.timestamp }}</td>
+                   <a href="{{ url_for('do_terminate', path=entry.dataset) }}"> terminate </a>
-                    <td>{{ entry.status.name }}</td>
+                 {% endif %}
-                    <td>{{ entry.message }}</td>
+               </td>
-                    <td>{{ entry.http_status }}</td>
+          </tr>
-                    <td>
+     {% endfor %}
-                         {% if entry.status.name == 'loaded' %}
+     </tbody>
-                         <a
-                              href="{{ url_for('do_terminate', path=entry.key.descriptor, source_name=entry.key.source_name) }}">
-                              terminate </a>
-                         {% endif %}
-                    </td>
-               </tr>
-               {% endfor %}
-          </tbody>
      </table>
      <script>
           $(() => {
-               $(".timestamp").each(function () {
+               $(".timestamp").each(function(){
                     const el = $(this);
                     const ts = el.text();
                     const dt = new Date(parseInt(ts * 1000));
@@ -80,5 +69,4 @@
           })
      </script>
 </body>
-
 </html>

cellxgene_gateway/templates/filecrawl.html

@@ -16,36 +16,19 @@
      <link rel="icon" type="image/png" href="{{ url_for('static', filename='nibr.ico') }}">
 	{% for script in extra_scripts %}
 	<script src="{{ script }}"></script>
-     {% endfor %}
+	{% endfor %}
-     <script src="{{ url_for('static', filename='js/annotation.js') }}"></script>
      <link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha384-MCw98/SFnGE8fJT3GXwEOngsV7Zt27NXFoaoApmYm81iuXoPkFOJwJ8ERdknLPMO" crossorigin="anonymous">
 </head>
 <body>
      <header class="navbar navbar-expand navbar-dark flex-column flex-md-row bd-navbar">
-          {% if path %}
+       <h3>Cellxgene Gateway - FILE CRAWLER</h3>
-          <h3>Cellxgene Gateway - {{ path }}</h3>
-          {% else %}
-          <h3>Cellxgene Gateway - FILE CRAWLER</h3>
-          {% endif %}
      </header>
+     <br>
 
      <h4>Please click on a dataset to view it in Cellxgene Server.</h4>
 
+     <br>
      {{ rendered_html|safe }}
-     <p>
+
-          Navigation:
-     <ul>
-     {% if path %}
-     <li><a href="/filecrawl.html">top level</a></li>
-     {% else %}
-     {% endif %}
-     <li><a href="/">homepage</a></li>
-     </ul>
-     </p>
-     <script>
-          $(() => {
-               $("a.new").click(new_annotation_callback);
-          })
-     </script>
 </body>
 </html>

cellxgene_gateway/templates/index.html

@@ -44,6 +44,47 @@
 			<u>Cache Status: view status of launched cellxgene servers.</u></a>
 	</div>
 	
+	{% if enable_upload %}
+	<br>
+	<h1 style="padding-left:35px">
+		How To Upload Data via HTTP:
+	</h1>
+	<ol style="padding-left:85px;">
+		<li>
+			Create a folder for your Username: 
+		</li>
+		<br>
+		<form action="{{ url_for('make_user') }}" method="post">
+		    Username <input type="text" name="directory">
+		    <input type="submit" value="Create">
+		</form>
+		<li>
+			Create a subdirectory under the selected Folder: 
+		</li>		
+		<br>
+		<form action="{{ url_for('make_subdir') }}" method="post">
+			<select name="usernames" id="usernames">
+				{% for user in users %}
+					<option value="{{ user }}">{{ user }}</option>
+				{% endfor %}
+			</select>
+			<br>
+			Subdirectory Name <input type="text" name="directory">
+		    <input type="submit" value="Create">
+		</form>
+		<li>Choose a folder to copy your data to, then upload your data file (must be in .h5ad format).</li>
+		<br>
+		<form action="{{ url_for('upload_file') }}" method="post" enctype="multipart/form-data">
+		Type in the name of the directory and subdirectory you wish to upload to, i.e. "USER/cells". <input type="text" name="path">
+		<br>
+		File: <input type="file" name="file"><br>
+		<input style="position:relative; top:10px;" type="submit" value="Upload">
+		</form>
+		<br>
+		<li>Take a look at your data using the file crawler link above</li>
+	</ol>
+	{% endif %}
+
 	<br>
 
 	<h1 style="padding-left:35px">

cellxgene_gateway/templates/loading.html

@@ -44,13 +44,9 @@
      </a>
      </div>
      <script>
-          var count = 0;
           window.setInterval(function(){
                var dots = document.getElementById('dots');
                dots.textContent = dots.textContent + '.';
-               if (count++ > 5) {
-                    window.location.reload();
-               }
           }, 1000);
      </script>
 </body>

environment-dev.yml

@@ -1,4 +1,4 @@
-name: cellxgene-gateway
+name: cellxgene-dev
 channels:
 - conda-forge
 dependencies:
@@ -6,8 +6,6 @@ dependencies:
 - requests
 - flask
 - psutil
-- black
-- pip
 - pip:
   - flask-api
-  - cellxgene>=0.15
+  - cellxgene

requirements.txt

@@ -1,4 +1,4 @@
-cellxgene>=0.15
+cellxgene
 flask
 flask_api
 psutil

run.sh.example

@@ -1,5 +1,8 @@
 export CELLXGENE_LOCATION=$(pwd)/.cellxgene-gateway/bin/cellxgene
 export CELLXGENE_DATA=../cellxgene_data
+export DEPLOYMENT_ENV=dev
+export GATEWAY_HOST=localhost:5005
+export GATEWAY_PROTOCOL=http
 export GATEWAY_IP=127.0.0.1
 
 #Once these are set, you run like a normal Flask app

setup.cfg

@@ -1,2 +0,0 @@
-[metadata]
-description-file = README.md

setup.py

@@ -1,69 +1,40 @@
-import codecs
 import os
-import sys
+from setuptools import setup
-
-from setuptools import find_packages, setup
-
-if sys.version_info < (3, 6):
-    sys.exit("Sorry, Python < 3.6 is not supported")
-
-
-def read(rel_path):
-    here = os.path.abspath(os.path.dirname(__file__))
-    with codecs.open(os.path.join(here, rel_path), "r") as fp:
-        return fp.read()
-
-
-def get_version(rel_path):
-    for line in read(rel_path).splitlines():
-        if line.startswith("__version__"):
-            delim = '"' if '"' in line else "'"
-            return line.split(delim)[1]
-    else:
-        raise RuntimeError("Unable to find version string.")
 
 
 def parse_requirements():
     reqs = []
     with open("requirements.txt", "r") as f:
-        for line in f.readlines():
+        for l in f.readlines():
-            reqs.append(line.strip("\n"))
+            reqs.append(l.strip("\n"))
     return reqs
 
 
-with open("README.md", "r") as fh:
-    long_description = fh.read()
-
 install_reqs = parse_requirements()
 
 setup(
     # mandatory
     name="cellxgene-gateway",
     # mandatory
-    version=get_version("cellxgene_gateway/__init__.py"),
+    version="0.1",
     # mandatory
     author="Niket Patel, Yohann Potier, Alok Saldanha",
     author_email="alok.saldanha@novartis.com",
     description=("Cellxgene Gateway"),
-    long_description=long_description,
-    long_description_content_type="text/markdown",
     license="MIT",
     keywords="visualization, genomics",
     url="http://github.com/Novartis/cellxgene-gateway",
-    packages=find_packages(),
+    packages=["cellxgene_gateway"],
     package_data={
         "cellxgene_gateway": [
             "static/css/homepagestyle.css",
-            "static/js/annotation.js",
             "static/nibr.ico",
-            "templates/*.html",
+            "templates/*.html"
-        ]
+    ]},
-    },
+    data_files=[('', ['Readme.md', 'LICENSE.txt'])],
-    data_files=[("", ["README.md", "LICENSE"])],
     install_requires=install_reqs,
     entry_points={
         "console_scripts": ["cellxgene-gateway=cellxgene_gateway.gateway:main"]
     },
     classifiers=["Topic :: Scientific/Engineering :: Visualization"],
-    python_requires=">=3.6",
 )

tests/test_cache_entry.py

@@ -1,35 +0,0 @@
-import unittest
-from cellxgene_gateway.cache_entry import CacheEntry, CacheEntryStatus
-from cellxgene_gateway.cache_key import CacheKey
-from cellxgene_gateway.items.item import ItemType
-from cellxgene_gateway.items.file.fileitem import FileItem
-from cellxgene_gateway.items.file.fileitem_source import FileItemSource
-
-key = CacheKey(
-    FileItem("/czi/", "pbmc3k.h5ad", ItemType.h5ad),
-    FileItemSource("/tmp", "local"),
-)
-
-
-class TestRenderEntry(unittest.TestCase):
-    def test_GIVEN_key_and_port_THEN_returns_loading_CacheEntry(self):
-        entry = CacheEntry.for_key("some-key", 1)
-        self.assertEqual(entry.status, CacheEntryStatus.loading)
-
-    def test_GIVEN_absolute_static_url_THEN_include_path(self):
-        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
-            "src:url(/static/assets/"
-        )
-        expected = "src:url(http://localhost:5005/source/local/view/czi/pbmc3k.h5ad/static/assets/"
-        self.assertEqual(actual, expected)
-
-    def test_GIVEN_absolute_src_THEN_include_path(self):
-        actual = CacheEntry.for_key(key, 8000).rewrite_text_content(
-            '<link rel="shortcut icon" href="/static/assets/favicon.ico">'
-        )
-        expected = '<link rel="shortcut icon" href="http://localhost:5005/source/local/view/czi/pbmc3k.h5ad/static/assets/favicon.ico">'
-        self.assertEqual(actual, expected)
-
-
-if __name__ == "__main__":
-    unittest.main()

tests/test_dir_util.py

@@ -0,0 +1,38 @@
+import unittest
+from unittest.mock import MagicMock, patch
+from cellxgene_gateway.dir_util import render_entry
+
+class TestRenderEntry(unittest.TestCase):
+    def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
+        entry = {
+                "path": "/somepath/",
+                "name": "entry",
+                "type": "file",
+            }
+        rendered = render_entry(entry)
+        self.assertIn('view/somepath', rendered)
+    def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
+        entry = {
+                "path": "/somepath",
+                "name": "entry",
+                "type": "file",
+            }
+        rendered = render_entry(entry)
+        self.assertIn('view/somepath', rendered)
+    def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
+        entry = {
+                "path": "somepath/",
+                "name": "entry",
+                "type": "file",
+            }
+        rendered = render_entry(entry)
+        self.assertIn('view/somepath', rendered)
+    def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
+        entry = {
+                "path": "somepath",
+                "name": "entry",
+                "type": "file",
+            }
+        rendered = render_entry(entry)
+        self.assertIn('view/somepath', rendered)
+        

tests/test_extra_scripts.py

@@ -1,26 +1,23 @@
 import unittest
 from unittest.mock import MagicMock, patch
-
 from cellxgene_gateway.extra_scripts import get_extra_scripts
 
-
 class TestExtraScripts(unittest.TestCase):
-    @patch("cellxgene_gateway.env.extra_scripts", new='["abc","def"]')
+    @patch('cellxgene_gateway.env.extra_scripts', new='["abc","def"]')
     def test_GIVEN_two_scripts_THEN_returns_two_strings(self):
-        self.assertEqual(get_extra_scripts(), ["abc", "def"])
+        self.assertEqual(get_extra_scripts(), ['abc', 'def'])
 
-    @patch("cellxgene_gateway.env.extra_scripts", new='["abc", "def"]')
+    @patch('cellxgene_gateway.env.extra_scripts', new='["abc", "def"]')
     def test_GIVEN_two_scripts_space_THEN_returns_two_strings(self):
-        self.assertEqual(get_extra_scripts(), ["abc", "def"])
+        self.assertEqual(get_extra_scripts(), ['abc', 'def'])
 
-    @patch("cellxgene_gateway.env.extra_scripts", new=None)
+    @patch('cellxgene_gateway.env.extra_scripts', new=None)
     def test_GIVEN_none_THEN_returns_empty_array(self):
         self.assertEqual(get_extra_scripts(), [])
 
-    @patch("cellxgene_gateway.env.extra_scripts", new="[]")
+    @patch('cellxgene_gateway.env.extra_scripts', new='[]')
     def test_GIVEN_empty_string_THEN_returns_empty_array(self):
         self.assertEqual(get_extra_scripts(), [])
 
-
+if __name__ == '__main__':
-if __name__ == "__main__":
     unittest.main()

tests/test_filecrawl.py

@@ -1,33 +0,0 @@
-import unittest
-from unittest.mock import MagicMock, patch
-
-from cellxgene_gateway.filecrawl import render_item
-from cellxgene_gateway.items.item import ItemType
-from cellxgene_gateway.items.file.fileitem import FileItem
-from cellxgene_gateway.items.file.fileitem_source import FileItemSource
-
-source = FileItemSource("/tmp")
-
-
-class TestRenderEntry(unittest.TestCase):
-    def test_GIVEN_path_both_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(
-            subpath="/somepath/", name="entry", type=ItemType.h5ad
-        )
-        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
-
-    def test_GIVEN_path_starts_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="/somepath", name="entry", type=ItemType.h5ad)
-        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
-
-    def test_GIVEN_path_ends_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="somepath/", name="entry", type=ItemType.h5ad)
-        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)
-
-    def test_GIVEN_path_no_slash_THEN_view_has_single_slash(self):
-        entry = FileItem(subpath="somepath", name="entry", type=ItemType.h5ad)
-        rendered = render_item(entry, source)
-        self.assertIn("view/somepath/entry/'", rendered)

tests/test_prune_process_cache.py

@@ -1,15 +1,13 @@
 import unittest
 from unittest.mock import MagicMock, patch
-
-from cellxgene_gateway.backend_cache import BackendCache
 from cellxgene_gateway.cache_entry import CacheEntry
-
+from cellxgene_gateway.backend_cache import BackendCache
 
 class TestPruneProcessCache(unittest.TestCase):
-    @patch("cellxgene_gateway.util.current_time_stamp", new=lambda: 0)
+    @patch('cellxgene_gateway.util.current_time_stamp', new=lambda:0)
-    @patch("cellxgene_gateway.env.ttl", new="10")
+    @patch('cellxgene_gateway.env.ttl', new='10')
-    @patch("cellxgene_gateway.cache_entry.CacheEntry")
+    @patch('cellxgene_gateway.cache_entry.CacheEntry')
-    @patch("cellxgene_gateway.cache_entry.CacheEntry")
+    @patch('cellxgene_gateway.cache_entry.CacheEntry')
     def test_GIVEN_one_old_one_new_THEN_prune_old(self, old, new):
         from cellxgene_gateway.prune_process_cache import PruneProcessCache
 
@@ -24,6 +22,5 @@ class TestPruneProcessCache(unittest.TestCase):
         self.assertEqual(len(cache.entry_list), 1)
         self.assertEqual(cache.entry_list[0], new)
 
-
+if __name__ == '__main__':
-if __name__ == "__main__":
     unittest.main()