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authorAdam Novak2020-04-09 15:52:23 -0700
committerAdam Novak2020-04-09 15:52:23 -0700
commit2cd6623aa0ddfe4e42b2d434e0523773bb3536ef (patch)
tree6c8a99afdf03837dba83e9d956f60316c09391d3
parentec6f3ad6268f576c1302101c7f0761fbf1d3dc55 (diff)
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Copy over/combine top-level project components
-rw-r--r--Dockerfile19
-rw-r--r--README.md45
-rw-r--r--bh20sequploader/main.py7
-rw-r--r--setup.py6
4 files changed, 71 insertions, 6 deletions
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..43fa8f2
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,19 @@
+# Dockerfile for containerizing the web interface
+FROM python:3.6-jessie
+WORKDIR /app
+
+RUN pip3 install gunicorn
+
+ADD LICENSE /app/
+ADD gittaggers.py /app/
+ADD setup.py /app/
+ADD README.md /app/
+ADD example /app/example
+ADD bh20seqanalyzer /app/bh20simplewebuploader
+ADD bh20sequploader /app/bh20sequploader
+ADD bh20simplewebuploader /app/bh20simplewebuploader
+
+RUN pip3 install -e .
+
+ENV PORT 8080
+CMD ["gunicorn", "-w", "4", "-b", "0.0.0.0:8080", "bh20simplewebuploader.main:app"]
diff --git a/README.md b/README.md
index a6fe052..4667310 100644
--- a/README.md
+++ b/README.md
@@ -159,4 +159,49 @@ odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5
For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
+# Web Interface
+
+This project comes with a simple web server that lets you use the sequence uploader from a browser. It will work as long as you install the packager with the `web` extra.
+
+To run it locally:
+
+```
+virtualenv --python python3 venv
+. venv/bin/activate
+pip install -e .[web]
+env FLASK_APP=bh20simplewebuploader/main.py flask run
+```
+
+Then visit [http://127.0.0.1:5000/](http://127.0.0.1:5000/).
+
+## Production
+
+For production deployment, you can use [gunicorn](https://flask.palletsprojects.com/en/1.1.x/deploying/wsgi-standalone/#gunicorn):
+
+```
+pip3 install gunicorn
+gunicorn bh20simplewebuploader.main:app
+```
+
+This runs on [http://127.0.0.1:8000/](http://127.0.0.1:8000/) by default, but can be adjusted with various [gunicorn options](http://docs.gunicorn.org/en/latest/run.html#commonly-used-arguments)
+
+## GNU Guix
+
+To run the web uploader in a GNU Guix environment
+
+```
+guix environment guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run
+```
+
+The containerized version looks like
+
+```
+guix environment -C guix --ad-hoc git python python-flask python-pyyaml nss-certs --network openssl
+```
+
+and
+
+```
+env FLASK_APP=bh20simplewebuploader/main.py flask run
+```
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 8b8fefe..d3ebc0c 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,7 +6,6 @@ import json
import urllib.request
import socket
import getpass
-from .qc_metadata import qc_metadata
ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -20,8 +19,6 @@ def main():
api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
- qc_metadata(args.metadata.name)
-
col = arvados.collection.Collection(api_client=api)
print("Reading FASTA")
@@ -32,8 +29,8 @@ def main():
f.write(r)
r = args.sequence.read(65536)
- print("Reading metadata")
- with col.open("metadata.yaml", "w") as f:
+ print("Reading JSONLD")
+ with col.open("metadata.jsonld", "w") as f:
r = args.metadata.read(65536)
print(r[0:20])
while r:
diff --git a/setup.py b/setup.py
index 48c25aa..41ace7b 100644
--- a/setup.py
+++ b/setup.py
@@ -16,6 +16,7 @@ except ImportError:
tagger = egg_info_cmd.egg_info
install_requires = ["arvados-python-client", "schema-salad"]
+web_requires = ["flask", "pyyaml"]
needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv)
pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else []
@@ -29,9 +30,12 @@ setup(
author="Peter Amstutz",
author_email="peter.amstutz@curii.com",
license="Apache 2.0",
- packages=["bh20sequploader", "bh20seqanalyzer"],
+ packages=["bh20sequploader", "bh20seqanalyzer", "bh20simplewebuploader"],
package_data={"bh20sequploader": ["bh20seq-schema.yml"]},
install_requires=install_requires,
+ extras_require={
+ 'web': web_requires
+ },
setup_requires=[] + pytest_runner,
tests_require=["pytest<5"],
entry_points={