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author | Adam Novak | 2020-04-09 15:52:23 -0700 |
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committer | Adam Novak | 2020-04-09 15:52:23 -0700 |
commit | 2cd6623aa0ddfe4e42b2d434e0523773bb3536ef (patch) | |
tree | 6c8a99afdf03837dba83e9d956f60316c09391d3 | |
parent | ec6f3ad6268f576c1302101c7f0761fbf1d3dc55 (diff) | |
download | bh20-seq-resource-2cd6623aa0ddfe4e42b2d434e0523773bb3536ef.tar.gz bh20-seq-resource-2cd6623aa0ddfe4e42b2d434e0523773bb3536ef.tar.lz bh20-seq-resource-2cd6623aa0ddfe4e42b2d434e0523773bb3536ef.zip |
Copy over/combine top-level project components
-rw-r--r-- | Dockerfile | 19 | ||||
-rw-r--r-- | README.md | 45 | ||||
-rw-r--r-- | bh20sequploader/main.py | 7 | ||||
-rw-r--r-- | setup.py | 6 |
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"] @@ -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: @@ -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={ |