diff options
| -rw-r--r-- | bh20simplewebuploader/__init__.py | 1 | ||||
| -rw-r--r-- | bh20simplewebuploader/api.py | 16 | ||||
| -rw-r--r-- | bh20simplewebuploader/main.py | 5 | ||||
| -rw-r--r-- | test/rest-api.org | 93 |
4 files changed, 110 insertions, 5 deletions
diff --git a/bh20simplewebuploader/__init__.py b/bh20simplewebuploader/__init__.py index e69de29..2dcc632 100644 --- a/bh20simplewebuploader/__init__.py +++ b/bh20simplewebuploader/__init__.py @@ -0,0 +1 @@ +import bh20simplewebuploader.api diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py new file mode 100644 index 0000000..8bd1a22 --- /dev/null +++ b/bh20simplewebuploader/api.py @@ -0,0 +1,16 @@ +# Public API for PubSeq + +import sys +import requests + +from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify +from bh20simplewebuploader.main import app + +@app.route('/api/version') +def version(): + return jsonify({ 'service': 'PubSeq', 'version': 0.10 }) + +@app.route('/api/ebi/sample-<id>.xml', methods=['GET']) +def ebi_sample(id): + page = render_template('ebi-sample.xml',**locals()) + return page diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index b40db6f..aad607d 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -936,8 +936,3 @@ def getSEQbyLocationAndSpecimenSource(): r = requests.get(baseURL, params=payload) result = r.json()['results']['bindings'] return str(result) - -@app.route('/api/ebi/sample-<id>.xml', methods=['GET']) -def ebi_sample(id): - page = render_template('ebi-sample.xml',**locals()) - return page diff --git a/test/rest-api.org b/test/rest-api.org new file mode 100644 index 0000000..c797cf3 --- /dev/null +++ b/test/rest-api.org @@ -0,0 +1,93 @@ +* PubSeq REST API + +Here we document the public REST API that comes with PubSeq. The tests +are written and run in the amazing emacs [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html][org-babel]]. Execute a code +block with C-c C-c. You may need to set + +#+begin_src elisp +(org-babel-do-load-languages + 'org-babel-load-languages + '((python . t))) +(setq org-babel-python-command "python3") +#+end_src + +#+RESULTS: +: python3 + +To skip confirmations you may also want to set + +: (setq org-confirm-babel-evaluate nil) + +** Check the version + +#+begin_src python :session +import requests +response = requests.get("http://localhost:5000/api/version") +response_body = response.json() +assert response_body["service"] == "PubSeq", "PubSeq API not found" +response_body +#+end_src + +#+RESULTS: +| service | : | PubSeq | version | : | 0.1 | + +** Fetch EBI XML + +#+begin_src python :session +requests.get("http://localhost:5000/api/ebi/sample-MT32690.1.xml").text +#+end_src + +#+RESULTS: +#+begin_example +<?xml version="1.0" encoding="UTF-8"?> +<SAMPLE_SET> + <SAMPLE alias="MT32690.1" center_name="COVID-19 PubSeq"> + <TITLE>COVID-19 PubSeq Sample</TITLE> + <SAMPLE_NAME> + <TAXON_ID>2697049</TAXON_ID> + <SCIENTIFIC_NAME>Severe acute respiratory syndrome coronavirus 2</SCIENTIFIC_NAME> + <COMMON_NAME>SARS-CoV-2</COMMON_NAME> + </SAMPLE_NAME> + <SAMPLE_ATTRIBUTES> + <SAMPLE_ATTRIBUTE> + <TAG>investigation type</TAG> + <VALUE></VALUE> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>sequencing method</TAG> + <VALUE></VALUE> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>collection date</TAG> + <VALUE></VALUE> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>geographic location (latitude)</TAG> + <VALUE></VALUE> + <UNITS>DD</UNITS> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>geographic location (longitude)</TAG> + <VALUE></VALUE> + <UNITS>DD</UNITS> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>geographic location (country and/or sea)</TAG> + <VALUE></VALUE> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>geographic location (region and locality)</TAG> + <VALUE></VALUE> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>environment (material)</TAG> + <VALUE></VALUE> + </SAMPLE_ATTRIBUTE> + <SAMPLE_ATTRIBUTE> + <TAG>ENA-CHECKLIST</TAG> + <VALUE>ERC000011</VALUE> + </SAMPLE_ATTRIBUTE> + </SAMPLE_ATTRIBUTES> + </SAMPLE> +</SAMPLE_SET> +#+end_example |