diff options
| -rw-r--r-- | bh20simplewebuploader/main.py | 6 | ||||
| -rw-r--r-- | test/rest-api.html | 110 | ||||
| -rw-r--r-- | test/rest-api.org | 4 |
3 files changed, 103 insertions, 17 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index aad607d..029c2e3 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -638,6 +638,11 @@ def export_page(): def demo_page(): return render_template('demo.html',menu='DEMO',load_map=True) +@app.route('/apidoc') +def apidoc_page(): + buf = get_html_body('test/rest-api.html',"https://github.com/arvados/bh20-seq-resource/blob/master/test/rest-api.org") + return render_template('blog.html',menu='BLOG',embed=buf) + @app.route('/blog',methods=['GET']) def blog_page(): blog_content = request.args.get('id') # e.g. using-covid-19-pubseq-part3 @@ -652,7 +657,6 @@ def about_page(): buf = get_html_body('doc/web/about.html','https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/about.org') return render_template('about.html',menu='ABOUT',embed=buf) - ## Dynamic API functions starting here ## This is quick and dirty for now, just to get something out and demonstrate the queries ## Feel free to rename the functions/endpoints, feel free to process result so we get nicer JSON diff --git a/test/rest-api.html b/test/rest-api.html index e0a10c7..c50d116 100644 --- a/test/rest-api.html +++ b/test/rest-api.html @@ -3,7 +3,7 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <head> -<!-- 2020-07-20 Mon 06:02 --> +<!-- 2020-07-20 Mon 06:13 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>‎</title> @@ -246,18 +246,18 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#orgc04a8fc">1. PubSeq REST API</a> +<li><a href="#orgb24ef14">1. PubSeq REST API</a> <ul> -<li><a href="#org239717f">1.1. Introduction</a></li> -<li><a href="#org6637383">1.2. Fetch EBI XML</a></li> +<li><a href="#orgd7c015d">1.1. Introduction</a></li> +<li><a href="#orgb2caa89">1.2. Fetch EBI XML</a></li> </ul> </li> -<li><a href="#org1577576">2. Configure emacs to run tests</a></li> +<li><a href="#org68f26b2">2. Configure emacs to run tests</a></li> </ul> </div> </div> -<div id="outline-container-orgc04a8fc" class="outline-2"> -<h2 id="orgc04a8fc"><span class="section-number-2">1</span> PubSeq REST API</h2> +<div id="outline-container-orgb24ef14" class="outline-2"> +<h2 id="orgb24ef14"><span class="section-number-2">1</span> PubSeq REST API</h2> <div class="outline-text-2" id="text-1"> <p> Here we document the public REST API that comes with PubSeq. The tests @@ -266,8 +266,8 @@ for running the tests inside emacs. </p> </div> -<div id="outline-container-org239717f" class="outline-3"> -<h3 id="org239717f"><span class="section-number-3">1.1</span> Introduction</h3> +<div id="outline-container-orgd7c015d" class="outline-3"> +<h3 id="orgd7c015d"><span class="section-number-3">1.1</span> Introduction</h3> <div class="outline-text-3" id="text-1-1"> <p> We built a REST API for COVID-19 PubSeq. The API source code can be @@ -299,11 +299,39 @@ assert response_body["service"] == "PubSeq", "PubSeq API not found" response_body </pre> </div> + +<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> + + +<colgroup> +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-right" /> +</colgroup> +<tbody> +<tr> +<td class="org-left">service</td> +<td class="org-left">:</td> +<td class="org-left">PubSeq</td> +<td class="org-left">version</td> +<td class="org-left">:</td> +<td class="org-right">0.1</td> +</tr> +</tbody> +</table> </div> </div> -<div id="outline-container-org6637383" class="outline-3"> -<h3 id="org6637383"><span class="section-number-3">1.2</span> Fetch EBI XML</h3> +<div id="outline-container-orgb2caa89" class="outline-3"> +<h3 id="orgb2caa89"><span class="section-number-3">1.2</span> Fetch EBI XML</h3> <div class="outline-text-3" id="text-1-2"> <p> PubSeq provides an API that is used to export formats that are @@ -315,12 +343,66 @@ documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq <pre class="src src-python">requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text </pre> </div> + +<pre class="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> +</pre> </div> </div> </div> -<div id="outline-container-org1577576" class="outline-2"> -<h2 id="org1577576"><span class="section-number-2">2</span> Configure emacs to run tests</h2> +<div id="outline-container-org68f26b2" class="outline-2"> +<h2 id="org68f26b2"><span class="section-number-2">2</span> Configure emacs to run tests</h2> <div class="outline-text-2" id="text-2"> <p> Execute a code @@ -346,7 +428,7 @@ To skip confirmations you may also want to set </div> </div> <div id="postamble" class="status"> -<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-20 Mon 06:02</small>. +<hr><small>Created by <a href="http://thebird.nl/">Pjotr Prins</a> (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!<br />Modified 2020-07-20 Mon 06:13</small>. </div> </body> </html> diff --git a/test/rest-api.org b/test/rest-api.org index fa4e9e6..6d118b5 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -22,7 +22,7 @@ curl http://covid19.genenetwork.org/api/version The Python3 version is -#+begin_src python :session +#+begin_src python :session :exports both import requests response = requests.get("http://covid19.genenetwork.org/api/version") response_body = response.json() @@ -39,7 +39,7 @@ PubSeq provides an API that is used to export formats that are suitable for uploading data to EBI/ENA from our [[http://covid19.genenetwork.org/export][EXPORT]] menu. This is documented [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][here]]. -#+begin_src python :session +#+begin_src python :session :exports both requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text #+end_src |