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| -rw-r--r-- | test/rest-api.html | 224 | ||||
| -rw-r--r-- | test/rest-api.org | 7 |
2 files changed, 206 insertions, 25 deletions
diff --git a/test/rest-api.html b/test/rest-api.html index 421d75a..6e5bf5a 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> -<!-- 2020-07-21 Tue 01:32 --> +<!-- 2020-07-21 Tue 05:38 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>PubSeq REST API</title> @@ -252,21 +252,21 @@ for the JavaScript code in this tag. <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> -<li><a href="#org0db7287">1. PubSeq REST API</a> +<li><a href="#orgc76638c">1. PubSeq REST API</a> <ul> -<li><a href="#orgd98cd95">1.1. Introduction</a></li> -<li><a href="#org8951ab6">1.2. Fetch EBI XML</a></li> +<li><a href="#org247cf63">1.1. Introduction</a></li> +<li><a href="#orgcc2b1b0">1.2. Search for an entry</a></li> +<li><a href="#org0ef2d2f">1.3. Fetch metadata</a></li> +<li><a href="#org82c693c">1.4. Fetch EBI XML</a></li> </ul> </li> -<li><a href="#orgbde9911">2. Configure emacs to run tests</a></li> +<li><a href="#org49153e2">2. Configure emacs to run tests</a></li> </ul> </div> </div> - - -<div id="outline-container-org0db7287" class="outline-2"> -<h2 id="org0db7287"><span class="section-number-2">1</span> PubSeq REST API</h2> +<div id="outline-container-orgc76638c" class="outline-2"> +<h2 id="orgc76638c"><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 @@ -275,8 +275,8 @@ for running the tests inside emacs. </p> </div> -<div id="outline-container-orgd98cd95" class="outline-3"> -<h3 id="orgd98cd95"><span class="section-number-3">1.1</span> Introduction</h3> +<div id="outline-container-org247cf63" class="outline-3"> +<h3 id="org247cf63"><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 @@ -302,7 +302,9 @@ The Python3 version is <div class="org-src-container"> <pre class="src src-python">import requests -response = requests.get("http://covid19.genenetwork.org/api/version") +baseURL="http://localhost:5000" # for development +# baseURL="http://covid19.genenetwork.org" +response = requests.get(baseURL+"/api/version") response_body = response.json() assert response_body["service"] == "PubSeq", "PubSeq API not found" response_body @@ -339,24 +341,196 @@ response_body </div> </div> -<div id="outline-container-org8951ab6" class="outline-3"> -<h3 id="org8951ab6"><span class="section-number-3">1.2</span> Fetch EBI XML</h3> +<div id="outline-container-orgcc2b1b0" class="outline-3"> +<h3 id="orgcc2b1b0"><span class="section-number-3">1.2</span> Search for an entry</h3> <div class="outline-text-3" id="text-1-2"> <p> +When you use the search box on PubSeq it queries the REST end point +for information on the search items. For example +</p> + +<div class="org-src-container"> +<pre class="src src-python">requests.get(baseURL+"/api/search?s=MT533203.1").json() +</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-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> +</colgroup> +<tbody> +<tr> +<td class="org-left">collection</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126</a></td> +<td class="org-left">fasta</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta</a></td> +<td class="org-left">id</td> +<td class="org-left">:</td> +<td class="org-left">MT533203.1</td> +<td class="org-left">info</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://identifiers.org/insdc/MT533203.1#sequence">http://identifiers.org/insdc/MT533203.1#sequence</a></td> +</tr> +</tbody> +</table> + +<p> +where collection is the raw uploaded data. The hash value in <code>c=</code> is +computed on the contents of the Arvados keep <a href="https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html">collection</a> and effectively +acts as a deduplication uuid. +</p> +</div> +</div> + +<div id="outline-container-org0ef2d2f" class="outline-3"> +<h3 id="org0ef2d2f"><span class="section-number-3">1.3</span> Fetch metadata</h3> +<div class="outline-text-3" id="text-1-3"> +<p> +Using above collection link you can fetch the metadata in JSON as it +was uploaded originally from the SHeX expression, e.g. using +<a href="https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/">https://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/</a> +</p> + +<p> +But better to use the more advanced sample metadata fetcher +because is does a bit more in terms of expansion +</p> + +<div class="org-src-container"> +<pre class="src src-python">requests.get(baseURL+"/api/sample/MT533203.1.json").json() +</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" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> + +<col class="org-left" /> +</colgroup> +<tbody> +<tr> +<td class="org-left">collection</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126</a></td> +<td class="org-left">date</td> +<td class="org-left">:</td> +<td class="org-right">2020-04-27</td> +<td class="org-left">fasta</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta">http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta</a></td> +<td class="org-left">id</td> +<td class="org-left">:</td> +<td class="org-left">MT533203.1</td> +<td class="org-left">info</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://identifiers.org/insdc/MT533203.1#sequence">http://identifiers.org/insdc/MT533203.1#sequence</a></td> +<td class="org-left">mapper</td> +<td class="org-left">:</td> +<td class="org-left">minimap v. 2.17</td> +<td class="org-left">sequencer</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://www.ebi.ac.uk/efo/EFO_0008632">http://www.ebi.ac.uk/efo/EFO_0008632</a></td> +<td class="org-left">specimen</td> +<td class="org-left">:</td> +<td class="org-left"><a href="http://purl.obolibrary.org/obo/NCIT_C155831">http://purl.obolibrary.org/obo/NCIT_C155831</a></td> +</tr> +</tbody> +</table> +</div> +</div> + + + +<div id="outline-container-org82c693c" class="outline-3"> +<h3 id="org82c693c"><span class="section-number-3">1.4</span> Fetch EBI XML</h3> +<div class="outline-text-3" id="text-1-4"> +<p> PubSeq provides an API that is used to export formats that are suitable for uploading data to EBI/ENA from our <a href="http://covid19.genenetwork.org/export">EXPORT</a> menu. This is documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6">here</a>. </p> <div class="org-src-container"> -<pre class="src src-python">requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text +<pre class="src src-python">requests.get(baseURL+"/api/ebi/sample-MT326090.1.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"> + <SAMPLE alias="MT326090.1" center_name="COVID-19 PubSeq"> <TITLE>COVID-19 PubSeq Sample</TITLE> <SAMPLE_NAME> <TAXON_ID>2697049</TAXON_ID> @@ -370,11 +544,11 @@ documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>sequencing method</TAG> - <VALUE></VALUE> + <VALUE>http://purl.obolibrary.org/obo/OBI_0000759</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>collection date</TAG> - <VALUE></VALUE> + <VALUE>2020-03-21</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>geographic location (latitude)</TAG> @@ -396,7 +570,7 @@ documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>environment (material)</TAG> - <VALUE></VALUE> + <VALUE>http://purl.obolibrary.org/obo/NCIT_C155831</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>ENA-CHECKLIST</TAG> @@ -410,8 +584,8 @@ documented <a href="http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq </div> </div> -<div id="outline-container-orgbde9911" class="outline-2"> -<h2 id="orgbde9911"><span class="section-number-2">2</span> Configure emacs to run tests</h2> +<div id="outline-container-org49153e2" class="outline-2"> +<h2 id="org49153e2"><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 @@ -423,6 +597,7 @@ block with C-c C-c. You may need to set 'org-babel-load-languages '((python . t))) (setq org-babel-python-command "python3") +(setq org-babel-eval-verbose t) </pre> </div> @@ -433,11 +608,16 @@ To skip confirmations you may also want to set <pre class="example"> (setq org-confirm-babel-evaluate nil) </pre> + + +<p> +To see output of the inpreter open then <b>Python</b> buffer. +</p> </div> </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 2020-07-21 Tue 01:32</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 2020-07-21 Tue 05:38</small>. </div> </body> </html> diff --git a/test/rest-api.org b/test/rest-api.org index 6dd6616..4b66147 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -77,6 +77,7 @@ requests.get(baseURL+"/api/sample/MT533203.1.json").json() #+end_src #+RESULTS: +| collection | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126 | date | : | 2020-04-27 | fasta | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence | mapper | : | minimap v. 2.17 | sequencer | : | http://www.ebi.ac.uk/efo/EFO_0008632 | specimen | : | http://purl.obolibrary.org/obo/NCIT_C155831 | @@ -108,11 +109,11 @@ requests.get(baseURL+"/api/ebi/sample-MT326090.1.xml").text </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>sequencing method</TAG> - <VALUE></VALUE> + <VALUE>http://purl.obolibrary.org/obo/OBI_0000759</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>collection date</TAG> - <VALUE></VALUE> + <VALUE>2020-03-21</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>geographic location (latitude)</TAG> @@ -134,7 +135,7 @@ requests.get(baseURL+"/api/ebi/sample-MT326090.1.xml").text </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>environment (material)</TAG> - <VALUE></VALUE> + <VALUE>http://purl.obolibrary.org/obo/NCIT_C155831</VALUE> </SAMPLE_ATTRIBUTE> <SAMPLE_ATTRIBUTE> <TAG>ENA-CHECKLIST</TAG> |