diff options
Diffstat (limited to 'test/rest-api.org')
| -rw-r--r-- | test/rest-api.org | 35 |
1 files changed, 30 insertions, 5 deletions
diff --git a/test/rest-api.org b/test/rest-api.org index 31fc792..1930d8b 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -10,8 +10,6 @@ #+HTML_HEAD: <link rel="Blog stylesheet" type="text/css" href="blog.css" /> - - * PubSeq REST API Here we document the public REST API that comes with PubSeq. The tests @@ -38,7 +36,9 @@ The Python3 version is #+begin_src python :session :exports both 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 @@ -47,9 +47,31 @@ response_body #+RESULTS: | service | : | PubSeq | version | : | 0.1 | +** Search for an entry + +When you use the search box on PubSeq it queries the REST end point +for information on the search items. For example + +#+begin_src python :session :exports both +requests.get(baseURL+"/api/search?s=MT326090.1").json() +#+end_src + +#+RESULTS: +| collection | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=10eaef75e0b875f81aa1f411c75370cf+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence | +| collection | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=5a4c815f3e076ad7760a91864c39dd07+126/sequence.fasta | id | : | MT326090.1 | info | : | http://identifiers.org/insdc/MT326090.1#sequence | + +where collection is the raw uploaded data. The hash value in ~c=~ is +computed on the contents of the Arvados keep [[https://doc.arvados.org/v2.0/user/tutorials/tutorial-keep-mount-gnu-linux.html][collection]] and effectively +acts as a deduplication uuid. + ** Fetch metadata +#+begin_src python :session :exports both +#+end_src + + + ** Fetch EBI XML PubSeq provides an API that is used to export formats that are @@ -57,14 +79,14 @@ suitable for uploading data to EBI/ENA from our [[http://covid19.genenetwork.org documented [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][here]]. #+begin_src python :session :exports both -requests.get("http://covid19.genenetwork.org/api/ebi/sample-MT32690.1.xml").text +requests.get(baseURL+"/api/ebi/sample-MT326090.1.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"> + <SAMPLE alias="MT326090.1" center_name="COVID-19 PubSeq"> <TITLE>COVID-19 PubSeq Sample</TITLE> <SAMPLE_NAME> <TAXON_ID>2697049</TAXON_ID> @@ -125,6 +147,7 @@ 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) #+end_src #+RESULTS: @@ -133,3 +156,5 @@ block with C-c C-c. You may need to set To skip confirmations you may also want to set : (setq org-confirm-babel-evaluate nil) + +To see output of the inpreter open then *Python* buffer. |