diff options
Diffstat (limited to 'test/rest-api.org')
| -rw-r--r-- | test/rest-api.org | 31 |
1 files changed, 17 insertions, 14 deletions
diff --git a/test/rest-api.org b/test/rest-api.org index 4b66147..66639c3 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -2,6 +2,10 @@ # C-c ! insert date (use . for active agenda, C-u C-c ! for date+time, C-u C-c . for time) # C-c C-t task rotate # RSS_IMAGE_URL: http://xxxx.xxxx.free.fr/rss_icon.png +# C-c C-c to run test blocks +# +# This page runs tests and the HTML export doubles as documentation on +# http://covid19.genenetwork.org/apidoc #+TITLE: PubSeq REST API #+AUTHOR: Pjotr Prins @@ -13,8 +17,8 @@ * PubSeq REST API Here we document the public REST API that comes with PubSeq. The tests -run in the amazing emacs [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html][org-babel]]. See the bottom of this document -for running the tests inside emacs. +run in emacs [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html][org-babel]]. See the bottom of this document for running +the tests inside emacs. See bottom of the page how to run tests. ** Introduction @@ -36,7 +40,7 @@ The Python3 version is #+begin_src python :session :exports both import requests -baseURL="http://localhost:5000" # for development +baseURL="http://localhost:5067" # for development # baseURL="http://covid19.genenetwork.org" response = requests.get(baseURL+"/api/version") response_body = response.json() @@ -57,7 +61,7 @@ requests.get(baseURL+"/api/search?s=MT533203.1").json() #+end_src #+RESULTS: -| collection | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#sequence | +| collection | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126 | fasta | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126/sequence.fasta | id | : | MT533203.1 | info | : | http://identifiers.org/insdc/MT533203.1#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 @@ -77,7 +81,7 @@ 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 | +| collection | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126 | date | : | 2020-04-27 | fasta | : | http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+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 | @@ -148,22 +152,21 @@ requests.get(baseURL+"/api/ebi/sample-MT326090.1.xml").text * Configure emacs to run tests -Execute a code -block with C-c C-c. You may need to set +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") -(setq org-babel-eval-verbose t) + (org-babel-do-load-languages + 'org-babel-load-languages + '((python . t))) + (setq org-babel-python-command "python3") + (setq org-babel-eval-verbose t) + (setq org-confirm-babel-evaluate nil) #+end_src #+RESULTS: -: python3 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. +To see output of the interpreter open then *Python* buffer. |