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-rw-r--r--test/rest-api.org31
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.