From f44cbe10ee5dc040d090d0350c626d1982fc6f6c Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 5 Nov 2020 11:22:26 +0000 Subject: Updated API doc --- test/rest-api.html | 148 ++++++++++++++++++++++------------------------------- test/rest-api.org | 25 +++++---- 2 files changed, 74 insertions(+), 99 deletions(-) diff --git a/test/rest-api.html b/test/rest-api.html index 6e5bf5a..2059ccb 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"> - + PubSeq REST API @@ -40,7 +40,7 @@ } pre.src { position: relative; - overflow: visible; + overflow: auto; padding-top: 1.2em; } pre.src:before { @@ -195,50 +195,26 @@ @@ -252,31 +228,31 @@ for the JavaScript code in this tag.

Table of Contents

-
-

1 PubSeq REST API

+
+

1 PubSeq REST API

Here we document the public REST API that comes with PubSeq. The tests -run in the amazing emacs org-babel. See the bottom of this document -for running the tests inside emacs. +run in emacs org-babel. See the bottom of this document for running +the tests inside emacs. See bottom of the page how to run tests.

- -
-

1.2 Search for an entry

+ -
-

1.3 Fetch metadata

+
+

1.3 Fetch metadata

Using above collection link you can fetch the metadata in JSON as it @@ -423,7 +399,7 @@ because is does a bit more in terms of expansion

-
requests.get(baseURL+"/api/sample/MT533203.1.json").json()
+
requests.get(baseURL+"/api/sample/MT533203.1.json").json()
@@ -483,13 +459,13 @@ because is does a bit more in terms of expansion collection : -http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126 +http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126 date : 2020-04-27 fasta : -http://collections.lugli.arvadosapi.com/c=0015b0d65dfd2e82bb3cee4436bf2893+126/sequence.fasta +http://collections.lugli.arvadosapi.com/c=b16901333ea1754a1e0409bf3caf7d22+126/sequence.fasta id : MT533203.1 @@ -513,8 +489,8 @@ because is does a bit more in terms of expansion -
-

1.4 Fetch EBI XML

+
+

1.4 Fetch EBI XML

PubSeq provides an API that is used to export formats that are @@ -523,11 +499,11 @@ documented -

requests.get(baseURL+"/api/ebi/sample-MT326090.1.xml").text
+
requests.get(baseURL+"/api/ebi/sample-MT326090.1.xml").text
-
+
 <?xml version="1.0" encoding="UTF-8"?>
 <SAMPLE_SET>
   <SAMPLE alias="MT326090.1" center_name="COVID-19 PubSeq">
@@ -584,20 +560,20 @@ documented 
-
2 Configure emacs to run tests

+

+
2 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
 

 
 

 
(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-babel-python-command "python3")
+(setq org-babel-eval-verbose t)
+(setq org-confirm-babel-evaluate nil)
 

 

 
@@ -617,7 +593,7 @@ To see output of the inpreter open then Python buffer.
 

 

 

-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-07-21 Tue 05:38.
+
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-11-05 Thu 05:21.
 

 
 
diff --git a/test/rest-api.org b/test/rest-api.org
index 4b66147..28d7559 100644
--- a/test/rest-api.org
+++ b/test/rest-api.org
@@ -13,8 +13,8 @@
 * 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 +36,7 @@ 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 +57,7 @@ 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 +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 |
+| 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 |
 
 
 
@@ -148,19 +148,18 @@ 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
 
-- 
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