From 2e96d0d87abd6357868114b0b59ee66b08985235 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 21 Jul 2020 07:52:13 +0100 Subject: Documenting exports and REST API --- bh20simplewebuploader/main.py | 5 +- bh20simplewebuploader/templates/export.html | 28 +-- doc/web/export.html | 307 ++++++++++++++++++++++++++++ doc/web/export.org | 32 +++ test/rest-api.html | 41 ++-- test/rest-api.org | 17 ++ 6 files changed, 388 insertions(+), 42 deletions(-) create mode 100644 doc/web/export.html create mode 100644 doc/web/export.org diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index 029c2e3..c306749 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -632,7 +632,8 @@ def validated_page(): @app.route('/export') def export_page(): - return render_template('export.html',menu='EXPORT') + buf = get_html_body('doc/web/export.html',"https://github.com/arvados/bh20-seq-resource/blob/master/doc/web/export.org") + return render_template('export.html',menu='EXPORT',embed=buf) @app.route('/demo') def demo_page(): @@ -641,7 +642,7 @@ def demo_page(): @app.route('/apidoc') def apidoc_page(): buf = get_html_body('test/rest-api.html',"https://github.com/arvados/bh20-seq-resource/blob/master/test/rest-api.org") - return render_template('blog.html',menu='BLOG',embed=buf) + return render_template('blog.html',menu='BLOG',embed=buf,blog=True) @app.route('/blog',methods=['GET']) def blog_page(): diff --git a/bh20simplewebuploader/templates/export.html b/bh20simplewebuploader/templates/export.html index aaceac9..3588e57 100644 --- a/bh20simplewebuploader/templates/export.html +++ b/bh20simplewebuploader/templates/export.html @@ -5,30 +5,10 @@ {% include 'banner.html' %} {% include 'menu.html' %} -

Export Data

-
- - COVID-19 PubSeq allows for exporting forms and data for other - services. - -

SPARQL

- -

- First of all, PubSeq exports a SPARQL endpoint - here that allows - you do do any query on the data. See this - document for - examples. -

- -

Export EBI/ENA Forms

- -

- Uploading data to EBI/ENA with PubSeq is described - here. To - export, first search for an uploaded entry through its - identifier: -

+ + {% if embed %} + {{ embed|safe }} + {% endif %}
diff --git a/doc/web/export.html b/doc/web/export.html new file mode 100644 index 0000000..cc92d4f --- /dev/null +++ b/doc/web/export.html @@ -0,0 +1,307 @@ + + + + + + + +About/FAQ + + + + + + +
+

About/FAQ

+ + +
+

1 Export data

+
+

+Apart from straight file downloads COVID-19 PubSeq allows for +exporting forms and data for other services. +

+
+
+ +
+

2 SPARQL API

+
+

+First of all, PubSeq exports a SPARQL endpoint here that allows you do +do any query on the data. See this document for examples. +

+
+
+ +
+

3 REST API

+
+

+In addition to above flexible SPARQL endpoint - which is essentially +is a query REST API - PubSeq exports its own +REST API. +

+
+
+ +
+

4 Export EBI/ENA Forms

+
+

+Uploading data to EBI/ENA with PubSeq is described here. +

+ +

+To export, +first search for an uploaded entry through its identifier: +

+
+
+
+
+
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 01:51. +
+ + diff --git a/doc/web/export.org b/doc/web/export.org new file mode 100644 index 0000000..aa7d680 --- /dev/null +++ b/doc/web/export.org @@ -0,0 +1,32 @@ +#+TITLE: About/FAQ +#+AUTHOR: Pjotr Prins + +* Table of Contents :TOC:noexport: + - [[#export-data][Export data]] + - [[#sparql-api][SPARQL API]] + - [[#rest-api][REST API]] + - [[#export-ebiena-forms][Export EBI/ENA Forms]] + +* Export data + +Apart from straight file [[http://covid19.genenetwork.org/download][downloads]] COVID-19 PubSeq allows for +exporting forms and data for other services. + +* SPARQL API + + +First of all, PubSeq exports a SPARQL endpoint [[http://sparql.genenetwork.org/sparql/][here]] that allows you do +do any query on the data. See this [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part1][document]] for examples. + +* REST API + +In addition to above flexible SPARQL endpoint - which is essentially +is a query REST API - PubSeq exports its own +[[http://covid19.genenetwork.org/apidoc][REST API]]. + +* Export EBI/ENA Forms + +Uploading data to EBI/ENA with PubSeq is described [[http://covid19.genenetwork.org/blog?id=using-covid-19-pubseq-part6][here]]. + +To export, +first search for an uploaded entry through its identifier: diff --git a/test/rest-api.html b/test/rest-api.html index c50d116..421d75a 100644 --- a/test/rest-api.html +++ b/test/rest-api.html @@ -3,10 +3,10 @@ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> - + -‎ +PubSeq REST API + -
+
+ UP + | + HOME +
+

PubSeq REST API

-
-

1 PubSeq REST API

+ + + +
+

1 PubSeq REST API

Here we document the public REST API that comes with PubSeq. The tests @@ -266,8 +275,8 @@ for running the tests inside emacs.

-
-

1.1 Introduction

+
+

1.1 Introduction

We built a REST API for COVID-19 PubSeq. The API source code can be @@ -330,8 +339,8 @@ response_body

-
-

1.2 Fetch EBI XML

+
+

1.2 Fetch EBI XML

PubSeq provides an API that is used to export formats that are @@ -401,8 +410,8 @@ documented -

2 Configure emacs to run tests

+
+

2 Configure emacs to run tests

Execute a code @@ -428,7 +437,7 @@ To skip confirmations you may also want to set

-
Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp!
Modified 2020-07-20 Mon 06:13. +
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 01:32.
diff --git a/test/rest-api.org b/test/rest-api.org index 6d118b5..31fc792 100644 --- a/test/rest-api.org +++ b/test/rest-api.org @@ -1,3 +1,17 @@ +# C-c C-e h h publish +# 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 + +#+TITLE: PubSeq REST API +#+AUTHOR: Pjotr Prins +#+HTML_LINK_HOME: http://covid19.genenetwork.org/apidoc +# OPTIONS: section-numbers: nil, with-drawers: t + +#+HTML_HEAD: + + + * PubSeq REST API Here we document the public REST API that comes with PubSeq. The tests @@ -33,6 +47,9 @@ response_body #+RESULTS: | service | : | PubSeq | version | : | 0.1 | +** Fetch metadata + + ** Fetch EBI XML PubSeq provides an API that is used to export formats that are -- cgit v1.2.3