From f368b3e047d14055bc63899771c782ebbb8c6553 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 20 Jul 2020 11:31:13 +0100
Subject: Start Public REST API

---
 bh20simplewebuploader/__init__.py |  1 +
 bh20simplewebuploader/api.py      | 16 +++++++
 bh20simplewebuploader/main.py     |  5 ---
 test/rest-api.org                 | 93 +++++++++++++++++++++++++++++++++++++++
 4 files changed, 110 insertions(+), 5 deletions(-)
 create mode 100644 bh20simplewebuploader/api.py
 create mode 100644 test/rest-api.org

diff --git a/bh20simplewebuploader/__init__.py b/bh20simplewebuploader/__init__.py
index e69de29..2dcc632 100644
--- a/bh20simplewebuploader/__init__.py
+++ b/bh20simplewebuploader/__init__.py
@@ -0,0 +1 @@
+import bh20simplewebuploader.api
diff --git a/bh20simplewebuploader/api.py b/bh20simplewebuploader/api.py
new file mode 100644
index 0000000..8bd1a22
--- /dev/null
+++ b/bh20simplewebuploader/api.py
@@ -0,0 +1,16 @@
+# Public API for PubSeq
+
+import sys
+import requests
+
+from flask import Flask, request, redirect, send_file, send_from_directory, render_template, jsonify
+from bh20simplewebuploader.main import app
+
+@app.route('/api/version')
+def version():
+    return jsonify({ 'service': 'PubSeq', 'version': 0.10 })
+
+@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
+def ebi_sample(id):
+    page = render_template('ebi-sample.xml',**locals())
+    return page
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index b40db6f..aad607d 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -936,8 +936,3 @@ def getSEQbyLocationAndSpecimenSource():
     r = requests.get(baseURL, params=payload)
     result = r.json()['results']['bindings']
     return str(result)
-
-@app.route('/api/ebi/sample-<id>.xml', methods=['GET'])
-def ebi_sample(id):
-    page = render_template('ebi-sample.xml',**locals())
-    return page
diff --git a/test/rest-api.org b/test/rest-api.org
new file mode 100644
index 0000000..c797cf3
--- /dev/null
+++ b/test/rest-api.org
@@ -0,0 +1,93 @@
+* PubSeq REST API
+
+Here we document the public REST API that comes with PubSeq. The tests
+are written and run in the amazing emacs [[https://orgmode.org/worg/org-contrib/babel/languages/ob-doc-python.html][org-babel]]. 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")
+#+end_src
+
+#+RESULTS:
+: python3
+
+To skip confirmations you may also want to set
+
+: (setq org-confirm-babel-evaluate nil)
+
+** Check the version
+
+#+begin_src python :session
+import requests
+response = requests.get("http://localhost:5000/api/version")
+response_body = response.json()
+assert response_body["service"] == "PubSeq", "PubSeq API not found"
+response_body
+#+end_src
+
+#+RESULTS:
+| service | : | PubSeq | version | : | 0.1 |
+
+** Fetch EBI XML
+
+#+begin_src python :session
+requests.get("http://localhost:5000/api/ebi/sample-MT32690.1.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">
+    <TITLE>COVID-19 PubSeq Sample</TITLE>
+    <SAMPLE_NAME>
+      <TAXON_ID>2697049</TAXON_ID>
+      <SCIENTIFIC_NAME>Severe acute respiratory syndrome coronavirus 2</SCIENTIFIC_NAME>
+      <COMMON_NAME>SARS-CoV-2</COMMON_NAME>
+    </SAMPLE_NAME>
+    <SAMPLE_ATTRIBUTES>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>investigation type</TAG>
+        <VALUE></VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>sequencing method</TAG>
+        <VALUE></VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>collection date</TAG>
+        <VALUE></VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (latitude)</TAG>
+        <VALUE></VALUE>
+     <UNITS>DD</UNITS>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (longitude)</TAG>
+        <VALUE></VALUE>
+     <UNITS>DD</UNITS>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+     <TAG>geographic location (country and/or sea)</TAG>
+     <VALUE></VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (region and locality)</TAG>
+        <VALUE></VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (material)</TAG>
+        <VALUE></VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>ENA-CHECKLIST</TAG>
+        <VALUE>ERC000011</VALUE>
+      </SAMPLE_ATTRIBUTE>
+    </SAMPLE_ATTRIBUTES>
+  </SAMPLE>
+</SAMPLE_SET>
+#+end_example
-- 
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