From f39e4aaf3cfd6c430097ab404f390dafc03da8a5 Mon Sep 17 00:00:00 2001
From: CinciaT <67963359+CinciaT@users.noreply.github.com>
Date: Thu, 17 Dec 2020 18:13:41 +0100
Subject: [PATCH] Import Json from accession ID

Write the curl command to extract json file from each sample.
---
 EGA_curation/Import_BSD_API.py | 39 ++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)
 create mode 100644 EGA_curation/Import_BSD_API.py

diff --git a/EGA_curation/Import_BSD_API.py b/EGA_curation/Import_BSD_API.py
new file mode 100644
index 0000000..f946b21
--- /dev/null
+++ b/EGA_curation/Import_BSD_API.py
@@ -0,0 +1,39 @@
+import sys
+
+
+"""
+    With file with samples accession BSD ID, get all json files.
+    WARNING: remove EOF of AccessionFile
+"""
+
+def main(AccessionFile, AAP_USERNAME, AAP_PASSWORD):
+    af = open(AccessionFile, 'r')
+    file1 = open('Import_json.sh', 'w')
+    file1.write('#!/bin/bash' + '\n' + '\n')
+    BSD_ID = af.read().split('\n')
+    j = 0
+    file1.write("curl -u " + AAP_USERNAME + ":" + AAP_PASSWORD + " https://api.aai.ebi.ac.uk/auth > aap.jwt" + '\n')
+    file1.write('TOKEN=`cat aap.jwt`' + '\n' + '\n')
+    for i in range (0,len(BSD_ID)):
+        j+=1
+        if j != 999:
+            accession = BSD_ID[i]
+            accession = accession.replace('\r','')
+            file1.write("curl 'https://www.ebi.ac.uk/biosamples/samples/"+ accession + "'"+ " -X GET -H " + '"Content-Type: application/json;charset=UTF-8"'
+                    + ' -H ' + '"Accept: application/hal+json"' +' -H '+ '"Authorization: Bearer $TOKEN" ' + '>> Json_EGA_samples.txt' + '\n' + '\n' + 'echo -e ' +"'\n'"+ '>> Json_EGA_samples.txt' + '\n' + '\n')
+        else:
+            j = 0
+            file1.write("curl -u " + AAP_USERNAME + ":" + AAP_PASSWORD + " https://api.aai.ebi.ac.uk/auth > aap.jwt" + '\n')
+            file1.write('TOKEN=`cat aap.jwt`' + '\n' + '\n')
+            accession = BSD_ID[i]
+            accession = accession.replace('\r','')
+            file1.write("curl 'https://www.ebi.ac.uk/biosamples/samples/"+ accession + "'"+ " -X GET -H " + '"Content-Type: application/json;charset=UTF-8"'
+                + ' -H ' + '"Accept: application/hal+json"' +' -H '+ '"Authorization: Bearer $TOKEN" ' + '>> Json_EGA_samples.txt' + '\n' + '\n' + 'echo -e ' +"'\n'"+ '>> Json_EGA_samples.txt' + '\n' + '\n')
+        
+
+
+if __name__ == "__main__":
+    main(sys.argv[1], sys.argv[2], sys.argv[3])
+
+
+