create IRODs example clients

see also https://gitlab.tuebingen.mpg.de/hpc-kyb/cast2irods-server

cast2irods1.py

+"""Get study metadata and subject attributes for all current studies."""
+
+import os
+import json
+
+import requests
+
+BASE_DIR = os.getenv('BASE_DIR', 'cast2irods')
+BASE_URL = os.getenv('BASE_URL', 'http://localhost:8000')
+TOKEN = os.getenv('TOKEN', '_YRJeCPMKH2-H7aNOFgTUy0iHCnm-2gp7OznR0qwxro')
+
+
+def fetch(path):
+    r = requests.get(BASE_URL + path, headers={'Authorization': 'token ' + TOKEN})
+    r.raise_for_status()
+    return r.json()
+
+
+if __name__ == '__main__':
+    studies = fetch('/studies/api/studies/?status=execution')
+    total = len(studies['studies'])
+    for i, study_id in enumerate(studies['studies']):
+        print("fetching study %i/%i" % (i + 1, total))
+        path = os.path.join(BASE_DIR, str(study_id))
+        os.makedirs(path, exist_ok=True)
+
+        info = fetch('/studies/api/studies/%i/' % study_id)
+        with open(os.path.join(path, 'study-info.json'), 'w') as fh:
+            json.dump(info, fh, indent=4)
+
+        domains = fetch('/execution/api/studies/%i/domains/' % study_id)
+        assert len(domains['domains']) == 1
+        domain = domains['domains'][0]['key']
+
+        subjects = []
+        pseudonyms = fetch('/execution/api/studies/%i/domains/%s/' % (study_id, domain))
+        for pseudonym in pseudonyms['pseudonyms']:
+            attributes = fetch('/execution/api/studies/%i/domains/%s/%s/attributes/' % (
+                study_id, domain, pseudonym
+            ))
+            subjects.append({'pseudonym': pseudonym, **attributes})
+
+        with open(os.path.join(path, 'subjects.json'), 'w') as fh:
+            json.dump(subjects, fh, indent=4)

cast2irods2.py

+"""Get internal pseudonym and attributes for a single subject."""
+
+import argparse
+import os
+
+import requests
+
+BASE_URL = os.getenv('BASE_URL', 'http://localhost:8000')
+TOKEN = os.getenv('TOKEN', '_YRJeCPMKH2-H7aNOFgTUy0iHCnm-2gp7OznR0qwxro')
+GENERAL_DOMAIN = os.getenv('GENERAL_DOMAIN', '35e61660-79e4-45f7-a3d4-a1ab35537b43')
+
+
+def fetch(path):
+    r = requests.get(BASE_URL + path, headers={'Authorization': 'token ' + TOKEN})
+    r.raise_for_status()
+    return r.json()
+
+
+def get_subject_data(study_id, study_pseudonym):
+    domains = fetch('/execution/api/studies/%i/domains/' % study_id)
+    assert len(domains['domains']) == 1
+    study_domain = domains['domains'][0]['key']
+
+    pseudonym = fetch('/execution/api/studies/%i/domains/%s/%s/%s/' % (
+        study_id, study_domain, study_pseudonym, GENERAL_DOMAIN
+    ))['pseudonym']
+    attributes = fetch('/subjects/api/subjects/%s/%s/attributes/' % (GENERAL_DOMAIN, pseudonym))
+    return {'pseudonym': pseudonym, **attributes}
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('study_id', type=int)
+    parser.add_argument('pseudonym')
+    args = parser.parse_args()
+
+    data = get_subject_data(args.study_id, args.pseudonym)
+    print(data)