new file: pc.upload_vcf.py

pc.upload_vcf.py

@@ -0,0 +1,222 @@
+#!/usr/bin/env python
+
+"""
+Usage: $0 PATIENT_ID VCF CREDENTIALS_FILE SERVER_NAME
+
+Upload the VCF file as an attachment for the given patient. For example:
+
+    $0 P0000102 path/to/file.vcf path/to/credentials.txt server_name
+
+credentials.txt should have one line with the form:
+
+    username:password
+"""
+
+from __future__ import with_statement
+
+import sys
+import os
+import logging
+import json
+
+try:
+    from httplib import HTTPConnection
+except ImportError:
+    from http.client import HTTPSConnection
+try:
+    from urllib import urlencode
+except ImportError:
+    from urllib.parse import urlencode
+from base64 import b64encode
+import xml.etree.ElementTree as ET
+
+# Set globally after parsing arguments
+CREDENTIALS = None
+SERVER = None
+
+def load_credentials(filename):
+    global CREDENTIALS
+    logging.info('Using credentials in file: {0}'.format(filename))
+    with open(filename) as ifp:
+        CREDENTIALS = ifp.read().strip()
+
+class Request(object):
+    def __init__(self, method, resource, content_type='text/plain', **kwargs):
+        auth = b64encode(CREDENTIALS.encode()).decode()
+        self._headers = {
+            'Authorization': 'Basic {0}'.format(auth),
+            'Content-Type': content_type,
+            'Accept': '*/*'
+            }
+        self._method = method
+        self._href = resource
+        self._kwargs = kwargs
+        self._conn = None
+
+    def __enter__(self):
+        self._conn = HTTPSConnection(SERVER)
+        #self._conn.set_debuglevel(1)
+        self._conn.request(self._method, self._href, headers=self._headers, **self._kwargs)
+        response = self._conn.getresponse()
+        return response
+
+    def __exit__(self, *args, **kwargs):
+        if self._conn:
+            self._conn.close()
+
+def get_consent(record_id):
+    logging.info('Loading Consents for record: {0}'.format(record_id))
+    href = '/rest/patients/{0}/consents/'.format(record_id)
+    result = 'no'
+    with Request('GET', href) as response:
+
+        assert response.status == 200, \
+            'ERROR getting PhenoTips.VCF object for record: {0}'.format(response.headers)
+
+        logging.info('Consents for record: {0}'.format(record_id))
+        # Convert bytes to string type and string type to dict
+        string = response.read().decode('utf-8')
+        json_obj = json.loads(string)
+        for consent in json_obj:
+            if consent['id'] == 'genetic':
+                result = consent['status']
+    return result
+
+def get_vcf_object(record_id):
+    href = '/rest/wikis/xwiki/spaces/data/pages/{0}/objects/PhenoTips.VCF'.format(record_id)
+    result = {}
+    with Request('GET', href) as response:
+        if response.status == 500:
+            # No VCF object for patient
+            logging.info('No PhenoTips.VCF object for record: {0}'.format(record_id))
+            return result
+
+        assert response.status == 200, \
+            'ERROR getting PhenoTips.VCF object for record: {0}'.format(response.headers)
+
+        logging.info('Found PhenoTips.VCF object for record: {0}'.format(record_id))
+        root = ET.fromstring(response.read())
+
+    # Server is Python 2.6.6, so does not support namespaces argument
+    # namespaces = {'xwiki': 'http://www.xwiki.org'}
+    summary = root.find('{http://www.xwiki.org}objectSummary')
+
+    if not summary:
+        logging.info('No VCF object exist in record: {0}'.format(record_id))
+        return None
+
+    for link in summary.findall('{http://www.xwiki.org}link'):
+        if link.get('rel') == 'http://www.xwiki.org/rel/object':
+            href = link.get('href')
+            logging.info('Found VCF object for {0}: {1}'.format(record_id, href))
+            result['href'] = href
+            break
+
+    result['headline'] = summary.findtext('{http://www.xwiki.org}headline', '').strip()
+    return result
+
+def set_vcf_properties(record_id, vcf_object, filename, reference_genome='GRCh37'):
+    method = 'PUT'
+    href = vcf_object.get('href') if vcf_object else None
+    if not href:
+        # Create VCF missing properties object
+        method = 'POST'
+        href = '/rest/wikis/xwiki/spaces/data/pages/{0}/objects'.format(record_id)
+
+    filebase = os.path.basename(filename)
+    params = {
+        'className': 'PhenoTips.VCF',
+        'property#filename': filebase,
+        'property#reference_genome': reference_genome,
+        }
+
+    content_type = 'application/x-www-form-urlencoded'
+
+    with Request(method, href, content_type=content_type, body=urlencode(params)) as response:
+        assert response.status in [201, 202], \
+            'Unexpected response ({0}) from setting VCF properties'.format(response.status)
+
+        if response.status == 201:
+            href = response.getheader('Location')
+            logging.info('Created VCF object: {0}'.format(href))
+            return href
+        elif response.status == 202:
+            logging.info('Updated VCF object: {0}'.format(href))
+            return vcf_object
+
+def delete_old_vcf_file(record_id):
+    attachment_name = '{0}.vcf'.format(record_id)
+    href = '/rest/wikis/xwiki/spaces/data/pages/{0}/attachments/{1}'.format(record_id, attachment_name)
+    with Request('HEAD', href) as response:
+        if response.status in [200, 500]:
+            logging.info('Found linked old-style VCF: {0}'.format(attachment_name))
+        else:
+            return
+
+    with Request('DELETE', href) as response:
+        assert response.status in [204, 500], \
+            'Unexpected response ({0}) from deleting VCF file'.format(response.status)
+        logging.info('Deleted attachment: {0}'.format(attachment_name))
+
+    with Request('DELETE', href) as response:
+        assert response.status == 404, \
+            'Failed to delete existing old-style VCF file'.format(response.status)
+
+def upload_vcf_file(record_id, filename):
+    attachment_name = os.path.basename(filename)
+    href = '/rest/wikis/xwiki/spaces/data/pages/{0}/attachments/{1}'.format(record_id, attachment_name)
+    with open(filename) as file:
+        with Request('PUT', href, content_type='text/plain', body=file) as response:
+            assert response.status in [201, 202], \
+                'Unexpected response ({0}) from uploading VCF file'.format(response.status)
+            if response.status == 201:
+                logging.info('Created attachment: {0}'.format(attachment_name))
+            elif response.status == 202:
+                logging.info('Updated attachment: {0}'.format(attachment_name))
+
+def script(record_id, vcf_filename, credentials_file, server_name):
+    global SERVER
+    SERVER = server_name
+
+    load_credentials(credentials_file)
+
+    consent_granted = get_consent(record_id)
+    if consent_granted == 'no':
+        logging.info('Record {0} has not granted genetic consent, can not upload VCF'.format(record_id))
+        return
+
+    vcf_object = get_vcf_object(record_id)
+
+    vcf_basename = os.path.basename(vcf_filename)
+    if vcf_object and vcf_object.get('headline', '') == vcf_basename:
+        # Filename already appears to be properly linked to record, skip
+        logging.info('Record {0} already has linked VCF file: {1}'.format(record_id, vcf_basename))
+    else:
+        href = set_vcf_properties(record_id, vcf_object, vcf_filename)
+
+        if href:
+            upload_vcf_file(record_id, vcf_filename)
+
+    # Optional, remove old VCF file
+    # delete_old_vcf_file(record_id)
+
+
+def parse_args(args):
+    from optparse import OptionParser
+    usage = "usage: %prog [options] PATIENT_ID VCF CREDENTIALS_FILE SERVER_NAME"
+    parser = OptionParser(usage=usage)
+    (options, args) = parser.parse_args()
+
+    if len(args) != 4:
+        parser.error('Invalid number of arguments')
+
+    return (options, args)
+
+def main(args=sys.argv[1:]):
+    options, args = parse_args(args)
+    kwargs = dict(options.__dict__)
+    logging.basicConfig(level=logging.DEBUG)
+    script(*args, **kwargs)
+
+if __name__ == '__main__':
+    sys.exit(main())