Updated by Yoochan Myung 2024-04-11

File get.py Modified

     if job_type == 'single':

-        req = requests.get(URL_single, data=params)

+        req = requests.get(URL_single, json=params)

         print(req.json())

         return True

     else:

                         help='Job identifier code generated upon submission')

     args = parser.parse_args()

-    main(args)

+    main(args)

Updated by Yoochan Myung 2024-04-10

View revision

File post.py Modified

 URL_single = "https://biosig.lab.uq.edu.au/csm_ab/api/prediction_single"

 URL_pose = "https://biosig.lab.uq.edu.au/csm_ab/api/prediction_pose"

 def main(args):

     if args.job_type == 'single':

-        pdb_file = args.pdb_file

-        pdb_accession = args.pdb_accession

-        if pdb_accession:

-            data = {"pdb_accession": pdb_accession}

-            req = requests.post(URL_single, data=data)

+        if args.pdb_accession:

+            data = {"pdb_accession": args.pdb_accession}

+            req = requests.post(URL_single, json=data)

             print(req.json())

         else:

-            pdb_to_submit = {"pdb_file": pdb_file}

-            req = requests.post(URL_single, files=pdb_to_submit)

+            files = {"pdb_file": open(args.pdb_file.name, 'rb')}

+            req = requests.post(URL_single, files=files)

             print(req.json())

-        return True

     else:

-        receptor_file = args.receptor_file

-        pose_file = args.pose_file

-        file_to_submit = {

-            'receptor_file': receptor_file, 'pose_file': pose_file}

-        req = requests.post(URL_pose, files=file_to_submit)

+        files = {'receptor_file': open(args.receptor_file.name, 'rb'), 'pose_file': open(args.pose_file.name, 'rb')}

+        req = requests.post(URL_pose, files=files)

         print(req.json())

 if __name__ == "__main__":

     parser = argparse.ArgumentParser(

         description='Job submission for CSM-AB')

-    parser.add_argument('job_type', type=str, choices=['single', 'pose'],

-                        help='choose between single and pose prediction')

-    parser.add_argument('--pdb_file', dest='pdb_file',

-                        type=argparse.FileType('r'), help='PDB file')

-    parser.add_argument('--pdb_accession', dest='pdb_accession',

-                        type=str, help='Type PDB-ID')

-    parser.add_argument('--receptor_file', dest='receptor_file',

-                        type=argparse.FileType('r'), help='PDB file')

-    parser.add_argument('--pose_file', dest='pose_file',

-                        type=argparse.FileType('r'), help='PDB file')

+    parser.add_argument('job_type', type=str, choices=['single', 'pose'], help='choose between single and pose prediction')

+    parser.add_argument('--pdb_file', dest='pdb_file', type=argparse.FileType('r'), help='PDB file')

+    parser.add_argument('--pdb_accession', dest='pdb_accession', type=str, help='Type PDB-ID')

+    parser.add_argument('--receptor_file', dest='receptor_file', type=argparse.FileType('r'), help='PDB file')

+    parser.add_argument('--pose_file', dest='pose_file', type=argparse.FileType('r'), help='PDB file')

     args = parser.parse_args()

-    print(args.job_type, args.pdb_file, args.pdb_accession)

     if args.job_type == 'single':

-        if (args.pdb_file == None and args.pdb_accession == None):

-            print(

-                'post.py: error: missing arguments: Please provide --pdb_file or --pdb_accession')

-            sys.exit(1)

+        if not (args.pdb_file or args.pdb_accession):

+            parser.error('For single job type, either --pdb_file or --pdb_accession must be provided.')

     else:

-        if args.receptor_file == None or args.pose_file == None:

-            print(

-                'post.py: error: missing arguments: Please provide --receptor_file or --pose_file')

-            sys.exit(1)

+        if not (args.receptor_file and args.pose_file):

+            parser.error('For pose job type, both --receptor_file and --pose_file must be provided.')

     main(args)

Updated by Yoochan Myung 2023-03-09

View revision

File post.py Modified

             print(req.json())

         else:

             pdb_to_submit = {"pdb_file": pdb_file}

-            req = requests.post(URL_pose, files=pdb_to_submit)

+            req = requests.post(URL_single, files=pdb_to_submit)

             print(req.json())

         return True

     else:

Updated by Yoochan Myung 2023-03-09

View revision

File get.py Modified

 import requests

 import sys

-URL_single = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_single"

-URL_pose = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_pose"

+URL_single = "https://biosig.lab.uq.edu.au/csm_ab/api/prediction_single"

+URL_pose = "https://biosig.lab.uq.edu.au/csm_ab/api/prediction_pose"

 def main(args):

File post.py Modified

 import requests

 import sys

-URL_single = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_single"

-URL_pose = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_pose"

+URL_single = "https://biosig.lab.uq.edu.au/csm_ab/api/prediction_single"

+URL_pose = "https://biosig.lab.uq.edu.au/csm_ab/api/prediction_pose"

 def main(args):

Updated by Yoochan Myung 2022-01-21

View revision

File get.py Modified

 import requests

 import sys

-URL = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_single"

+URL_single = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_single"

+URL_pose = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_pose"

 def main(args):

+    job_type = args.job_type

     job_id = args.job_id

     params = {

         "job_id": job_id,

-    req = requests.get(URL, data=params)

-    print(req.json())

-    return True

+    if job_type == 'single':

+        req = requests.get(URL_single, data=params)

+        print(req.json())

+        return True

+    else:

+        req = requests.get(URL_pose, data=params)

+        print(req.json())

+        return True

 if __name__ == "__main__":

-    parser = argparse.ArgumentParser(description='Retrieve job results for single prediction - CSM-AB')

-    parser.add_argument('--job_id', dest='job_id', type=str, help='Job identifier code generated upon submission', required=False, default=None)

+    parser = argparse.ArgumentParser(

+        description='Retrieve job results for CSM-AB')

+    parser.add_argument('job_type', type=str, choices=['single', 'pose'],

+                        help='choose between single and pose prediction')

+    parser.add_argument('job_id', type=str,

+                        help='Job identifier code generated upon submission')

     args = parser.parse_args()

-    if args.job_id == None:

-        print('usage: get.py [-h] [--job_id JOB_ID]')

-        print('get.py: error: missing arguments: Please provide --job_id')

-        sys.exit(1)

     main(args)

File post.py Modified

 import requests

 import sys

-URL = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_single"

+URL_single = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_single"

+URL_pose = "http://biosig.unimelb.edu.au/csm_ab/api/prediction_pose"

 def main(args):

-    pdb_file = args.pdb_file

-    pdb_accession = args.pdb_accession

-    if pdb_accession:

-        data = {"pdb_accession":pdb_accession}

-        req = requests.post(URL, data=data)

-        print(req.json())

+    if args.job_type == 'single':

+        pdb_file = args.pdb_file

+        pdb_accession = args.pdb_accession

+        if pdb_accession:

+            data = {"pdb_accession": pdb_accession}

+            req = requests.post(URL_single, data=data)

+            print(req.json())

+        else:

+            pdb_to_submit = {"pdb_file": pdb_file}

+            req = requests.post(URL_pose, files=pdb_to_submit)

+            print(req.json())

+        return True

     else:

-        pdb_to_submit = {"pdb_file": pdb_file}

-        req = requests.post(URL, files=pdb_to_submit)

+        receptor_file = args.receptor_file

+        pose_file = args.pose_file

+        file_to_submit = {

+            'receptor_file': receptor_file, 'pose_file': pose_file}

+        req = requests.post(URL_pose, files=file_to_submit)

         print(req.json())

-    return True

 if __name__ == "__main__":

-    parser = argparse.ArgumentParser(description='Job submission for single prediction - CSM-AB')

-    parser.add_argument('--pdb_file', dest='pdb_file', type=argparse.FileType('r'), help='PDB file')

-    parser.add_argument('--pdb_accession', dest='pdb_accession', type=str, help='Type PDB-ID')

+    parser = argparse.ArgumentParser(

+        description='Job submission for CSM-AB')

+    parser.add_argument('job_type', type=str, choices=['single', 'pose'],

+                        help='choose between single and pose prediction')

+    parser.add_argument('--pdb_file', dest='pdb_file',

+                        type=argparse.FileType('r'), help='PDB file')

+    parser.add_argument('--pdb_accession', dest='pdb_accession',

+                        type=str, help='Type PDB-ID')

+    parser.add_argument('--receptor_file', dest='receptor_file',

+                        type=argparse.FileType('r'), help='PDB file')

+    parser.add_argument('--pose_file', dest='pose_file',

+                        type=argparse.FileType('r'), help='PDB file')

     args = parser.parse_args()

-    if args.pdb_file == None and args.pdb_accession == None:

-        print('usage: post.py [-h] [--pdb_file PDB_FILE] [--pdb_accession pdb_accession]')

-        print('post.py: error: missing arguments: Please provide --pdb_file or --pdb_accession')

-        sys.exit(1)

+    print(args.job_type, args.pdb_file, args.pdb_accession)

+    if args.job_type == 'single':

+        if (args.pdb_file == None and args.pdb_accession == None):

+            print(

+                'post.py: error: missing arguments: Please provide --pdb_file or --pdb_accession')

+            sys.exit(1)

+    else:

+        if args.receptor_file == None or args.pose_file == None:

+            print(

+                'post.py: error: missing arguments: Please provide --receptor_file or --pose_file')

+            sys.exit(1)

     main(args)

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Biosig Lab CSM-AB_single_prediction_API

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File get.py Modified

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