.gitignore

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+mirri/biolomics/secrets.py
+.vscode/launch.json
+*.pyc

bin/upload_strains_to_mirri_is_NEWDB.py

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+#!/usr/bin/env python3
+import argparse
+from cmath import nan
+import sys
+from collections import Counter
+
+#
+from mirri.biolomics.pipelines.growth_medium import get_or_create_or_update_growth_medium
+from mirri.biolomics.pipelines.strain import get_or_create_or_update_strain
+from mirri.biolomics.remote.biolomics_client import BiolomicsMirriClient
+from mirri.io.parsers.mirri_excel import parse_mirri_excel
+from mirri.validation.excel_validator import validate_mirri_excel
+
+##Database
+from sqlalchemy import create_engine, MetaData
+import pymysql
+import pandas as pd
+from pathlib import Path
+import numpy as np
+
+# DEFINE THE DATABASE CREDENTIALS
+user = 'mirridev'
+password = 'estramboticandolotodo'
+host = 'mirri-is.mirri.org'
+port = 33066
+database = 'mirri-db'
+
+TEST_SERVER_URL = 'https://webservices.bio-aware.com/mirri_test'
+PROD_SERVER_URL = 'https://webservices.bio-aware.com/mirri'
+
+def show_stats(counter, kind, out_fhand):
+    out_fhand.write(f'{kind}\n')
+    line = ''.join(['-'] * len(kind))
+    out_fhand.write(f"{line}\n")
+    for kind2, value in counter.most_common(5):
+        out_fhand.write(f'{kind2}: {value}\n')
+    out_fhand.write('\n')
+
+
+def get_cmd_args():
+    desc = "Upload strains to MIRRI-IS"
+    parser = argparse.ArgumentParser(description=desc)
+    parser.add_argument('-i'                , '--input', required=True, help='Validated Excel file', type=argparse.FileType('rb'))
+    parser.add_argument('-v'                , '--spec_version', default='20200601', help='Version of he specification of the given excel file')
+    parser.add_argument('-u'                , '--ws_user', help='Username of the web service')
+    parser.add_argument('-p'                , '--ws_password', required=True, help='Password of the web service user')
+    parser.add_argument('-c'                , '--client_id', required=True, help='Client id of the web service')
+    parser.add_argument('-s'                , '--client_secret', required=True, help='Client secret of the web service')
+    parser.add_argument('--force_update'    , required=False, action='store_true', help='Use it if you want to update the existing strains')
+    parser.add_argument('--verbose'         , action='store_true', help='use it if you want a verbose output')
+    parser.add_argument('--prod'            , action='store_true', help='Use production server')
+    parser.add_argument('--dont_add_gm'     , default=True, action='store_false', help="Don't add growth media")
+    parser.add_argument('--dont_add_strains', default=True, action='store_false', help="Don't add growth media")
+    parser.add_argument('--skip_first_num'  , type=int, help='skip first X strains to the tool')
+
+    args = parser.parse_args()
+
+    return {'input_fhand': args.input
+            ,'user': args.ws_user
+            ,'version': args.spec_version
+            ,'password': args.ws_password
+            ,'client_id': args.client_id
+            ,'client_secret': args.client_secret
+            ,'update': args.force_update
+            ,'verbose': args.verbose
+            ,'use_production_server': args.prod
+            ,'add_gm': args.dont_add_gm
+            ,'add_strains': args.dont_add_strains
+            ,'skip_first_num': args.skip_first_num
+        }
+
+
+def write_errors_in_screen(errors, fhand=sys.stderr):
+    for key, errors_by_type in errors.items():
+        fhand.write(f'{key}\n')
+        fhand.write('-' * len(key) + '\n')
+        for error in errors_by_type:
+            if error.pk:
+                fhand.write(f'{error.pk}: ')
+            fhand.write(f'{error.message} - {error.code}\n')
+        fhand.write('\n')
+
+
+def create_or_upload_strains(client, strains, update=False, counter=None, out_fhand=None, seek=None):
+
+    for index, strain in enumerate(strains):
+        if seek is not None and index < seek:
+            continue
+        # if strain.id.strain_id != 'CECT 5766':
+        #     continue
+        result = get_or_create_or_update_strain(client, strain, update=update)
+
+        new_strain = result['record']
+        created = result['created']
+        updated = result.get('updated', False)
+        if updated:
+            result_state = 'updated'
+        elif created:
+            result_state = 'created'
+        else:
+            result_state = 'not modified'
+
+        if counter is not None:
+            counter[result_state] += 1
+        if out_fhand is not None:
+            out_fhand.write(f'{index}: Strain {new_strain.id.strain_id}: {result_state}\n')
+        # break
+
+
+def create_or_upload_growth_media(client, growth_media, update=False, counter=None, out_fhand=None):
+
+    for gm in growth_media:
+        result = get_or_create_or_update_growth_medium(client, gm, update)
+
+        new_gm = result['record']
+        created = result['created']
+        updated = result.get('updated', False)
+        if updated:
+            result_state = 'updated'
+        elif created:
+            result_state = 'created'
+        else:
+            result_state = 'not modified'
+        if counter is not None:
+            counter[result_state] += 1
+        if out_fhand is not None:
+            out_fhand.write(f'Growth medium {new_gm.record_name}: {result_state}\n')
+
+  
+def get_connection():
+    # PYTHON FUNCTION TO CONNECT TO THE MYSQL DATABASE AND
+    # RETURN THE SQLACHEMY ENGINE OBJECT
+    return create_engine(url="mysql+pymysql://{0}:{1}@{2}:{3}/{4}".format(user, password, host, port, database))
+  
+def main():
+    ## Load Excel
+    path = Path('C://data//brclims_excel.xlsx')
+    Excel_Data = pd.read_excel(path, sheet_name = None)
+    cc_id=1
+
+    ## Load Database
+    sqlEngine  = get_connection()
+    engine     = sqlEngine.connect()
+
+    ## Create new file upload
+    with engine.connect() as conn:
+        metaDats = MetaData(conn, schema=database)
+        metaDats.reflect(bind=conn)
+        table = metaDats.tables['mirri-db.file_upload']
+        stmt = table.insert().values(filename=path.name,cc_id=cc_id)
+        aux=conn.execute(stmt).inserted_primary_key[0]
+
+        ## Load all Sheet from Excel to DB
+        for key in Excel_Data.keys():
+            #print(key)
+            n=Excel_Data[key].replace(np.nan, '', regex=True).astype(str)
+            n.columns = n.columns.str.replace(' ','_')
+            n['f_id']=aux
+            n.to_sql(key, engine, index=False, if_exists='append')
+
+    
+
+
+"""    
+    args = get_cmd_args()
+    input_fhand = args['input_fhand']
+    spec_version = args['version']
+    out_fhand = sys.stdout
+    error_log = validate_mirri_excel(input_fhand, version=spec_version)
+    errors = error_log.get_errors()
+    skip_first_num = args['skip_first_num']
+    if errors:
+        write_errors_in_screen(errors, out_fhand)
+        sys.exit(1)
+
+    input_fhand.seek(0)
+    parsed_objects = parse_mirri_excel(input_fhand, version=spec_version)
+    strains = list(parsed_objects['strains'])
+    growth_media = list(parsed_objects['growth_media'])
+
+    server_url = PROD_SERVER_URL if args['use_production_server'] else TEST_SERVER_URL
+
+    client = BiolomicsMirriClient(server_url=server_url,  api_version='v2',
+                                  client_id=args['client_id'],
+                                  client_secret=args['client_secret'],
+                                  username=args['user'],
+                                  password=args['password'],
+                                  verbose=args['verbose'])
+
+    if args['add_gm']:
+        client.start_transaction()
+        counter = Counter()
+        try:
+            create_or_upload_growth_media(client, growth_media, update=args['update'],
+                                          counter=counter, out_fhand=out_fhand)
+        except (Exception, KeyboardInterrupt) as error:
+            out_fhand.write('There were some errors in the Growth media upload\n')
+            out_fhand.write(str(error) + '\n')
+            out_fhand.write('Rolling back\n')
+            client.rollback()
+            raise
+        client.finish_transaction()
+        show_stats(counter, 'Growth Media', out_fhand)
+
+    if args['add_strains']:
+        client.start_transaction()
+        counter = Counter()
+        try:
+            create_or_upload_strains(client, strains, update=args['update'],
+                                     counter=counter,
+                                     out_fhand=out_fhand, seek=skip_first_num)
+            client.finish_transaction()
+        except (Exception, KeyboardInterrupt) as error:
+            out_fhand.write('There were some errors in the Strain upload\n')
+            out_fhand.write(str(error) + '\n')
+            out_fhand.write('rolling back\n')
+            # client.rollback()
+            raise
+        client.finish_transaction()
+        show_stats(counter, 'Strains', out_fhand)
+"""
+
+if __name__ == '__main__':
+    main()

bin/validateNEW.py

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+#!/usr/bin/env python
+import sys
+from pathlib import Path
+from mirri.validation.excel_validator import validate_mirri_excel
+import warnings
+warnings.simplefilter("ignore")
+
+
+def main():
+    # path = Path(sys.argv[1])
+    path = Path( 'C:/data/brclims_excel.xlsx')
+    
+    error_log = validate_mirri_excel(path.open("rb"))
+
+    for errors in error_log.get_errors().values():
+        for error in errors:
+            print(error.pk, error.message, error.code)
+
+
+if __name__ == "__main__":
+    main()