Remove calls to AAP as it is not supported anymore (#249)

* Remove calls to AAP as it is not supported anymore

* fix test

* Add to requirements.txt

Author: tcezard

bin/check_existing_sample_ownership.py

@@ -17,10 +17,10 @@
 import argparse
 import csv
 
+from ebi_eva_common_pyutils.biosamples_communicators import WebinHALCommunicator
 from ebi_eva_common_pyutils.config import cfg
 from ebi_eva_common_pyutils.logger import logging_config as log_cfg
 
-from eva_submission.biosample_submission.biosamples_submitters import AAPHALCommunicator
 from eva_submission.submission_config import load_config
 from eva_submission.xlsx.xlsx_parser_eva import EvaXlsxReader
 
@@ -41,9 +41,10 @@ def main():
     # Load the config_file from default location
     load_config()
     metadata_reader = EvaXlsxReader(args.metadata_file)
-    communicator = AAPHALCommunicator(cfg.query('biosamples', 'aap_url'), cfg.query('biosamples', 'bsd_url'),
-                                      cfg.query('biosamples', 'username'), cfg.query('biosamples', 'password'),
-                                      cfg.query('biosamples', 'domain'))
+    communicator = WebinHALCommunicator(
+        cfg.query('biosamples', 'webin_url'), cfg.query('biosamples', 'bsd_url'),
+        cfg.query('biosamples', 'webin_username'), cfg.query('biosamples', 'webin_password')
+    )
     with open(args.output, 'w') as open_ouptut:
         sample_attrs = ['accession', 'name', 'domain', 'webinSubmissionAccountId', 'status']
         writer = csv.DictWriter(open_ouptut, fieldnames=sample_attrs + ['owner'])

eva_submission/biosample_submission/biosamples_submitters.py

@@ -17,7 +17,7 @@
 from datetime import datetime, date
 from functools import lru_cache
 
-from ebi_eva_common_pyutils.biosamples_communicators import AAPHALCommunicator, WebinHALCommunicator
+from ebi_eva_common_pyutils.biosamples_communicators import WebinHALCommunicator
 from ebi_eva_common_pyutils.config import cfg
 from ebi_eva_common_pyutils.logger import AppLogger
 
@@ -267,27 +267,11 @@ class SampleSubmitter(AppLogger):
 
     def __init__(self, submit_type):
         communicators = []
-
-        if 'override' in submit_type:
-            assert len(submit_type) == 1, f'override can only be used as a single action'
-            communicators.append(AAPHALCommunicator(
-                cfg.query('biosamples', 'aap_url'), cfg.query('biosamples', 'bsd_url'),
-                cfg.query('biosamples', 'aap_super_user'), cfg.query('biosamples', 'aap_super_password'),
-                cfg.query('biosamples', 'aap_super_domain')
-            ))
         # If the config has the credential for using webin with BioSamples use webin first
-        if cfg.query('biosamples', 'webin_url') and cfg.query('biosamples', 'webin_username') and \
-                cfg.query('biosamples', 'webin_password'):
-            communicators.append(WebinHALCommunicator(
-                cfg.query('biosamples', 'webin_url'), cfg.query('biosamples', 'bsd_url'),
-                cfg.query('biosamples', 'webin_username'), cfg.query('biosamples', 'webin_password')
-            ))
-        communicators.append(AAPHALCommunicator(
-            cfg.query('biosamples', 'aap_url'), cfg.query('biosamples', 'bsd_url'),
-            cfg.query('biosamples', 'username'), cfg.query('biosamples', 'password'),
-            cfg.query('biosamples', 'domain')
+        communicators.append(WebinHALCommunicator(
+            cfg.query('biosamples', 'webin_url'), cfg.query('biosamples', 'bsd_url'),
+            cfg.query('biosamples', 'webin_username'), cfg.query('biosamples', 'webin_password')
         ))
-
         self.submitter = BioSamplesSubmitter(communicators, submit_type)
         self.sample_data = None
 

eva_submission/xlsx/xlsx_validation.py

@@ -5,7 +5,7 @@
 import yaml
 from cerberus import Validator
 from ebi_eva_common_pyutils.assembly_utils import retrieve_genbank_assembly_accessions_from_ncbi
-from ebi_eva_common_pyutils.biosamples_communicators import AAPHALCommunicator
+from ebi_eva_common_pyutils.biosamples_communicators import WebinHALCommunicator
 from ebi_eva_common_pyutils.config import cfg
 from ebi_eva_common_pyutils.logger import AppLogger
 from ebi_eva_common_pyutils.reference import NCBIAssembly
@@ -32,10 +32,9 @@ def __init__(self, metadata_file):
             self.metadata[worksheet] = self.reader._get_all_rows(worksheet)
 
         self.error_list = []
-        self.communicator = AAPHALCommunicator(
-            cfg.query('biosamples', 'aap_url'), cfg.query('biosamples', 'bsd_url'),
-            cfg.query('biosamples', 'username'), cfg.query('biosamples', 'password'),
-            cfg.query('biosamples', 'domain')
+        self.communicator = WebinHALCommunicator(
+            cfg.query('biosamples', 'webin_url'), cfg.query('biosamples', 'bsd_url'),
+            cfg.query('biosamples', 'webin_username'), cfg.query('biosamples', 'webin_password')
         )
 
 

requirements.txt

@@ -1,6 +1,6 @@
 cached-property
 cerberus
-ebi-eva-common-pyutils[eva-internal]>=0.6.17, ==0.*
+ebi-eva-common-pyutils[eva-internal]>=0.7.0, ==0.*
 eva-vcf-merge>=0.0.8
 eva_sub_cli>=0.4.6
 humanize

tests/test_biosamples_submission.py

@@ -7,7 +7,7 @@
 import pytest
 import yaml
 
-from ebi_eva_common_pyutils.biosamples_communicators import AAPHALCommunicator, HALCommunicator, WebinHALCommunicator
+from ebi_eva_common_pyutils.biosamples_communicators import HALCommunicator, WebinHALCommunicator
 
 from eva_submission import ROOT_DIR
 from eva_submission.biosample_submission import biosamples_submitters
@@ -56,7 +56,6 @@ def tearDown(self):
         'release': '2020-07-06T19:09:29.090Z'}
     ]
 
-# BioSamples does not support AAP login so we have to use credentials from Webin.
 @pytest.mark.skip(reason='You need to set a config file with correct Webin credential to run these test')
 class TestBSDSubmitter(BSDTestCase):
     """

tests/test_vep_utils.py

@@ -153,7 +153,7 @@ def test_get_species_and_assembly(self):
 
     def test_get_releases(self):
         with get_ftp_connection(ensembl_ftp_url) as ftp:
-            assert get_releases(ftp, 'pub', current_only=True) == {113: 'pub/release-113'}
+            assert get_releases(ftp, 'pub', current_only=True) == {115: 'pub/release-115'}
 
         with get_ftp_connection(ensembl_genome_ftp_url) as ftp:
             assert get_releases(ftp, ensembl_genome_dirs[0], current_only=True) == {60: 'ensemblgenomes/pub/plants/release-60'}