minor refinements

files/files.py

@@ -162,7 +162,7 @@ def copy_raw_files_from_dir(self, accession, source_base_directory):
         """
 
         # get the full path where you can find the raw files in the file system
-        # to support that, data should be written in following format:
+        # to support that, data should be written in the following format:
         # base/path/ + yyyy/mm/accession/ + submitted/
         path_fragment = self.get_submitted_file_path_prefix(accession)
         complete_source_dir = source_base_directory + "/" + path_fragment + "/submitted/"

pridepy.py

@@ -14,7 +14,6 @@
 from project.project import Project
 from protein.protein import Protein
 from spectra.spectra import Spectra
-from util.api_handling import Util
 from util.file_handling import FileHanding
 
 
@@ -101,8 +100,8 @@ def update_metadata(filename, username, password):
     token = authentication.get_token(username, password)
 
     # Format extracted metadata to compatible with PRIDE API endpoint
-    fileHandling = FileHanding()
-    fileHandling.wrap_with_ms_run_metadata(filename)
+    file_handling = FileHanding()
+    file_handling.wrap_with_ms_run_metadata(filename)
 
     # Update msrun metatdata
     msrun = MsRun()

project/project.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-import json
 
 from util.api_handling import Util
 
@@ -24,7 +23,8 @@ def get_projects(self, page_size, page, sort_direction, sort_conditions):
            :param sort_conditions: Field(s) for sorting the results on
            :return: paged peptide_evidences in json format
        """
-        request_url = self.API_BASE_URL + "projects?" + "pageSize=" + str(page_size) + "&page=" + str(page) + "&sortDirection=" + sort_direction + "&sortConditions=" + sort_conditions
+        request_url = self.API_BASE_URL + "projects?" + "pageSize=" + str(page_size) + "&page=" + str(
+            page) + "&sortDirection=" + sort_direction + "&sortConditions=" + sort_conditions
         headers = {"Accept": "application/JSON"}
         response = Util.get_api_call(request_url, headers)
         return response.json()
@@ -66,7 +66,8 @@ def get_files_by_accession(self, accession, query_filter, page_size, page, sort_
         if query_filter:
             request_url = request_url + "filter=" + query_filter + "&"
 
-        request_url = request_url + "pageSize=" + str(page_size) + "&page=" + str(page) + "&sortDirection=" + sort_direction + "&sortConditions=" + sort_conditions
+        request_url = request_url + "pageSize=" + str(page_size) + "&page=" + str(
+            page) + "&sortDirection=" + sort_direction + "&sortConditions=" + sort_conditions
 
         headers = {"Accept": "application/JSON"}
         response = Util.get_api_call(request_url, headers)
@@ -78,12 +79,12 @@ def get_private_files_by_accession(self, accession, user, passwd):
         request_url = self.PRIVATE_API_BASE_URL + "getAAPTokenWeb"
         headers = {"Content-Type": "application/json;charset=UTF-8"}
 
-        data =  {"Credentials":{"username": user,"password": passwd}}
-        aapToken = Util.post_api_call(request_url, headers, data)
-        print(aapToken.text)
+        data = {"Credentials": {"username": user, "password": passwd}}
+        aap_token = Util.post_api_call(request_url, headers, data)
+        print(aap_token.text)
 
         request_url = self.PRIVATE_API_BASE_URL + "projects/" + accession + "/files"
-        headers = {"Authorization": "Bearer " + aapToken.text}
+        headers = {"Authorization": "Bearer " + aap_token.text}
 
         while True:
             response = Util.get_api_call(request_url, headers)
@@ -113,7 +114,8 @@ def get_similar_projects_by_accession(self, accession):
         response = Util.get_api_call(request_url, headers)
         return response.json()
 
-    def search_by_keywords_and_filters(self, keyword, query_filter, page_size, page, date_gap, sort_direction, sort_fields):
+    def search_by_keywords_and_filters(self, keyword, query_filter, page_size, page, date_gap, sort_direction,
+                                       sort_fields):
         """
         search PRIDE API projects by keyword and filters
         :param keyword: keyword to search projects

requirements.txt

@@ -1,7 +1,8 @@
-requests
-ratelimit
-click
-pytest
-setuptools
-plotly
-boto3
+requests~=2.31.0
+ratelimit~=2.2.1
+click~=8.1.7
+pytest~=8.0.2
+setuptools~=58.0.4
+plotly~=5.22.0
+boto3~=1.34.61
+botocore~=1.34.74

spectra/spectra.py

@@ -32,8 +32,8 @@ def spectra_evidences(self, usi, project_accession, assay_accession, peptide_seq
         request_url = self.api_base_url + "spectra?"
 
         if usi:
-            usiArray = usi.split("\\n")
-            for usiElement in usiArray:
+            usi_array = usi.split("\\n")
+            for usiElement in usi_array:
                 request_url = request_url + "usi=" + usiElement + "&"
 
         if project_accession:

tests/test_search.py

@@ -4,7 +4,6 @@
 from peptide.peptide import Peptide
 from project.project import Project
 from protein.protein import Protein
-from spectra.spectra import Spectra
 
 
 class TestSearch(TestCase):