Included credentials as validation method, linting

bu_isciii/__main__.py

@@ -205,7 +205,12 @@ def new_service(ctx, resolution, path, no_create_folder, ask_path):
     Create new service, it will create folder and copy template depending on selected service.
     """
     new_ser = bu_isciii.new_service.NewService(
-        resolution, path, no_create_folder, ask_path, ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        path,
+        no_create_folder,
+        ask_path,
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     new_ser.create_new_service()
 
@@ -251,7 +256,13 @@ def scratch(ctx, resolution, path, tmp_dir, direction, ask_path):
     Copy service folder to scratch directory for execution.
     """
     scratch_copy = bu_isciii.scratch.Scratch(
-        resolution, path, tmp_dir, direction, ask_path, ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        path,
+        tmp_dir,
+        direction,
+        ask_path,
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     scratch_copy.handle_scratch()
 
@@ -302,7 +313,9 @@ def clean(ctx, resolution, path, ask_path, option):
     Service cleaning. It will either remove big files, rename folders before copy, revert this renaming,
     show removable files or show folders for no copy.
     """
-    clean = bu_isciii.clean.CleanUp(resolution, path, ask_path, option, ctx.obj["api_user"], ctx.obj["api_password"])
+    clean = bu_isciii.clean.CleanUp(
+        resolution, path, ask_path, option, ctx.obj["api_user"], ctx.obj["api_password"]
+    )
     clean.handle_clean()
 
 
@@ -336,7 +349,12 @@ def copy_sftp(ctx, resolution, path, ask_path, sftp_folder):
     Copy resolution FOLDER to sftp, change status of resolution in iskylims and generate md, pdf, html.
     """
     new_del = bu_isciii.copy_sftp.CopySftp(
-        resolution, path, ask_path, sftp_folder, ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        path,
+        ask_path,
+        sftp_folder,
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     new_del.copy_sftp()
 
@@ -379,22 +397,43 @@ def finish(ctx, resolution, path, ask_path, sftp_folder, tmp_dir):
     """
     print("Starting cleaning scratch directory: " + tmp_dir)
     clean_scratch = bu_isciii.clean.CleanUp(
-        resolution, tmp_dir, ask_path, "clean", ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        tmp_dir,
+        ask_path,
+        "clean",
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     clean_scratch.handle_clean()
     print("Starting copy from scratch directory: " + tmp_dir + " to service directory.")
     copy_scratch2service = bu_isciii.scratch.Scratch(
-        resolution, path, tmp_dir, "Scratch_to_service", ask_path, ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        path,
+        tmp_dir,
+        "Scratch_to_service",
+        ask_path,
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     copy_scratch2service.handle_scratch()
     print("Starting renaming of the service directory.")
     rename_databi = bu_isciii.clean.CleanUp(
-        resolution, path, ask_path, "rename_nocopy", ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        path,
+        ask_path,
+        "rename_nocopy",
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     rename_databi.handle_clean()
     print("Starting copy of the service directory to the SFTP folder")
     copy_sftp = bu_isciii.copy_sftp.CopySftp(
-        resolution, path, ask_path, sftp_folder, ctx.obj["api_user"], ctx.obj["api_password"]
+        resolution,
+        path,
+        ask_path,
+        sftp_folder,
+        ctx.obj["api_user"],
+        ctx.obj["api_password"],
     )
     copy_sftp.copy_sftp()
     print("Service correctly in SFTP folder")
@@ -454,7 +493,15 @@ def finish(ctx, resolution, path, ask_path, sftp_folder, tmp_dir):
 )
 @click.pass_context
 def bioinfo_doc(
-    ctx, type, resolution, path, ask_path, sftp_folder, report_md, results_md, email_psswd
+    ctx,
+    type,
+    resolution,
+    path,
+    ask_path,
+    sftp_folder,
+    report_md,
+    results_md,
+    email_psswd,
 ):
     """
     Create the folder documentation structure in bioinfo_doc server
@@ -467,7 +514,7 @@ def bioinfo_doc(
         sftp_folder,
         report_md,
         results_md,
-        ctx.obj["api_user"], 
+        ctx.obj["api_user"],
         ctx.obj["api_password"],
         email_psswd,
     )
@@ -535,7 +582,7 @@ def archive(
         service_file,
         ser_type,
         option,
-        ctx.obj["api_user"], 
+        ctx.obj["api_user"],
         ctx.obj["api_password"],
         skip_prompts,
         date_from,

bu_isciii/clean.py

@@ -276,7 +276,7 @@ def rename(self, to_find, add, verbose=True):
         path_content = self.scan_dirs(to_find=to_find)
         unfiltered_path_content = [f.path for f in os.scandir(self.full_path)]
         for directory_to_rename in path_content:
-            renamed_directory = str(directory_to_rename+add)
+            renamed_directory = str(directory_to_rename + add)
             if renamed_directory in unfiltered_path_content:
                 stderr.print(
                     "[orange]WARNING: Directory %s already renamed to %s Omitting..."

bu_isciii/drylab_api.py

@@ -20,7 +20,7 @@ def __init__(self, server, url, user, password):
         self.request_url = server + url
         self.headers = {
             "accept": "application/json",
-            "Content-Type": "application/json"
+            "Content-Type": "application/json",
         }
         if not user:
             stderr.print("[red]Missing user for api request")
@@ -87,7 +87,9 @@ def put_request(
     def post_request(self, request_info, data, safe=True):
         url_http = self.request_url + request_info
         try:
-            req = requests.post(url_http, data=data, headers=self.headers, auth=self.auth)
+            req = requests.post(
+                url_http, data=data, headers=self.headers, auth=self.auth
+            )
             if req.status_code > 201:
                 if safe:
                     log.error(
@@ -103,19 +105,21 @@ def post_request(self, request_info, data, safe=True):
             log.error("Unable to open connection towards iSkyLIMS, aborting")
             sys.exit(1)
             return False
- 
+
     def basic_authentication(self):
         # Pseudo-code for credentials validation, returns error 404 right now
         from requests.auth import HTTPBasicAuth
+
         user, password = self.auth[0], self.auth[1]
-        url_http = (self.request_url)
+        url_http = self.request_url
         response = requests.get(url_http, auth=HTTPBasicAuth(user, password))
         print("Response status code", response.status_code)
         if response.status_code <= 200:
             return True
         else:
             return False
 
+
 """ Example usage
     rest_api = RestServiceApi("http://localhost:8000/", "drylab/api/")
     services_queue = rest_api.get_request("service/", "state", "queued")