Solved issue BU-ISCIII#312 warnings when running the install.sh

Author: luissian

wetlab/utils/collection_index.py

@@ -73,7 +73,7 @@ def get_collection_index_name(input_file):
     collection_name = ""
     with open(input_file, encoding="utf-8") as fh:
         for line in fh:
-            found_collection_name = re.search("^\[Name\]", line)
+            found_collection_name = re.search(r"^\[Name\]", line)
             if found_collection_name:
                 found_name = True
                 continue
@@ -305,7 +305,7 @@ def store_collection_kits_file(collection_file):
     # fetch the file from user form and  build the file name  including
     # the date and time on now to store in database
 
-    split_filename = re.search("(.*)(\.\w+$)", collection_file.name)
+    split_filename = re.search(r"(.*)(\.\w+$)", collection_file.name)
     f_name = split_filename[1]
     f_extension = split_filename[2]
     fs_index_lib = FileSystemStorage()

wetlab/utils/common.py

@@ -186,7 +186,7 @@ def find_xml_tag_text(input_file, search_tag):
     fh = open(input_file, "r")
     search_line = "<" + search_tag + ">(.*)</" + search_tag + ">"
     for line in fh:
-        found_tag = re.search("^\s+ %s" % search_line, line)
+        found_tag = re.search(r"^\s+ %s" % search_line, line)
         if found_tag:
             fh.close()
             return found_tag.group(1)

wetlab/utils/crontab_process.py

@@ -720,7 +720,7 @@ def get_latest_run_procesing_log(conn, log_folder, experiment_name):
             continue
         file_remote = sfh.filename
         if file_remote.endswith(".log"):
-            log_file = re.search(".*_Cycle(\d+)_.*", file_remote)
+            log_file = re.search(r".*_Cycle(\d+)_.*", file_remote)
 
             cycle_number = int(log_file.group(1))
             if cycle_number > max_cycle:

wetlab/utils/library.py

@@ -804,7 +804,7 @@ def get_library_code_and_unique_id(sample_id, molecule_id):
             sample_id=sample_obj, molecule_id=molecule_obj
         ).last()
         last_lib_prep_code_id = lib_prep_obj.get_lib_prep_code()
-        split_code = re.search("(.*_)(\d+)$", last_lib_prep_code_id)
+        split_code = re.search(r"(.*_)(\d+)$", last_lib_prep_code_id)
         index_val = int(split_code.group(2))
         new_index = str(index_val + 1).zfill(2)
         lib_prep_code_id = split_code.group(1) + new_index

wetlab/utils/samplesheet.py

@@ -106,7 +106,7 @@ def get_adapters(file_lines):
             else:
                 adapter2 = adapter_code
                 break
-        data_found = re.search("^\[Data]", line)
+        data_found = re.search(r"^\[Data]", line)
         if data_found:
             break
 
@@ -205,7 +205,7 @@ def get_reads(file_lines):
             continue
         if "[Settings]" in line:
             break
-        if read_found and re.search("^\w+", line):
+        if read_found and re.search(r"^\w+", line):
             reads.append(line.split(",")[0])
     return reads
 
@@ -392,7 +392,7 @@ def get_projects_in_run(in_file: str) -> dict:
                     continue
             else:
                 # ignore the empty lines separated by commas
-                valid_line = re.search("^\w+", line)
+                valid_line = re.search(r"^\w+", line)
                 if not valid_line:
                     continue
                 # store the project name and the user name (Description) inside projects dict
@@ -442,7 +442,7 @@ def get_index_library_name(in_file):
 def update_library_kit_field(library_file_name, library_kit_name, library_name):
     # result_directory='documents/wetlab/BaseSpaceMigrationFiles/'
     timestr = time.strftime("%Y%m%d-%H%M%S")
-    tmp = re.search("(.*)\d{8}-\d+.*\.csv", library_file_name)
+    tmp = re.search(r"(.*)\d{8}-\d+.*\.csv", library_file_name)
     absolute_path = str(settings.BASE_DIR + "/")
     out_file = str(
         absolute_path
@@ -517,7 +517,7 @@ def create_unique_sample_id_values(infile, index_file):
             continue
         if found_sample_line:
             # discard the empty lines or the lines that contains empty lines separated by comma
-            if line == "\n" or re.search("^\W", line):
+            if line == "\n" or re.search(r"^\W", line):
                 continue
 
             data_line = line.split(",")
@@ -592,7 +592,7 @@ def set_user_names_in_sample_sheet(in_file, user_names):
             continue
         if found_sample_line:
             # discard the empty lines or the lines that contains empty lines separated by comma
-            if line == "\n" or re.search("^\W", line):
+            if line == "\n" or re.search(r"^\W", line):
                 continue
 
             data_line = line.split(",")