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Hotfix for tmp folder creation in remote home #269

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merged 4 commits into from
Jun 3, 2024
Merged

Hotfix for tmp folder creation in remote home #269

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1f71b84
Fixed tmp folder creation in /home
Shettland May 28, 2024
2320724
Removed pdb imports
Shettland May 28, 2024
8a78ef7
read-excel error handling when header flag is not found
Shettland May 28, 2024
e7a839c
Fixed tmp folder creation in /home. lint
Shettland May 28, 2024
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3 changes: 2 additions & 1 deletion relecov_tools/sftp_handle.py
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Original file line number Diff line number Diff line change
Expand Up @@ -202,7 +202,8 @@ def recursive_list(folder_name):

if recursive:
directory_list = recursive_list(folder_name)
directory_list.append(folder_name)
if folder_name != ".":
directory_list.append(folder_name)
return directory_list
try:
directory_list = [
Expand Down
5 changes: 0 additions & 5 deletions relecov_tools/upload_ena_protocol.py
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Expand Up @@ -232,9 +232,6 @@ def update_json(self, updated_schemas_df, json_data):

def xml_submission(self, json_data, schemas_dataframe, batch_index=None):
"""The metadata is submitted in an xml format"""
import pdb

pdb.set_trace()
schema_targets = extract_targets(self.action, schemas_dataframe)

tool = self.config_json.get_configuration("ENA_fields")["tool"]
Expand Down Expand Up @@ -266,9 +263,7 @@ def xml_submission(self, json_data, schemas_dataframe, batch_index=None):
schema_xmls["submission"] = submission_xml

stderr.print(f"\nProcessing submission to ENA server: {self.url}")
import pdb

pdb.set_trace()
receipt = send_schemas(schema_xmls, self.url, self.user, self.passwd).text
if not os.path.exists(self.output_path):
os.mkdir(self.output_path)
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9 changes: 6 additions & 3 deletions relecov_tools/utils.py
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Expand Up @@ -64,9 +64,12 @@ def read_excel_file(f_name, sheet_name, header_flag, leave_empty=True):
"""
wb_file = openpyxl.load_workbook(f_name, data_only=True)
ws_metadata_lab = wb_file[sheet_name]
heading_row = [
idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x
][0]
try:
heading_row = [
idx + 1 for idx, x in enumerate(ws_metadata_lab.values) if header_flag in x
][0]
except IndexError:
raise KeyError(f"Header flag '{header_flag}' could not be found in {f_name}")
heading = [str(i.value).strip() for i in ws_metadata_lab[heading_row] if i.value]
ws_data = []
for row in islice(ws_metadata_lab.values, heading_row, ws_metadata_lab.max_row):
Expand Down
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