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authorBonfaceKilz2021-11-23 17:20:18 +0300
committerBonfaceKilz2021-11-23 17:44:24 +0300
commit66960bdbd7cd313ebe5a7136568b7389dc7d7fed (patch)
treebe1d627fb971bcc3a6da02ff3dfbf6a2083a7150
parentc398af6b98f89917065457153b0f7e55be28e835 (diff)
downloadgenenetwork2-66960bdbd7cd313ebe5a7136568b7389dc7d7fed.tar.gz
wqflask: metadata_edits: Remove "\n\n" check with something else
In excel, "\n\n" is replaced with ",,,," and this leads to a value error.
-rw-r--r--wqflask/wqflask/metadata_edits.py13
1 files changed, 9 insertions, 4 deletions
diff --git a/wqflask/wqflask/metadata_edits.py b/wqflask/wqflask/metadata_edits.py
index 572db080..21b73cb4 100644
--- a/wqflask/wqflask/metadata_edits.py
+++ b/wqflask/wqflask/metadata_edits.py
@@ -1,6 +1,7 @@
import datetime
import json
import os
+import re
from collections import namedtuple
from itertools import groupby
@@ -250,17 +251,21 @@ def update_phenotype(dataset_id: str, name: str):
file_.save(new_file_name)
publishdata_id = ""
lines = []
+ split_point = ""
with open(new_file_name, "r") as f:
lines = f.read()
- first_line = lines.split('\n', 1)[0]
- publishdata_id = first_line.split("Id:")[-1].strip()
+ for line in lines.split("\n"):
+ if "# Publish Data Id:" in line:
+ split_point = line
+ publishdata_id = re.findall(r'\b\d+\b', line)[0]
+ break
with open(new_file_name, "w") as f:
- f.write(lines.split("\n\n")[-1])
+ f.write(lines.split(f"{split_point}\n")[-1].strip())
csv_ = get_trait_csv_sample_data(conn=conn,
trait_name=str(name),
phenotype_id=str(phenotype_id))
with open(uploaded_file_name, "w") as f_:
- f_.write(csv_.split("\n\n")[-1])
+ f_.write(csv_.split(str(publishdata_id))[-1].strip())
r = run_cmd(cmd=("csvdiff "
f"'{uploaded_file_name}' '{new_file_name}' "
"--format json"))