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authorFrederick Muriuki Muriithi2023-12-20 06:28:06 +0300
committerFrederick Muriuki Muriithi2023-12-20 06:28:06 +0300
commitcb7f6b866672f44d730f303639e6372d2ae2babe (patch)
tree52a868382ab81c407a738bbeef45c3f603d5293e
parentbf0013bceac63c852b1baf5842f9c7b560f3330d (diff)
downloadgn-uploader-cb7f6b866672f44d730f303639e6372d2ae2babe.tar.gz
Fix ID column key
Fix the wrong assumption that the ID key will always be "ProbeSetID". The key for the ID column could change from study to study or dataset to dataset.
-rw-r--r--scripts/insert_data.py8
1 files changed, 5 insertions, 3 deletions
diff --git a/scripts/insert_data.py b/scripts/insert_data.py
index 63e85ef..0ac3799 100644
--- a/scripts/insert_data.py
+++ b/scripts/insert_data.py
@@ -67,9 +67,10 @@ def strains_info(
def read_datavalues(filepath, headings, strain_info):
"""Read numerical, data values from the file."""
+ id_key = headings[0]
return {
- str(row["ProbeSetID"]): tuple({
- "ProbeSetName": str(row["ProbeSetID"]),
+ str(row[id_key]): tuple({
+ "ProbeSetName": str(row[id_key]),
"StrainId": strain_info[sname]["Id"],
"DataValue": float(row[sname])
} for sname in headings[1:])
@@ -79,9 +80,10 @@ def read_datavalues(filepath, headings, strain_info):
def read_probesets(filepath, headings):
"""Read the ProbeSet names."""
+ id_key = headings[0]
for row in (dict(zip(headings, line))
for line in read_file_contents(filepath)):
- yield {"Name": str(row["ProbeSetID"])}
+ yield {"Name": str(row[id_key])}
def last_data_id(dbconn: mdb.Connection) -> int:
"Get the last id from the database"