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authorFrederick Muriuki Muriithi2022-10-18 13:02:58 +0300
committerFrederick Muriuki Muriithi2022-10-18 13:06:28 +0300
commit2469cd822a91992d8661f6ec33bfe86f0725765c (patch)
tree913a7ee0e078a853c3674072e7c3326a692d54dd /issues
parent42d9cfff96bce98ec14c37ddb8ba7175b24062d3 (diff)
downloadgn-gemtext-2469cd822a91992d8661f6ec33bfe86f0725765c.tar.gz
Issues (correlation-missing-file): Update issue
* issues/correlation-missing-file.gmi: Update issue with findings and a fix for the issue.
Diffstat (limited to 'issues')
-rw-r--r--issues/correlation-missing-file.gmi18
1 files changed, 17 insertions, 1 deletions
diff --git a/issues/correlation-missing-file.gmi b/issues/correlation-missing-file.gmi
index 95f4e68..4bf82e5 100644
--- a/issues/correlation-missing-file.gmi
+++ b/issues/correlation-missing-file.gmi
@@ -20,4 +20,20 @@ GeneNetwork tux01:gene:2.11-rc2-gn_20221013-4eb4beafd
[Errno 2] No such file or directory: '/home/gn2/production/tmp/gn2/gn2/ProbeSetFreezeId_886_EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)' (error)
```
-This obviously has something to do with the sample data files, though not sure what yet.
+This obviously has something to do with the sample data files, though not sure what yet.
+
+### 2022-10-18
+
+I (fredm) was able to successfully reproduce the issue.
+
+The issue here is that the code
+=> https://github.com/genenetwork/genenetwork2/blob/testing/wqflask/wqflask/correlation/pre_computes.py#L212-L219
+generates the file name does not sanitize the input from the database, leading to issues with the final path.
+
+In this case, the dataset name used to generate the file is (** Note the forward slash **):
+```
+EPFL/ETHZ BXD Liver Proteome CD-HFD (Nov19)
+```
+
+The following commit should fix the issue for most part:
+=> https://github.com/genenetwork/genenetwork2/commit/c8f606b0080a7dd343515c7c2ae830dfeecdf341