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| author | Frederick Muriuki Muriithi | 2022-10-18 13:02:58 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2022-10-18 13:06:28 +0300 |
| commit | 2469cd822a91992d8661f6ec33bfe86f0725765c (patch) | |
| tree | 913a7ee0e078a853c3674072e7c3326a692d54dd | |
| parent | 42d9cfff96bce98ec14c37ddb8ba7175b24062d3 (diff) | |
| download | gn-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.
| -rw-r--r-- | issues/correlation-missing-file.gmi | 18 |
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 |