- csv export meta data are not commented out
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
csv export meta data are not commented out
## Tags
* assigned: zsloan
* priority: high
* type: bug
* status: unclear
* keywords: CSV, from github, meta data
## Description...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...in progress
* keywords: slow query
# Tasks
* [ ] upgrade mariadb on production
* [ ] switch character type on ProbeSet table from latin1/utf8mb3 to utf8mb4 (and any other tables) - depends on mariadb...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...query returns detailed information for transcript expression traits, but not for traits from the 'Publish' database.
### Describe the solution you'd like
For example, downloading the data as CSV via...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
## Tags
* assigned: Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419 From GitHub...
- Search results for SNP looks weird
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables from GUIX from...
- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
...do not match the query.
Searching for a gene gives correct coordinates in the search box at http://www.genenetwork.org/snp_browser, but the results are for the same coordinates in mm9 (see screenshot).
- Global search does not close connections properly (and is slow)
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
...[Warning] Aborted connection 45219 to db: 'db_webqtl' user: 'webqtlout' host: '127.0.0.1' (CLOSE_CONNECTION)
```
generating 6Mb of log file info.
In fact, every row in the table has a SQL query...
- Capture Data on the BXDs in RDF
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...metadata from RDF
Work on dumping RDF has already been done in:
=> https://github.com/genenetwork/dump-genenetwork-database dump-genenetwork-database
Also, vector/matrix data should be put in lmdb...
- 'TempDataSet' object has no attribute 'query_for_group' (error)
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Sep 28 2022 by Alexander_Kabui
...as a batch file in the old version of genenetwork.
The trait data that I tried to upload and check on GN2 was the
median-lateral position of the representation of visual space on V1. It was
old data...
- Adding principal component to collection returns an error
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Alexander Kabui
.../app.py", line 1950, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/guix-profiles/gn-latest-20201216/lib/python3.8/site-packages/flask/app.py", line 1936, in...
- Multi-trait heat map failed
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...trimmed_values)
IndexError: reaper: the length of the strain list and the value list are different,
```
One of my traits had missing data, deselecting this trait fixed the problem. Record 20761.
- Error when attempt to zoom to a chromosome after mapping a PCA trait
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
...68, in create_dataset
dataset_type = Dataset_Getter(dataset_name)
File "/export/local/home/gn2/production/gene/wqflask/base/data_set.py", line 120, in __call__
return self.datasets...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...have ?php are in ./infoshare. Try
```
gn1@tux01:~/production/gnshare/gn-pjotr-test$ grep '?php' -r > phpfiles.txt
```
they end in .htm and .html so we need to wire that together.
So adding a test in...
- Automatically find broken links on GN2
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 2 of 2 tasks done
.../app.py", line 1926, in dispatch_request
self.raise_routing_exception(req)
File "/usr/local/guix-profiles/gn-latest-20200513/lib/python2.7/site-packages/flask/app.py", line 1908, in...
- correlation error: 'NoneType' object is not iterable
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 13 2022 by Alexander Kabui
...Feb 19, 2020)
'NoneType' object is not iterable (error)
File "/export/local/home/gn2/production/gene/wqflask/wqflask/correlation/show_corr_results.py", line 473, in process_samples
for sample in...
- Unable to open new tab for mapping/ correlations with Chrome
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 18 2023 by Munyoki Kilyungi
- GN1 annotation page broken
issue opened on Dec 23 2022 by Pjotr Prins
.../421 From GitHub
=> http://gn1.genenetwork.org/webqtl/main.py?FormID=annotation The annotations page in GN1
is broken. An exception stack trace is displayed, instead of the annotations page content.
- BXD102xBXD077F1 Error
✓ issue opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
.../612 From GitHub
> Hi,
>
> There is an error when I click on Compute in Calculate Correlations. It does not load the correlations. This is the error:
> GeneNetwork tux01:gene:2.11-rc2-testing-c16e361c4...