6 files changed, 219 insertions, 0 deletions

diff --git a/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip b/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip
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--- /dev/null
+++ b/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip
diff --git a/issues/genenetwork3/broken-aliases.gmi b/issues/genenetwork3/broken-aliases.gmi
new file mode 100644
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+++ b/issues/genenetwork3/broken-aliases.gmi
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+# Broken Aliases
+
+## Tags
+
+* type: bug
+* status: open
+* priority: high
+* assigned: fredm
+* interested: pjotrp
+* keywords: aliases, aliases server
+
+
+## Repository
+
+=> https://github.com/genenetwork/gn3
+
+## Bug Report
+
+### Actual
+
+* Go to https://genenetwork.org/gn3/gene/aliases2/Shh,Brca2
+* Not that an exception is raised, with a "404 Not Found" message
+
+### Expected
+
+* We expected a list of aliases to be returned for the given symbols as is done in https://fallback.genenetwork.org/gn3/gene/aliases2/Shh,Brca2
+
diff --git a/issues/genenetwork3/check-for-mandatory-settings.gmi b/issues/genenetwork3/check-for-mandatory-settings.gmi
new file mode 100644
index 0000000..16a2f8a
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+++ b/issues/genenetwork3/check-for-mandatory-settings.gmi
@@ -0,0 +1,40 @@
+# Check for Mandatory Settings
+
+## Tags
+
+* status: open
+* priority: high
+* type: bug, improvement
+* interested: fredm, bonz
+* assigned: jnduli, rookie101
+* keywords: GN3, gn3, genenetwork3, settings, config, configs, configurations
+
+## Explanation
+
+Giving defaults to some important settings leads to situations where the correct configuration is not set up correctly leading at best to failure, and at worst, to subtle failures that can be difficult to debug: e.g. When a default URI to a server points to an active domain, just not the correct one.
+
+We want to make such (arguably, sensitive) configurations explicit, and avoid giving them defaults. We want to check that they are set up before allowing the application to run, and fail loudly and obnoxiously if they are not provided.
+
+Examples of configuration variables that should be checked for:
+
+* All external URIs (external to app/repo under consideration)
+* All secrets (secret keys, salts, tokens, etc)
+
+We should also eliminate from the defaults:
+
+* Computed values
+* Calls to get values from ENVVARs (`os.environ.get(…)` calls)
+
+### Note on ENVVARs
+
+The environment variables should be used for overriding values under specific conditions, therefore, it should both be explicit and the last thing loaded to ensure they actually override settings. 
+
+=> https://git.genenetwork.org/gn-auth/tree/gn_auth/__init__.py?id=3a276642bea934f0a7ef8f581d8639e617357a2a#n70 See this example for a possible way of allowing ENVVARs to override settings.
+
+The example above could be improved by maybe checking for environment variables starting with a specific value, e.g. the envvar `GNAUTH_SECRET_KEY` would override the `SECRET_KEY` configuration. This allows us to override settings without having to change the code.
+
+## Tasks
+
+* [ ] Explicitly check configs for ALL external URIs
+* [ ] Explicitly check configs for ALL secrets
+* [ ] Explicitly load ENVVARs last to override settings
diff --git a/issues/genenetwork3/ctl-maps-error.gmi b/issues/genenetwork3/ctl-maps-error.gmi
new file mode 100644
index 0000000..6726357
--- /dev/null
+++ b/issues/genenetwork3/ctl-maps-error.gmi
@@ -0,0 +1,46 @@
+# CTL Maps Error
+
+## Tags
+
+* type: bug
+* status: open
+* priority: high
+* assigned: alexm, zachs, fredm
+* keywords: CTL, CTL Maps, gn3, genetwork3, genenetwork 3
+
+## Description
+
+Trying to run the CTL Maps feature in the collections page as described in
+=> /issues/genenetwork2/broken-collections-feature
+
+We get an error in the results page of the form:
+
+```
+{'error': '{\'code\': 1, \'output\': \'Loading required package: MASS\\nLoading required package: parallel\\nLoading required package: qtl\\nThere were 13 warnings (use warnings() to see them)\\nError in xspline(x, y, shape = 0, lwd = lwd, border = col, lty = lty, : \\n invalid value specified for graphical parameter "lwd"\\nCalls: ctl.lineplot -> draw.spline -> xspline\\nExecution halted\\n\'}'}
+```
+
+on the CLI the same error is rendered:
+```
+Loading required package: MASS
+Loading required package: parallel
+Loading required package: qtl
+There were 13 warnings (use warnings() to see them)
+Error in xspline(x, y, shape = 0, lwd = lwd, border = col, lty = lty,  : 
+  invalid value specified for graphical parameter "lwd"
+Calls: ctl.lineplot -> draw.spline -> xspline
+Execution halted
+```
+
+On my local development machine, the command run was
+```
+Rscript /home/frederick/genenetwork/genenetwork3/scripts/ctl_analysis.R /tmp/01828928-26e6-4cad-bbc8-59fd7a7977de.json
+```
+
+Here is a zipped version of the json file (follow the link and click download):
+=> https://github.com/genenetwork/gn-gemtext-threads/blob/main/issues/genenetwork3/01828928-26e6-4cad-bbc8-59fd7a7977de.json.zip
+
+Troubleshooting a while, I suspect
+=> https://github.com/genenetwork/genenetwork3/blob/27d9c9d6ef7f37066fc63af3d6585bf18aeec925/scripts/ctl_analysis.R#L79-L80 this is the offending code.
+
+=> https://cran.r-project.org/web/packages/ctl/ctl.pdf The manual for the ctl library
+indicates that our call above might be okay, which might mean something changed in the dependencies that the ctl library used.
diff --git a/issues/genenetwork3/generate-heatmaps-failing.gmi b/issues/genenetwork3/generate-heatmaps-failing.gmi
new file mode 100644
index 0000000..522dc27
--- /dev/null
+++ b/issues/genenetwork3/generate-heatmaps-failing.gmi
@@ -0,0 +1,64 @@
+# Generate Heatmaps Failing
+
+## Tags
+
+* type: bug
+* status: open
+* priority: medium
+* assigned: fredm, zachs, zsloan
+* keywords: genenetwork3, gn3, GN3, heatmaps
+
+## Reproduce
+
+* Go to https://genenetwork.org/
+* Under "Select and Search" menu, enter "synap*" for the "Get Any" field
+* Click "Search"
+* In search results page, select first 10 traits
+* Click "Add"
+* Under "Create a new collection" enter the name "newcoll" and click "Create collection"
+* In the collections page that shows up, click "Select All" once
+* Ensure all the traits are selected
+* Click "Generate Heatmap" and wait
+* Note how system fails silently with no heatmap presented
+
+### Notes
+
+On https://gn2-fred.genenetwork.org the heatmaps fails with a note ("ERROR: undefined"). In the logs, I see "Module 'scipy' has no attribute 'array'" which seems to be due to a change in numpy.
+=> https://github.com/MaartenGr/BERTopic/issues/1791
+=> https://github.com/scipy/scipy/issues/19972
+
+This issue should not be present with python-plotly@5.20.0 but since guix-bioinformatics pins the guix version to `b0b988c41c9e0e591274495a1b2d6f27fcdae15a`, we are not able to pull in newer versions of packages from guix.
+
+
+### Update 2025-04-08T10:59CDT
+
+Got the following error when I ran the background command manually:
+
+```
+$ export RUST_BACKTRACE=full
+$ /gnu/store/dp4zq4xiap6rp7h6vslwl1n52bd8gnwm-profile/bin/qtlreaper --geno /home/frederick/genotype_files/genotype/genotype/BXD.geno --n_permutations 1000 --traits /tmp/traits_test_file_n2E7V06Cx7.txt --main_output /tmp/qtlreaper/main_output_NGVW4sfYha.txt --permu_output /tmp/qtlreaper/permu_output_MJnzLbrsrC.txt
+thread 'main' panicked at src/regression.rs:216:25:
+index out of bounds: the len is 20 but the index is 20
+stack backtrace:
+   0:     0x61399d77d46d - <unknown>
+   1:     0x61399d7b5e13 - <unknown>
+   2:     0x61399d78b649 - <unknown>
+   3:     0x61399d78f26f - <unknown>
+   4:     0x61399d78ee98 - <unknown>
+   5:     0x61399d78f815 - <unknown>
+   6:     0x61399d77d859 - <unknown>
+   7:     0x61399d77d679 - <unknown>
+   8:     0x61399d78f3f4 - <unknown>
+   9:     0x61399d6f4063 - <unknown>
+  10:     0x61399d6f41f7 - <unknown>
+  11:     0x61399d708f18 - <unknown>
+  12:     0x61399d6f6e4e - <unknown>
+  13:     0x61399d6f9e93 - <unknown>
+  14:     0x61399d6f9e89 - <unknown>
+  15:     0x61399d78e505 - <unknown>
+  16:     0x61399d6f8d55 - <unknown>
+  17:     0x75ee2b945bf7 - __libc_start_call_main
+  18:     0x75ee2b945cac - __libc_start_main@GLIBC_2.2.5
+  19:     0x61399d6f4861 - <unknown>
+  20:                0x0 - <unknown>
+```
diff --git a/issues/genenetwork3/rqtl2-mapping-error.gmi b/issues/genenetwork3/rqtl2-mapping-error.gmi
new file mode 100644
index 0000000..480c7c6
--- /dev/null
+++ b/issues/genenetwork3/rqtl2-mapping-error.gmi
@@ -0,0 +1,42 @@
+# R/qtl2 Maps Error
+
+## Tags
+
+* type: bug
+* status: open
+* priority: high
+* assigned: alexm, zachs, fredm
+* keywords: R/qtl2, R/qtl2 Maps, gn3, genetwork3, genenetwork 3
+
+## Reproduce
+
+* Go to https://genenetwork.org/
+* In the "Get Any" field, enter "synap*" and press the "Enter" key
+* In the search results, click on the "1435464_at" trait
+* Expand the "Mapping Tools" accordion section
+* Select the "R/qtl2" option
+* Click "Compute"
+* In the "Computing the Maps" page that results, click on "Display System Log"
+
+### Observed
+
+A traceback is observed, with an error of the following form:
+
+```
+⋮
+FileNotFoundError: [Errno 2] No such file or directory: '/opt/gn/tmp/gn3-tmpdir/JL9PvKm3OyKk.txt'
+```
+
+### Expected
+
+The mapping runs successfully and the results are presented in the form of a mapping chart/graph and a table of values.
+
+### Debug Notes
+
+The directory "/opt/gn/tmp/gn3-tmpdir/" exists, and is actually used by other mappings (i.e. The "R/qtl" and "Pair Scan" mappings) successfully.
+
+This might imply a code issue: Perhaps
+* a path is hardcoded, or
+* the wrong path value is passed
+
+The same error occurs on https://cd.genenetwork.org but does not seem to prevent CD from running the mapping to completion. Maybe something is missing on production — what, though?