10 files changed, 554 insertions, 0 deletions

diff --git a/issues/genenetwork2/broken-collections-features.gmi b/issues/genenetwork2/broken-collections-features.gmi
new file mode 100644
index 0000000..4239929
--- /dev/null
+++ b/issues/genenetwork2/broken-collections-features.gmi
@@ -0,0 +1,44 @@
+# Broken Collections Features
+
+## Tags
+
+* type: bug
+* status: open
+* priority: high
+* assigned: zachs, fredm
+* keywords: gn2, genenetwork2, genenetwork 2, collections
+
+## Descriptions
+
+There are some features in the search results page, and/or the collections page that are broken — these are:
+
+* "CTL" feature
+* "MultiMap" feature
+* "Partial Correlations" feature
+* "Generate Heatmap" feature
+
+### Reproduce Issue
+
+* Go to https://genenetwork.org
+* Select "Mouse (Mus musculus, mm10) for "Species"
+* Select "BXD Family" for "Group"
+* Select "Traits and Cofactors" for "Type"
+* Select "BXD Published Phenotypes" for "Dataset"
+* Type "locomotion" in the "Get Any" field (without the quotes)
+* Click "Search"
+* In the results page, select the traits with the following "Record" values: "BXD_10050", "BXD_10051", "BXD_10088", "BXD_10091", "BXD_10092", "BXD_10455", "BXD_10569", "BXD_10570", "BXD_11316", "BXD_11317"
+* Click the "Add" button and add them to a new collection
+* In the resulting collections page, click the button for any of the listed failing features above
+
+### Failure modes
+
+* The "CTL" and "WCGNA" features have a failure mode that might have been caused by recent changes making use of AJAX calls, rather than submitting the form manually.
+* The "MultiMap" and "Generate Heatmap" features raise exceptions that need to be investigated and resolved
+* The "Partial Correlations" feature seems to run forever
+
+## Break-out Issues
+
+We break-out the issues above into separate pages to track the progress of the fixes for each feature separately.
+
+=> /issues/genenetwork3/ctl-maps-error
+=> /issues/genenetwork3/generate-heatmaps-failing
diff --git a/issues/genenetwork2/fix-display-for-time-consumed-for-correlations.gmi b/issues/genenetwork2/fix-display-for-time-consumed-for-correlations.gmi
new file mode 100644
index 0000000..0c8e9c8
--- /dev/null
+++ b/issues/genenetwork2/fix-display-for-time-consumed-for-correlations.gmi
@@ -0,0 +1,15 @@
+# Fix Display for the Time Consumed for Correlations
+
+## Tags
+
+* type: bug
+* status: closed, completed
+* priority: low
+* assigned: @alexm, @bonz
+* keywords: gn2, genenetwork2, genenetwork 2, gn3, genenetwork3 genenetwork 3, correlations, time display
+
+## Description
+
+The breakdown of the time consumed for the correlations computations, displayed at the bottom of the page, is not representative of reality. The time that GeneNetwork3 (or background process) takes for the computations is not actually represented in the breakdown, leading to wildly inaccurate displays of total time.
+
+This will need to be fixed.
diff --git a/issues/genenetwork2/genenetwork2_configurations.gmi b/issues/genenetwork2/genenetwork2_configurations.gmi
new file mode 100644
index 0000000..4ba0a89
--- /dev/null
+++ b/issues/genenetwork2/genenetwork2_configurations.gmi
@@ -0,0 +1,81 @@
+# Genenetwork2 Configurations
+
+## Tags
+
+* assigned: fredm
+* priority: normal
+* status: closed, obsoleted
+* keywords: configuration, config, gn2, genenetwork, genenetwork2
+* type: bug
+
+## Description
+
+The current way the configuration in Genenetwork2 works is as follows:
+
+* The configuration setup begins in `bin/genenetwork` script in the genenetwork2 repository. This script sets up the `GN2_PROFILE` environment variable, and all other environment variables depending on it: see the "`GN2_PROFILE`-Dependent Environment Variables" section below.
+* In `wqflask/wqflask/__init__.py` the settings in the file pointed to by `GN2_SETTINGS` environment variable are then loaded. If there is no such file, then it defaults to loading the settings in the `etc/default_settings.py` within the genenetwork2 repository.
+* In `wqflask/utility/tools.py` in the genenetwork2 repository, the settings loaded thus far, can then have their values overriden by values set in the environment variables. There is an "OVERRIDES" value that is currently not in use and can be ignored.
+* Some other minor configurations are updated/overriden in `wqflask/utility/startup_config.py`
+
+From these, `GN2_PROFILE` is the only environment variable that needs to be set up. All the other variables can be set in the settings file.
+
+The file `wqflask/base/webqtlConfig.py` also has some configurations that need to be handled.
+
+The sub-sections that follow will contain more information on variables and what needs to be done
+
+### `GN2_PROFILE`-Dependent Environment Variables
+
+* `PATH`: Exposes the binaries within the profile
+* `PYTHONPATH`: Exposes the Python modules within the profile
+* `R_LIBS_SITE`: Exposes the R module within the profile
+* `JS_GUIX_PATH`: Exposes the Javascript modules within the profile
+* `GUIX_GTK3_PATH`: Exposes the GTK modules within the profile
+* `GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
+* `XDG_DATA_DIRS`: Exposes the "share" directories within the profile
+* `GIO_EXTRA_MODULES`: Expose the GIO modules
+* `GUIX_GENENETWORK_FILES`: Expose the Genenetwork shared files
+* `PLINK_COMMAND`: Point to the "PLINK" binary
+* `GEMMA_COMMAND`: Point to the "GEMMA" binary
+* `GEMMA_WRAPPER_COMMAND`: Point to the `GEMMA` wrapper binary
+
+### `wqflask/utility/tools.py`
+
+This is our biggest pain-point. The following are some actions that can be taken to reduce the pain in this module:
+
+* Refactor functions in to take the "application object" as one of their arguments, to decouple the module from the module where the application is declared
+* Remove all settings from this module, instead, override any of the variables that need it at the application creation step, possibly within the `wqflask/wqflask/__init__.py` module.
+* Replace all uses of variables from this module with configurations from `flask.current_app.config` as appropriate
+* Get rid of this module entirely if possible, moving the functions elsewhere.
+
+### Modules with Routes but no Blueprints
+
+These modules are:
+
+* `wqflask/run_gunicorn.py`
+* `wqflask/wqflask/user_session.py`
+* `wqflask/wqflask/collect.py`
+* `wqflask/wqflask/views.py`
+* `wqflask/wqflask/partial_correlations_views.py`
+* `wqflask/wqflask/user_login.py`
+* `wqflask/wqflask/api/router.py`
+* `wqflask/base/trait.py`
+
+Except for `wqflask/run_gunicorn.py`, each module will have its own Blueprint and then we'll have some top-level Blueprint that import all the others and sets them up. The top-level blueprint will then be registered with the app at the application-creation time.
+
+For `wqflask/run_gunicorn.py`, the route can remain as is, since this is an entry-point module.
+
+### `wqflask/wqflask/__init__.py`
+
+* Move application initialisation into an application factory function
+* Replace all uses of `wqflask.app` variable with `flask.current_app` or `create_app()` as necessary
+
+### Non-Executable Configuration Files
+
+Eschew executable formats (*.py) for configuration files and prefer non-executable formats e.g. *.cfg, *.json, *.conf etc
+
+
+## Closed as obsoleted
+
+I am closing this issue as obsoleted, since a lot of things have changed since this issue was set up. The `bin/genenetwork2` script no longer exists and most of the paths mentioned have changed.
+
+The configuration issue(s) mentioned above still abound, but the changes will have to be incremental to avoid breaking the system.
diff --git a/issues/genenetwork2/haley-knott-regression-mapping-error.gmi b/issues/genenetwork2/haley-knott-regression-mapping-error.gmi
new file mode 100644
index 0000000..25bb221
--- /dev/null
+++ b/issues/genenetwork2/haley-knott-regression-mapping-error.gmi
@@ -0,0 +1,80 @@
+# Haley-Knott Regression Mapping Error
+
+## Tags
+
+* type: bug
+* status: closed, completed
+* priority: high
+* assigned: fredm
+* keywords: gn2, genenetwork2, genenetwork 2, mapping, haley-knott
+
+## Description
+
+To run the mapping:
+
+* Do a search
+* Click on any trait in the results
+* On the trait page, expand the "Mapping Tools" section
+* Select the "Haley-Knott Regression" option under "Mapping Tools"
+* Click "Compute"
+
+On running the mapping as above, we got the following error:
+
+```
+      GeneNetwork 2.11-rc2  https://gn2-fred.genenetwork.org/run_mapping ( 6:14AM UTC Sep 11, 2024) 
+Traceback (most recent call last):
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/flask/app.py", line 1523, in full_dispatch_request
+    rv = self.dispatch_request()
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/flask/app.py", line 1509, in dispatch_request
+    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/gn2/wqflask/views.py", line 1004, in mapping_results_page
+    gn1_template_vars = display_mapping_results.DisplayMappingResults(
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/gn2/wqflask/marker_regression/display_mapping_results.py", line 651, in __init__
+    self.perm_filename = self.drawPermutationHistogram()
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/gn2/wqflask/marker_regression/display_mapping_results.py", line 3056, in drawPermutationHistogram
+    Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD,
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/gn2/utility/Plot.py", line 184, in plotBar
+    scaleFont = ImageFont.truetype(font=COUR_FILE, size=11)
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/PIL/ImageFont.py", line 959, in truetype
+    return freetype(font)
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/PIL/ImageFont.py", line 956, in freetype
+    return FreeTypeFont(font, size, index, encoding, layout_engine)
+  File "/gnu/store/hgcvlkn4bjl0f9wqiakpk5w66brbfxk6-profile/lib/python3.10/site-packages/PIL/ImageFont.py", line 247, in __init__
+    self.font = core.getfont(
+OSError: cannot open resource
+```
+
+### Hypothesis
+
+My hypothesis is that the use of relative paths[fn:1] is the cause of the failure.
+
+When running the application with the working directory being the root of the GeneNetwork2 repository, use of the relative paths works well. Unfortunately, that assumption breaks quickly if the application is ever run outside of the root of the GN2 repo.
+
+Verification:
+
+*Question*: Does the application run on root of GN2 repository/package?
+
+* Log out the path of the font file and use the results to answer the question
+* https://github.com/genenetwork/genenetwork2/commit/ca8018a61f2e014b4aee4da2cbd00d7b591b2f6a
+* https://github.com/genenetwork/genenetwork2/commit/01d56903ba01a91841d199fe393f9b307a7596a2
+
+*Answer*: No! The application does not run with the working directory on the root of the GN2 repository/package, as evidenced by this snippet from the logs:
+
+```
+2024-09-11 07:41:13 [2024-09-11 07:41:13 +0000] [494] [DEBUG] POST /run_mapping
+2024-09-11 07:41:18 [2024-09-11 07:41:18 +0000] [494] [DEBUG] Font file path: /gn2/wqflask/static/fonts/courbd.ttf
+2024-09-11 07:41:18 DEBUG:gn2.wqflask:Font file path: /gn2/wqflask/static/fonts/courbd.ttf
+2024-09-11 07:41:18 [2024-09-11 07:41:18 +0000] [494] [ERROR] https://gn2-fred.genenetwork.org/run_mapping ( 7:41AM UTC Sep 11, 2024)
+2024-09-11 07:41:18 Traceback (most recent call last):
+```
+
+We see from this that the application seems to be running with the working directory being "/" rather than the root for the application's package files.
+
+### Fixes
+
+* https://github.com/genenetwork/genenetwork2/commit/d001c1e7cae8f69435545b8715038b1d0fc1ee62
+* https://git.genenetwork.org/guix-bioinformatics/commit/?id=7a1bf5bc1c3de67f01eabd23e1ddc0150f81b22b
+
+# Footnotes
+
+[fn:1] https://github.com/genenetwork/genenetwork2/blob/50fc0b4bc4106164745afc7e1099bb150f6e635f/gn2/utility/Plot.py#L44-L46
diff --git a/issues/genenetwork2/handle-oauth-errors-better.gmi b/issues/genenetwork2/handle-oauth-errors-better.gmi
new file mode 100644
index 0000000..77ad7ad
--- /dev/null
+++ b/issues/genenetwork2/handle-oauth-errors-better.gmi
@@ -0,0 +1,21 @@
+# Handle OAuth Errors Better
+
+## Tags
+
+* type: bug
+* status: closed, completed
+* priority: high
+* assigned: fredm
+* interested: zachs, robw
+* keywords: gn2, genenetwork2, ui, user interface, oauth, oauth errors
+
+## Description
+
+When a session expires, for whatever reason, a notification is displayed to the user as shown in the image below:
+=> ./session_expiry_oauth_error.png
+
+The message is a little jarring to the end user. Make it gentler, and probably more informative, so the user is not as surprised.
+
+## Close as complete
+
+This should be fixed at this point. Closing this as complete.
diff --git a/issues/genenetwork2/mapping-error.gmi b/issues/genenetwork2/mapping-error.gmi
new file mode 100644
index 0000000..7e7d0a7
--- /dev/null
+++ b/issues/genenetwork2/mapping-error.gmi
@@ -0,0 +1,66 @@
+# Mapping Error
+
+## Tags
+
+* type: bug
+* status: closed
+* priority: medium
+* assigned: zachs, fredm, flisso
+* keywords: gn2, genenetwork2, genenetwork 2, mapping
+
+## Reproduction
+
+* Go to https://staging.genenetwork.org/
+* For 'Species' select "Arabidopsis (Arabidopsis thaliana, araTha1)"
+* For 'Group' select "BayXSha(RIL by sib-mating)"
+* For 'Type' select "arabidopsis seeds"
+* For 'Dataset' select "Arabidopsis BayXShaXRIL_expr_reg _ATH1"
+* Leave 'Get Any' blank
+* Enter "*" for "Combined"
+* Click "Search"
+* On the search results page, click on "AT1G01010"
+* Expand the "Mapping Tools" section
+* For 'Chromosome' select "All"
+* For 'Minor Allele ≥' enter "0.05"
+* For 'Use LOCO' select "Yes"
+* Ignore covariates
+* Click "Compute"
+
+### Expected
+
+The system would compute the maps and display the mapping diagram(s) and data.
+
+### Actual
+
+The computation fails with:
+
+```
+      GeneNetwork 2.11-rc2  https://staging.genenetwork.org/loading ( 6:50PM UTC Jul 03, 2024) 
+Traceback (most recent call last):
+  File "/gnu/store/jsvqai0gz6fn40k7kx3r12yq4hzfini6-profile/lib/python3.10/site-packages/flask/app.py", line 1523, in full_dispatch_request
+    rv = self.dispatch_request()
+  File "/gnu/store/jsvqai0gz6fn40k7kx3r12yq4hzfini6-profile/lib/python3.10/site-packages/flask/app.py", line 1509, in dispatch_request
+    return self.ensure_sync(self.view_functions[rule.endpoint])(**req.view_args)
+  File "/gnu/store/jsvqai0gz6fn40k7kx3r12yq4hzfini6-profile/lib/python3.10/site-packages/gn2/wqflask/views.py", line 812, in loading_page
+    for sample in samples:
+TypeError: 'NoneType' object is not iterable
+```
+
+### Updates
+
+This is likely just because the genotype file doesn't exist in the necessary format (BIMBAM). We probably need to convert the R/qtl2 genotypes to BIMBAM.
+
+## Stalled
+
+This is currently stalled, until we can upload genotypes via the uploader.
+
+
+## Notes
+
+### 2025-12-31
+
+I am closing this issue as WONTFIX because of the following reasons:
+
+- Better fix is to prevent mapping in the first place, if no genotypes exist for the given trait(s)
+- Issue relies on non-implemented feature (Genotypes upload) to fix it
+- Issue does not exist on production
diff --git a/issues/genenetwork2/mechanical-rob-add-partial-correlations-tests.gmi b/issues/genenetwork2/mechanical-rob-add-partial-correlations-tests.gmi
new file mode 100644
index 0000000..e38f653
--- /dev/null
+++ b/issues/genenetwork2/mechanical-rob-add-partial-correlations-tests.gmi
@@ -0,0 +1,22 @@
+# mechanical-rob: Add Partial Correlations Tests
+
+## Tags
+
+* assigned: fredm
+* priority: medium
+* status: open
+* keywords: genenetwork2, gn2, mechanical-rob, partial correlations, tests, regression
+* type: enhancement
+
+## Description
+
+Add regression tests to verify that the partial correlations feature still works
+as expected.
+
+### TODOS
+
+- [-] Tests for "entry-point" page
+- [x] Tests for partial correlation using Pearson's R against select traits
+- [ ] Tests for partial correlation using Spearman's Rho against select traits
+- [ ] Tests for partial correlation using Pearson's R against an entire dataset
+- [ ] Tests for partial correlation using Spearman's Rho against an entire dataset
diff --git a/issues/genenetwork2/refresh-token-failure.gmi b/issues/genenetwork2/refresh-token-failure.gmi
new file mode 100644
index 0000000..c488820
--- /dev/null
+++ b/issues/genenetwork2/refresh-token-failure.gmi
@@ -0,0 +1,111 @@
+# Refresh Token Failure
+
+## Tags
+
+* status: closed, obsoleted
+* priority: high
+* type: bug
+* assigned: fredm, zsloan, zachs
+* keywords: gn2, genenetwork2
+
+## Description
+
+* Go to https://genenetwork.org
+* Click "Sign in" and sign in to the application
+* Wait 15 minutes
+* Close the entire browser
+* Open the browser and go to https://genenetwork.org
+* Observe the "ERROR" message at the "Collections" link's badge
+
+The expectation is that the Collections badge would list the number of collection the user has, rather than the error message.
+
+The logs fail with an 'invalid_client' error:
+
+```
+2025-01-08 20:48:56     raise self.oauth_error_class(
+2025-01-08 20:48:56 authlib.integrations.base_client.errors.OAuthError: invalid_client: 
+2025-01-08 20:48:56 ERROR:gn2.wqflask:Error loading number of collections
+2025-01-08 20:48:56 Traceback (most recent call last):
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/gn2/wqflask/__init__.py", 
+line 55, in numcoll
+2025-01-08 20:48:56     return num_collections()
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/gn2/wqflask/oauth2/collect
+ions.py", line 13, in num_collections
+2025-01-08 20:48:56     all_collections = all_collections + oauth2_get(
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/gn2/wqflask/oauth2/client.
+py", line 168, in oauth2_get
+2025-01-08 20:48:56     resp = oauth2_client().get(
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/requests/sessions.py", lin
+e 600, in get
+2025-01-08 20:48:56     return self.request("GET", url, **kwargs)
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/integrations/reque
+sts_client/oauth2_session.py", line 109, in request
+2025-01-08 20:48:56     return super(OAuth2Session, self).request(
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/requests/sessions.py", lin
+e 573, in request
+2025-01-08 20:48:56     prep = self.prepare_request(req)
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/requests/sessions.py", lin
+e 484, in prepare_request
+2025-01-08 20:48:56     p.prepare(
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/requests/models.py", line 
+372, in prepare
+2025-01-08 20:48:56     self.prepare_auth(auth, url)
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/requests/models.py", line 
+603, in prepare_auth
+2025-01-08 20:48:56     r = auth(self)
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/integrations/reque
+sts_client/oauth2_session.py", line 24, in __call__
+2025-01-08 20:48:56     self.ensure_active_token()
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/integrations/reque
+sts_client/oauth2_session.py", line 20, in ensure_active_token
+2025-01-08 20:48:56     if self.client and not self.client.ensure_active_token(self.token):
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/oauth2/client.py",
+ line 262, in ensure_active_token
+2025-01-08 20:48:56     self.refresh_token(url, refresh_token=refresh_token)
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/oauth2/client.py",
+ line 252, in refresh_token
+2025-01-08 20:48:56     return self._refresh_token(
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/oauth2/client.py",
+ line 373, in _refresh_token
+2025-01-08 20:48:56     token = self.parse_response_token(resp)
+2025-01-08 20:48:56   File "/gnu/store/3n1cl5cxal3qk7p9q363qgm2ag45a177-profile/lib/python3.10/site-packages/authlib/oauth2/client.py",
+ line 340, in parse_response_token
+2025-01-08 20:48:56     raise self.oauth_error_class(
+2025-01-08 20:48:56 authlib.integrations.base_client.errors.OAuthError: invalid_client:
+```
+
+
+### Troubleshooting
+
+The following commits were done as part of the troubleshooting:
+
+=> https://github.com/genenetwork/genenetwork2/commit/55da5809d851a3c8bfa13637947b019a2c02cc93
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=d1cada0f0933732eb68b7786fb04ea541d8c51c9
+=> https://github.com/genenetwork/genenetwork2/commit/93dd7f7583af4e0bdd3c7b9c88d375fdc4b40039
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=5fe04ca1545f740cbb91474576891c7fd1dff13a
+=> https://github.com/genenetwork/genenetwork2/commit/2031da216f3b62c23dca64eb6d1c533c07dc81f1
+=> https://github.com/genenetwork/genenetwork2/commit/125c436f5310b194c10385ce9d81135518ac0adf
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=758e6f0fbf6af4af5b94b9aa5a9264c31f050153
+=> https://github.com/genenetwork/genenetwork2/commit/8bf483a3ab23ebf25d73380e78271c368ff06b2d
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=f1ee97a17e670b12112d48bea8969e2ee162f808
+=> https://github.com/genenetwork/genenetwork2/commit/de01f83090184fc56dce2f9887d2dc910edc60fe
+=> https://github.com/genenetwork/genenetwork2/commit/91017b97ee346e73bed9b77e3f3f72daa4acbacd
+=> https://github.com/genenetwork/genenetwork2/commit/7e6bfe48167c70d26e27b043eb567608bc1fda84
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=1f71a1e78af87266e7a4170ace8860111a1569d6
+=> https://github.com/genenetwork/genenetwork2/commit/9bdc8ca0b17739c1df9dc504f8cd978296b987dd
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=02a9a99e7e3c308157f7d740a244876ab4196337
+=> https://github.com/genenetwork/genenetwork2/commit/236a48835dc6557ba0ece6aef6014f496ddb163e
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=f928be361d2e331d72448416300c331e47341807
+=> https://github.com/genenetwork/genenetwork2/commit/5fb56c51ad4eaff13a7e24b6022dffb7d82aa41d
+=> https://github.com/genenetwork/genenetwork2/commit/c6c9ef71718d650f9c19ae459d6d4e25e72de00a
+=> https://github.com/genenetwork/genenetwork2/commit/dc606f39fb4aad74004959a6a15e481fa74d52ff
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=4ab597b734968916af5bae6332756af8168783b3
+=> https://github.com/genenetwork/genenetwork2/commit/854639bd46293b6791c629591fd934d1f34038ac
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=7e0083555150d151e566cebed4bd82d69e347eb6
+=> https://github.com/genenetwork/genenetwork2/commit/c4508901027a2d3ea98e1e9b3f8767a455cad02f
+=> https://git.genenetwork.org/guix-bioinformatics/commit/?id=955e4ce9370be9811262d7c73fa5398385cc04d8
+
+
+# Closed as Obsolete
+
+We no longer rely on refresh tokens. This issue is no longer present.
diff --git a/issues/genenetwork2/remove-bin-genenetwork2-script.gmi b/issues/genenetwork2/remove-bin-genenetwork2-script.gmi
new file mode 100644
index 0000000..da11be7
--- /dev/null
+++ b/issues/genenetwork2/remove-bin-genenetwork2-script.gmi
@@ -0,0 +1,114 @@
+# Remove `bin/genenetwork2` Script
+
+## Tags
+
+* type: improvement
+* status: closed, completed
+* priority: medium
+* assigned: fredm, bonfacem, alexm, zachs
+* interested: pjotrp, aruni
+* keywords: gn2, bin/genenetwork2, startup script
+
+## Description
+
+The `bin/genenetwork2` script was used for a really long time to launch Genenetwork2, and has served that purpose with honour and dedication. We applaud that.
+
+It is, however, time to retire the script, since at this point in time, it serves more to obfuscate the startup that as a helpful tool.
+
+On production, we have all but abandoned the use of the script, and we need to do the same for CI/CD, and eventually, development.
+
+This issue tracks the process, and problems that come up during the move to retire the script.
+
+### Process
+
+* [x] Identify how to run unit tests without the script
+* [x] Document how to run unit tests without the script
+* [x] Identify how to run mechanical-rob tests without the script
+* [x] Document how to run mechanical-rob tests without the script
+* [x] Update CI/CD definitions to get rid of the references to the script
+* [x] Delete the script from the repository
+
+### Setup
+
+First, we need to setup the following mandatory environment variables:
+
+* GN2_PROFILE
+* GN2_SETTINGS
+* JS_GUIX_PATH
+* GEMMA_COMMAND
+* PLINK_COMMAND
+* GEMMA_WRAPPER_COMMAND
+* REQUESTS_CA_BUNDLE
+
+Within a guix shell, you could do that with something like:
+
+```
+export GN2_PROFILE="${GUIX_ENVIRONMENT}"
+export GN2_SETTINGS="/home/frederick/genenetwork/gn2_settings.conf"
+export JS_GUIX_PATH="${GN2_PROFILE}/share/genenetwork2/javascript"
+export GEMMA_COMMAND="${GN2_PROFILE}/bin/gemma"
+export PLINK_COMMAND="${GN2_PROFILE}/bin/plink2"
+export GEMMA_WRAPPER_COMMAND="${GN2_PROFILE}/bin/gemma-wrapper"
+export REQUESTS_CA_BUNDLE="${GUIX_ENVIRONMENT}/etc/ssl/certs/ca-certificates.crt"
+```
+
+Note that, you can define all the variables derived from "GN2_PROFILE" in your settings file, if such a settings file is computed.
+
+### Running Unit Tests
+
+To run unit tests, run pytest at the root of the repository.
+
+```
+$ cd /path/to/genenetwork2
+$ pytest
+```
+
+### Running "mechanical-rob" Tests
+
+At the root of the repository, run something like:
+
+```
+python test/requests/test-website.py --all http://localhost:5033
+```
+
+Change the port, as appropriate.
+
+
+### Launching Application
+
+In addition to the minimum set of envvars defined in the "Setup" section above, we need the following variables defined to get the application to launch:
+
+* FLASK_APP
+
+In a guix shell, you could do:
+
+```
+export FLASK_APP="gn2.wsgi"
+```
+
+Now you can launch the application with flask with something like:
+
+```
+flask run --port=5033 --with-threads
+```
+
+or with green unicorn with something like:
+
+```
+gunicorn --reload \
+         --workers 3 \
+         --timeout 1200 \
+         --log-level="debug" \
+         --keep-alive 6000 \
+         --max-requests 10 \
+         --bind="127.0.0.1:5033" \
+         --max-requests-jitter 5 \
+         gn2.wsgi:application
+```
+
+You can change the gunicorn setting to fit your scenario.
+
+
+## Close as completed
+
+The script has been deleted.
diff --git a/issues/genenetwork2/session_expiry_oauth_error.png b/issues/genenetwork2/session_expiry_oauth_error.png
new file mode 100644
index 0000000..34e2dda
--- /dev/null
+++ b/issues/genenetwork2/session_expiry_oauth_error.png
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