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The original code (using the homebrew ORM system) would simply ignore
values that were `None` when doing updates - the new code using direct
queries was not.
My (fredmanglis) initial fix to provide a default for values in DB
that did not accept NULL was incorrect; instead, I needed to remove
any key-value pairs from the incoming data that were set to `None` to
fix the bug.
The fix still feels incorrect: maybe we should do direct comparisons
for all old-new value pairs, and set the data to be updated based on
the differences, rather than relying on `None`s.
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including 'chr'
As far as I can tell, the regex from before wasn't necessary; it seems like a simple matter of extracting the 'chr' substring from the chromosome search term
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Provide a means to paginate the data items in the resources page.
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Fetch the `metadata_audit` trails for phenotypes and probesets using
direct queries rather than the ORM-dependent functions.
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Create a 'metadata_audit' record with a direct query rather than using
the ORM-dependent function to create it.
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Ensure that changes the database are committed if the query is
successful, or rolled back if not.
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For editing, ensure the user is logged in before even attempting to
check the authorisation privileges.
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Display the "Edit" button for all the users to ensure that they are
aware of the feature.
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Protect the actual "approve" or "reject" steps, rather than just the
UI elements.
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* Add missing `.now()`
* Provide defaults (not `None`) for required fields
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Replace the ORM functions for fetching and updating the publication
with non-ORM equivalents.
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traits export
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Avoid the use of the ORM code for fetching data from the database, and
instead use direct queries that indicate easily what is being fetched
from the database.
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Use the reworked `retrieve_phenotype_group_name` to fetch the group
name for phenotype datasets.
== Bug Description ==
There was a subtle bug in the original calls to `retrieve_group_name`
function where the `dataset_id` was passed in as an argument, rather
than the group id.
For some Datasets, the `group_id` and `dataset_id` share the same
value, and would end up querying the correct values, but that was a
fluke where doing the wrong thing ended up with the expected values.
This commit fixes that by using the reworked function, which does the
correct indirection from `dataset_id` to the appropriate `group_id`.
See
https://github.com/genenetwork/genenetwork3/commit/088b6181457ef4e528b7dcbf04b7aca29b274d1f
for the reworked function.
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Serialize values to JSON using the custom encoder that is aware of
data types the default encoder might not be aware of.
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Change the input elements from all "<textarea ...>" to more closely
adhere to the data that each element is concerned with.
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Assign the value to group within the db connection's context
manager. Initialise the group to an empty tuple at the very begining.
Fixes the error noted in
https://github.com/genenetwork/gn-docs/blob/master/api/questions-to-ask-GN.md
and should now allow the curl invocation:
curl -s https://genenetwork.org/api/v_pre1/group/BXD
to work as expected.
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The `str.isnumeric()` function returns false for numbers such as
'9.99', '88.8' etc. This commit provides a slightly more robust check
for strings that are numbers. It will fail for numbers with exponents
though.
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* wqflask/utility/json/__init__.py: Custom JSON for serialising UUIDs
into a JSON representantion
* wqflask/utility/json/encoders.py: Custom JSON for serialising UUIDs
into a JSON representation
* wqflask/wqflask/metadata_edits.py: Use new sessions for author
information
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Change how the check for user login works.
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Apparently collections/add needs the input to be passed as POST
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Update the sort-key functions to use the correct dictionary keys to
retrieve the comparison value for the sort.
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The code filtering the diffs to ensure that only the diffs for the
traits that the user has access to are visible was leading to the
diffs that relate to the same trait showing up more than once. This
commit fixes that, ensuring that each diff shows up once.
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* wqflask/wqflask/metadata_edits.py: Filter out diffs that the user
has access to before sending them to the template.
* wqflask/wqflask/templates/display_files.html: Remove access control
code in the UI template.
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work
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The bug was caused by PCA traits not having description_display
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Add GN3 Github link
Move News Twitter feed below Links (at least until the Twitter embed
starts working again)
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I think this bug was caused by changing the /run_mapping endpoint to
accept both GET and POST requests, and it only seemed to occur for some
users (only Rob that I'm aware of).
I'm still not sure why it was happening, but I addressed it by returning
/run_mapping to being only POST requests, and instead allowing the
mapping hashes to be linked to with the pattern /run_mapping/<hash>
(instead of the GET request /run_mapping?hash=<hash>). This appears to
have prevented the problem from happening.
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The main code should only ever get its configs from the application
configurations, and not directly from the envvars. This helps with
maintenance by ensuring that the application configurations are done
in one place, and can be traced for debugging purposes.
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The `OVERRIDES` variable has no actual use in the application,
therefore, this commit removes it and its dependent code.
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The individual parts of the URI to the database are not used in the
application and thus serve no purpose.
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