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This was just caused by the correlation code not directly being passed the PMID (and instead only being passed the link and the text), so the logic in the table code needed to be changed to check for the link instead of the PMID
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I think it now gets the SQL_URI from settings
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Enable search when user types in search box. Filter out any selected
datasets.
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Move the javascript to an external file to ease development.
Generalise some functions to make it easier to reuse the code down the line.
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Genenetwork2 configs are a tad weird, and instead of using the configs
in `flask.current_app`, we need to use those in `utility.tools`.
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Remove use of deprecated function and fix a myriad of bugs that rise
from its removal.
Issue: https://issues.genenetwork.org/issues/bugfix_coupling_current_app_and_db_utils
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When a user selects a dataset in the search table, automatically add
it to the link table and remove it from the search table.
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Simplify the implementation by dropping the use of the jQuery
DataTables plugin - this avoids a lot of arising bugs while retaining
the UI look and feel until we have something working.
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Try auto-selecting datasets on user click: not successful at this
point.
There are some weird bugs with the DataTables that I have not been
able to resolve yet.
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Since the table data could change depending on user input, save the
state in the `data-*` attributes to enable update of tables on
changes.
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Filter out data as the user types, with a short delay to prevent
searching on each and every character.
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Provide a UI for the phenotype datasets with a search
interface (currently inactive) that is eventually going to allow for
linking the traits to user groups.
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The previous code caused an error when the mean was N/A (when trying to
take the float() of it)
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* wqflask/wqflask/metadata_edits.py (update_phenotype): Add url to
diff page in flash message.
* wqflask/wqflask/templates/edit_phenotype.html: Render flash message
with HTML.
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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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ATM, editing case-attributes is very buggy.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: Delete.
* wqflask/wqflask/decorators.py: Remove:
gn3.authentication.get_groups_by_user_uid import.
(case_attributes_edit_access): Delete.
* wqflask/tests/integration/wqflask/test_metadata_edits.py: Remove
wqflask.decorators.case_attributes_edit_access,
gn3.db.case_attributes.get_case_attributes,
gn3.db.case_attributes.get_unreviewed_diffs,
gn3.db.case_attributes.insert_case_attribute_audit,
gn3.db.case_attributes.reject_case_attribute and
gn3.db.case_attributes.approve_case_attribute.
(display_phenotype_metadata): Remove headers arg when rendering
template.
(update_phenotype): Remove case attribute headers list when updating a
phenotype.
(show_case_attribute_columns, update_case_attributes): Delete.
(reject_case_attribute_data, approve_case_attribute_data): Ditto.
* wqflask/wqflask/templates/edit_phenotype.html: Remove link that
shows all the listed case-attributes.
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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In order to enable searching through the existing datasets for linking
with the auth system, we need a way to filter the data.
In this commit, I load the menu and load it onto a dropdown box as a
proof of concept to give an idea of some of the filters I can use down
the road to fetch the data.
This commit breaks the data-linking code. I will need to rework the
data-linking code entirely to get it working again.
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List/link the phenotypes at the trait level rather than at the dataset level.
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In the case that the JSON output from the correlations computation is
malformed, we capture that into a new exception an re-raise it to help
with debugging and fixing issues.
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Edit Sample Data and Edit Metadata are now two separate sections, and Edit Sample Data appears first
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searchform is already used for the regular search)
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