Display the name of the user instead of their ID in the notification emails.

Fixes aces#9202

In the uploadForm.js file is modified to increase / decrease the numFiles value according to whether a file was actually selected or not. If a file is selected, the numFiles increases. If a file is not selected, the numFiles decreases.

This prevents the bug where "File to Upload" field is added indefinitely if the file is browsed and then cancelled.

Fixes aces#9136

The recruitment graphs on the dashboard provided by the
statistics module are not efficient. They run one SQL query
per month per year per site for each graph that is displayed.
This is highly inefficient for large projects.

This replaces the single queries in the inner loops with a
single group-by query which it processes into the same format.

The result should be significantly faster load times on the dashboard
when the statistics module is loaded.

The value expected by the field is the number id, but the fetch statement was returning the name - so I modified the sql statement to fetch the project ID.

Fixes aces#9134

Display correct error message for files that are too large

Resolves aces#9163

…tion function (aces#9208)

An error regarding the non-existence of a notification_module with module: publication and operation: download prevented the downloading of files.

The notification function was overridden for this module to bypass the LorisException thrown by the non-existence of entries. It appeared by far to be a simpler solution than checking for and adding extra logic when the entries do not exist.

Resolves  aces#9133.

-The loris baseURL is now sent from the react pages to the ajax scripts on submit for both editing and uploading a new publication, and then is sent in the email.
- I did it this way as \NDB_Factory::singleton()->settings()->getBaseURL() does not work in ajax files, and since it is deprecated it made more sense to do a hotfix rather than investigating the issue with ajax.
- This was noticed and fixed for files in php folders in  PR#7807, however that same fix does not work for ajax. Thankfully publication is the only module with ajax still that uses getBaseUrl().

Resolves aces#9132

Fix display of long help text or help text when scrolled past the start of the page.

Resolves aces#9180

This updates the candidate_list module to use format=binary
format instead of format=json. For large projects with many
candidates the encoding of the data to JSON can use up all
the server's memory and then crash with an out-of-memory error.

Since the format=binary format is a line-based streamable format,
it does not require loading the entire result set into memory before
transmitting it to the client and larger data sets can be loaded into
LORIS.

Document required configurations for spm

Fixes aces#9153

Add missing import

Fixes aces#9152

Use a batch insert instead of a prepared statement loop to
populate temporary table in new DQT for SQLQueryEngine.

This makes the SQLQueryEngine use the same logic as
modules/dataquery/php/query.class.inc, which is much more
efficient for large data sets.

…s#9211)

Fixes aces#9185

Fix insert statement when too many roles are added by converting the fields from varchar(255) to text.

Fixes aces#9173

…ils (aces#9214)

Remove unnecessary newline in dicom archive display.

Only re-build instrument data dictionaries, not all data dictionaries, to ensure all names are unique.

…ces#9183)

This adds the query parameter showFeedback=true to trigger auto-opening the feedback panel on-load.

Fixes aces#8056.

This modifies the test plan for the genomic browser module. The changes are mostly cosmetics but also include corrections of the permission names and table headers mentioned in the plan.

Resolves aces#9151

…9188)

Permissions are check now before allowing to add examiner to site.
Before this, a user with only the permission Examiner: Add and Certify Examiners - Own Sites was able to add examiners to sites it don't belongs to. Now this feature is only granted to users with the corresponding level of permission.

Fixes aces#9149