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LIMS-1759: Add pages to create and view ligands#957

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ndg63276 merged 5 commits intopre-release/2025-R5.1from
improvement/LIMS-1759/create-and-view-ligands
Oct 28, 2025
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LIMS-1759: Add pages to create and view ligands#957
ndg63276 merged 5 commits intopre-release/2025-R5.1from
improvement/LIMS-1759/create-and-view-ligands

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@ndg63276 ndg63276 commented Jul 10, 2025

JIRA ticket: LIMS-1759

Summary:

Now that we have the Ligand, Ligand_has_PDB and BLSample_has_Ligand tables, we should have Synchweb pages to create, view, edit ligands, and add them to samples.

Changes:

  • Make a copy of the View (all) Proteins page as a View (all) Ligands, with different columns
  • Make a copy of the Add Protein page as an Add Ligand page, with different fields
  • Make a copy of the View/Edit Protein page as a View/Edit Ligand page, with different fields, but keeping the Add PDB functionality, and also keeping the view of associated samples, containers and data collections
  • Add an Add Ligand field to both the View Sample pages (there are separate ones for pucks and plates), copying the Add Component functionality

To test:

  • Log into an mx proposal (eg mx23694), and select Ligands from the main menu. Click Add Ligand from the top right
  • Populate the form (including testing weird characters for SMILES code) and click Add Ligand. Check you are taken to a view of the ligand.
  • Add PDBs to the ligand, using Existing Code, File Upload, and Code options.
  • Delete PDBs, check they stay removed after a refresh. If no other proteins or ligands use a PDB, check the PDB is deleted from the database.
  • Check you can edit the other fields on the ligand
  • Add a few more ligands and check the list at /ligands displays them all
  • Go to a sample from a puck (eg /samples/sid/6615286), check you can add multiple ligands to it and delete them as well
  • Go to a plate (eg /containers/cid/338373) and click on one of the wells. Check you can add multiple ligands to each sample in the plate (you may need to add some ligands to this proposal first), and delete them as well.

@ndg63276 ndg63276 marked this pull request as ready for review July 10, 2025 12:07
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gfrn commented Oct 9, 2025

Hello! Are we still going ahead with the original plan of deploying this and getting users to test it instead of the usual PR procedure? If not, I can review it

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ndg63276 commented Oct 9, 2025

I think just go ahead and review it, otherwise I'll get confused with what is deployed.

@ndg63276 ndg63276 changed the base branch from master to pre-release/2025-R5.1 October 28, 2025 11:26
@ndg63276 ndg63276 merged commit fcc4f4b into pre-release/2025-R5.1 Oct 28, 2025
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@ndg63276 ndg63276 deleted the improvement/LIMS-1759/create-and-view-ligands branch October 28, 2025 11:28
ndg63276 added a commit that referenced this pull request Nov 11, 2025
* LIMS-1759: Add pages to create and view ligands (#957)

* LIMS-1759: Add pages to add/view/list ligands, add PDBS, and add to samples

* LIMS-1759: Add ligands to samples in plates

* LIMS-1759: Fix bug where ligands were added multiple times

* LIMS-1759: Fix error with too few args

---------

Co-authored-by: Mark Williams <[email protected]>

* LIMS-1926: Hide barcode field when viewing a puck (#991)

Co-authored-by: Mark Williams <[email protected]>

* LIMS-1963: Load all logins for a proposal (#998)

Co-authored-by: Mark Williams <[email protected]>

* LIMS-1917: Track status of strategy pipelines (#993)

* LIMS-1917: Track status of strategy pipelines

* LIMS-1917: Hide strategy pipelines from downstream results

---------

Co-authored-by: Mark Williams <[email protected]>

---------

Co-authored-by: Mark Williams <[email protected]>
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