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    December 21, 2023

    CDD Vault Update (December 2023 #3): New Password Algorithm and API Parameter Updates (ELN, Plates, Runs)

    New Password Algorithm

    CDD Vault will now use the Zxcvbn password algorithm when users set their passwords. This algorithm analyzes a proposed password and gives it a rating based on how hard it is for hacking software to guess. CDD Vault will require a zxcvbn score of 4 (out of 4).

    Update ELN Entries via the API

    A new PUT ELN Entries API call can be used to modify the content of existing ELN Entries. Update the title, project, ELN fields and even the body; adding links, text, and files using a new parameter, append_to_body.

    This new parameter is an array of JSON objects, each with a specific type and associated parameters:

    • TEXT: { "type": "text", "text": "required text goes here" }
    • LINK: { "type": "link", "url": "required URL goes here, same scheme rules as frontend", "label": "optional label override goes here" }
    • FILE: { "type": "file", "file": <file id> }

    This API call:

    PUT .../vaults/<vault_id>/eln/entries/<entry_id>

    ... using this JSON:

       {"append_to_body": [

         {"type": "text", "text": "Description of this experiment"},

         {"type": "link", "url": "https://www.collaborativedrug.com", "label": "This is a link to CDD"},

         {"type": "file", "file": 12345}

         ]}

    ... will append the content to the existing ELN Entry.

    The POST ELN Entries API call can now update the status of an ELN Entry. As an example, to reopen a finalized ELN entry.

    For Vaults with Witnessing enabled, these parameters may be used

    • { status_action: submit, witness: required user id }
    • { status_action: approve }
    • { status_action: reject, reason: required string }
    • { status_action: cancel }

    For Vaults without Witnessing, this parameter may be used:

    • { status_action: finalize }

    And these parameters are available for all ELN enabled Vaults:

    • { status_action: reopen, reason: (string, required) }
    • { status_action: discard }

    To submit an Entry for witnessing use this API call:

    POST .../vaults/<vault_id>/eln/entries/<eln_entry_id>/status

    ... using this JSON:

    {

           "status_action":"submit",

           "witness":"10276"

    }

    To reject an ELN Entry use this API call:

    POST .../vaults/<vault_id>/eln/entries/<eln_entry_id>/status

    ... using this JSON:

    {

           "status_action":"reject",

           "reason":"Not enough data"

    }

    To approve/finalize an ELN Entry use this API call:

    POST .../vaults/<vault_id>/eln/entries/<eln_entry_id>/status

    ... using this JSON:

    {

           "status_action":"approve"

    }.

    PUT Runs API Update

    Values for custom Run Fields may be updated using PUT Runs.

    PUT .../vaults/4493/runs/649838

    ... using this JSON:

    {

       "run_fields":

           {"CRO":"Graceland CRO"}

    }

    ... will update the value of the CRO Run field for the specified Run.

    New PUT/POST Calls for the Plates API Endpoint

    The new PUT and POST endpoints are now supported for creating/updating Plate objects.

    POST .../vaults/4493/plates

    PUT .../vaults/4493/plates/12345

    When creating a new Plate, the name and projects parameters must be included.

    This JSON will create a new Plate:

    { "name": "New Plate 20231219",
      "projects":["Internal Data"] }

    The following JSON is returned:

    {
        "id": 1239120,
        "class": "plate",
        "created_at": "2023-12-20T15:46:00.000Z",
        "modified_at": "2023-12-20T15:46:00.000Z",
        "name": "CW Plate 20231219",
        "volume": 0.0,
        "concentration": 0.0
    }

    These parameters can also be used when creating/updating Plates:

    • concentration
    • concentration_unit_label
    • volume
    • volume_unit_label
    • location

    To associate Batches to the various Plate Wells, either when creating the Plate or updating a Plate, use the wells parameter (which must be an array).

    The JSON for using the concentration, volume and location parameters, along with the well parameter, should resemble:

    { "name": "CW Plate 20231219e",
      "projects":["Internal Data"],
      "concentration":"10",
      "concentration_unit_label":"uM",
      "volume":"100",
      "volume_unit_label":"mL",
      "location":"LabB",
      "wells":[
        {"pos":"A01","batch":142517171},
        {"pos":"A02","batch":126705604},
        {"pos":"A03","batch":126705581}
              ]
     }

    Note: The GET Plates API call also has an only_ids parameter for returning only the internal Plate IDs.

    GET .../vaults/4493/plates

    … using JSON like this:

    { "only_ids":"true" }

    … returns the following JSON results:

    {
        "count": 5,
        "offset": 0,
        "page_size": 50,
        "objects": [
            282199,
            282200,
            306728,
            366630,
            537940
        ]
    }

    This blog is authored by members of the CDD Vault community. CDD Vault is a hosted drug discovery informatics platform that securely manages both private and external biological and chemical data. It provides core functionality including chemical registrationdata visualization, inventory, and electronic lab notebook capabilities.

     

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