Workflow

Sources

The Sources are used for defining forms, structure checkers and registration options.

After defining a new source, the administrator should define a registration form for the given source and a set of structure checkers and the list of registration options. In order to make the new source the default selection during single registration and bulk uploads, drag and drop it to the beginning of the list of Known sources and save your changes.


The Sources menu that contains the list of sources

{primary} Before version 24.3.2 the source name had to be written in all capitals without spaces, for example NEWSOURCE. Since version 24.3.2 the source name can be lowercase as well. "Default" can be a valid source name. The source parameter of the request body accepted by the /autoRegister, /advancedAutoRegister, and /advancedRegister endpoints is going to be case-sensitive. (E.g. to register with "REGISTRAR" the string "REGISTRAR" will be accepted but not "registrar").

Registration Options

Using the Registration options (formerly system switchers) you can define actions to be used during the registration .


Registration options

Register new lots

When the switcher is set to false, the registration of new lots under a matching version is not allowed. The submission will fall to the Staging area with "OperationNotAllowed" status message. The submission can be picked up and registered from the Staging area through the Submission page.
Register new versions

When the switcher is set to false, the registration of new versions is not allowed. The submission will fall to the Staging area with "OperationNotAllowed" status message. The submission can be picked up and registered from the Staging area through the Submission page.
Register with unknown CST

If during registration an unknown CST (Chemically Significant Text) is provided, registration will be allowed only if the switcher is set to true. Otherwise, it will fall to the Staging area. From the Staging area again the submission can be successfully registered only if the switcher is set to true.

"UnknownCST" is considered a CST that is not present in the CST dictionary.
Register Restricted matches

When the switcher is set to false, the registration of compounds having a positive integer other than 0 for the restriction value is not allowed.
Register 2D Parent Matches

When the switcher is set to false, the registration of structures that are stereo and/or CST matches of already existing ones is not allowed. The submission will fall to the Staging area with "Parent2DMatch" status message. The submission can be picked up and registered from the Staging area through the Submission page.

Structure to be registered Registered structure Match type

2D (stereroisomer)

2D (CST different)
Register Tautomer Parent Matches

When the switcher is set to false, the registration of structures that are tautomer matches of already existing ones is not allowed. The submission will fall to the Staging area with "ParentTautomerMatch" status message. The submission can be picked up and registered from the Staging area through the Submission page if the switcher will be enabled.

Structure to be registered Registered structure Match type

Tautomer
Register 2D_Tautomer Parent Matches

When the switcher is set to false, the registration of structures that are stereo-tautomer matches of already existing ones is not allowed. The submission will fall to the Staging area with "Parent2DTautomerMatch" status message. The submission can be picked up and registered from the Staging area through the Submission page if the switcher will be enabled.

Structure to be registered Registered structure Match type

Tautomer & 2D (Tautomer and stereo)
Perform Quality Checks

Quality Checks are defined at the level of the entire registration service. This source-dependent system switcher controls whether the quality check should run or not.
Analyze Salt/Solvate

Analyze Salt/Solvate is a procedure capable of automated extraction of salt/solvate fragment from a compound's chemical structure and replace them with references to the corresponding records in the salts and solvates dictionary . It can be activated or deactivated as a part of the system switchers . The switcher is on by default for some sources, and can be applied manually to the records in the Staging area .
Stereo Comment Check

When the switcher is false, no stereo comment is required to be set in the corresponding Stereochemistry and Geometric isomerism fields and if values are provided those are not validated, they will be stored as provided. More info can be found here.
Reject Duplicate Id

If this switcher is on, a submission that has failed because of a duplicate Id error (like LnbRefDuplicated or LotIdDuplicated), will have a "Rejected Id" for the status and will be excluded from the Staging area. Users will not be able to retrieve these submissions, unless they specifically type the submission Id in the URL, like: https://your.domain.com/RegistryCxn/client/index.html#/submission? submissionId=xxx.

The "Reject Duplicate Id" switcher is turned off by default: in case of a duplicate Id, the submission will fall to the Staging area, where the user can correct the Id in order to register the submission.

Structure to be registered	Registered structure	Match type
		Tautomer

Structure to be registered	Registered structure	Match type
		Tautomer & 2D (Tautomer and stereo)

Workflow Steps

In the Compound Registration system the following workflows are available and configurable:

A detailed explanation of the configurable workflow steps is available:

Description of the workflow steps

{info} After changing the workflow steps you need to click on the "Save" button in order to apply the changes.

{info} Since version 20.8.0 when you click to the "Save" button the workflow change is done immediately. In older versions a server restart is necessary after you save the workflow change.

Auto registration


Auto registration Workflow steps

Since version 21.20.0 there is a new workflow step: WarningCheckerValidator. If the workflow contains the WarningCheckerValidator workflow step, the configured quality warnings will run globally in the system. This configuration can be done on the Structure Checkers administration page.

Quality Warnings configuration is empty by default, so it does not run any checkers. When it is configured with checkers, all of the checkers and fixers will run based on the FixMode and FixerClassName configuration. Quality Warnings are executed for each registration, do not prevent registration if unfixed, just generate warnings.

Structure Warnings will be visible in the submission history if the workflow contains the WarningCheckerValidator workflow step.

Advanced registration


Advanced registration Workflow steps

Register to existing compound (Register lot)


Register lot Workflow steps

Auto registration Virtual compounds


Auto registration Virtual compounds Workflow steps

Advanced registration Virtual compounds


Advanced registration Virtual compounds Workflow steps

Amend parent level


Amend parent level Workflow steps

Amend version level


Amend version level Workflow steps

Amend lot level


Amend lot level Workflow steps

Update additional data on parents


Update additional data on parent level Workflow steps

Update additional data on versions


Update additional data on version level Workflow steps

Update additional data on lots


Update additional data on lot level Workflow steps

The description of the workflow steps:

Workflow step	Description
SourceValidator	Check if the source is known according to the Administration/Workflow/Sources setting.
LotIdValidator	Check if it is required according to the Administration/Integration/Identifiers setting. In case when LotId is provided it is checked if it is valid (e.g. not a negative number). The "REJECT_DUPLICATED_IDS" switcher is checked. If the switcher is on and the LotId is already present in the DB, the submission will be sent to the Staging with “Rejected” status. If the switcher is off, and the LotId is already present in the DB, the submission will be sent to the Staging with “LotIdDuplicated” status. Note: Unique LotIds are not searched among deleted compounds.
LnbRefValidator	Check if LnbRef validation is set. If validation is on, check if the provided LnbRef corresponds to the configured regular expressions defined within the Administration/Integration/Identifiers setting. Check if LnbRef considers the “autoCompleteEmptyLnbRefWithLns” switcher. The "REJECT_DUPLICATED_IDS" switcher is checked. If the switcher is on and the LnbRef is already present in the DB, the submission will be sent to the Staging with “Rejected” status. If the switcher is off, and the LnbRef is already present in the DB, the submission will be sent to the Staging with “LnbRefDuplicated” status.Note: Unique LnbRefs are also searched among deleted compounds.
LnbRefChangeValidation	After changing the LnbRef on the Submission page LnbRef validation runs again.
StructureTypeValidator	Check if the provided structure corresponds to the selected structure type.
RejectMarkushValidator	If present, all Markush structures (“Single Structure” structures types) are sent to the Staging area.
FieldValidator	Check if the values of the additional fields correspond to the configured field settings.
FieldGenerator	Configured auto-generated fields (e.g. chemical terms) are populated in this step.
MarkushStructureValidator	Recognized Markush structures are being validated. You can find more info about Markush structures here.
StandardizerErrorValidator	Configured general standardizer actions run in this step.
AmfValidator	Check if the provided multi-component compound corresponds to the configured Alternate, Mixture or Formulation.
PolymerValidator	Check if the provided multi-component compound corresponds to the configured Polymer.
SaltSolvateValidator	Check if added salt/solvate components are valid salts/solvates.
ParentMultiplicityValidator	In the case of salt/solvate components, the parent multiplicity is validated and the rounded parent multiplicity value will be set.
SaltFragmentsValidator	Check if the fragments of the compound to be registered are present in the salts/solvates list.
ChargeValidator	Check if the compound charge is balanced.
StructureCheckerValidator	Validates structures according to the Structure Checkers for the “source” section in the Structure Checkers settings.
StructureQualityCheckerValidator	Validate structures according to the Quality Checkers section in the Structure Checkers settings.
StereoCommentsValidator	If the Calculate Stereo Comments Registration option is on, in this step the provided and calculated stereo comments are compared or if not provided, the calculated comments (Stereochemistry and Geometric isomerism) will be stored.
WarningCheckerValidator	Validates structures according to the Quality Warnings section in the Structure Checkers settings.
ParentFieldValidator	Parent-level additional data field validations according to the Administration/Forms&Fields field settings.
VersionFieldValidator	Version-level additional data field validations according to the Administration/Forms&Fields field settings.
PreparationFieldValidator	Lot-level additional data field validations according to the Administration/Forms&Fields field settings.
EmptyStructureValidator	It prevents registration when the submission does not contain a structure or CST.
AmendmentIdTypeValidator	Check if the amendment workflow type matches the submitted identifier level. E.g. AmendVersion is only possible if the submitted identifier is the CN ID type.
IdExistsValidator	It validates that the submitted identifier is not in use by another compound.
RejectParentStructureTypeChangeValidator	This validator prevents the following structure-type transitions: Isomer -> AMFP, Single -> Polymer, Single -> AMF, but only when the single compound has the same parent identifier as one of the AMF's component.
StructureChangeForAmendmentValidator	Verifies that the amendment source and target structure are different.
CollectionFieldValidator	Verifies the collection form to correspond to the table form. If the numbering order is incorrect or a field is missing the registration is prevented.

Post identification steps during registration

Since version 24.3.0 there a post identification extension capability is available in Compound Registration for registration customizations.


Post identification steps