Updates to registration of specimen handled by external lab

[Nicklas Nordborg]

The registration of specimen handled by external lab has been implemented in ticket #1349, #1347 and #1295. There is still a problem with the ordering. The current implementation requires that JSON files are imported first before the pathology referral form can be registered. The first version that used FutureSpecimen required the opposite order.

To provide more flexibility the registration should be re-designed to be independent of the order. The FutureSpecimen solution was a bit complex so we need something simpler. The suggestion is:

1. The pathology referral form should be used to register NoSpecimen items with a special option that data is expected to come in later. A special value should be set on the ReasonIfNoSpecimen annotation. In this "mode" it should also be possible to register more information that is normally not available when registering a NoSpecimen (RNA later date+time, Other path. note, etc.).

2. When a JSON-file with data arrives it can be matched against an existing NoSpecimen item. Values that are missing in the JSON file can be taken from the NoSpecimen item. If there are values in both places it should be verified that they are equal. The NoSpecimen item is converted to a Specimen item.

Some changes are required in other parts:

• NoSpecimen items that are waiting for data should not be included in data releases. This is because it is not possible to change the type of an item on the relax server.

• The case summary should probably have some indication that data is expected to come in later.

• More...?

[Nicklas Nordborg]

In 6572:

References #1360: Updates to registration of specimen handled by external lab

Added a validator implementation that can use values from an existing NoSpecimen item if they are missing in the JSON file.

[Nicklas Nordborg]

In 6573:

References #1360: Updates to registration of specimen handled by external lab

The importer now searches for an existing NoSpecimen and converts that to a Specimen item. Laterality, PAD, Sampling date and RNA later date are used from the NoSpecimen item if they are missing from the JSON file.

[Nicklas Nordborg]

In 6574:

References #1360: Updates to registration of specimen handled by external lab

Changes in the "Pathology referral form" wizard that adds an option to mark a NoSpecimen item as "Specimen exists at external lab". When this option is enabled the registration form also allows an "Operator" and "LiasonComment" to be entered as well as full date and time for sampling date and RNA later date.

[Nicklas Nordborg]

In 6575:

References #1360: Updates to registration of specimen handled by external lab

Fixed issues with automatically going to second step when a patient was already registred.

[Nicklas Nordborg]

In 6576:

References #1360: Updates to registration of specimen handled by external lab

The importer now checks that NoSpecimen items have the ExternalSpecimenExists annotation set to "Yes".

[Nicklas Nordborg]

In 6577:

References #1360: Updates to registration of specimen handled by external lab

Added a check for duplicate Clarity ID values.

[Nicklas Nordborg]

In 6578:

References #1360: Updates to registration of specimen handled by external lab

A NoSpecimen item can only be used by one JSON file. If there are more than one specimen tube, the second JSON should create a new item instead.

[Nicklas Nordborg]

In 6579:

References #1360: Updates to registration of specimen handled by external lab

Updated Case summary to display information about existing specimen for NoSpecimen items.

[Nicklas Nordborg]

In 6580:

References #1360: Updates to registration of specimen handled by external lab

The release exporter now ignore NoSpecimen items with ExternalSpecimenExists=Yes.

[Nicklas Nordborg]

In 6581:

References #1360: Updates to registration of specimen handled by external lab

Re-factored the code so that data can be copied from a different sample than the NoSpecimen that has been pre-registered. The intention is that if there are multiple JSON files coming in for a single NoSpecimen it should be possible to first convert the NoSpecimen and then copy from the same item for the second JSON (this is not yet implemented).

[Nicklas Nordborg]

In 6582:

References #1360: Updates to registration of specimen handled by external lab

Include all NoSpecimen items that have been annotated with ExternalSpecimenExists=Yes in the Import list with some information about sampling and registration date.

[Nicklas Nordborg]

In 6583:

References #1360: Updates to registration of specimen handled by external lab

When searching for existing items that match the SCAN-B id we now also check if there are NoSpecimen without the "ExternalSpecimenExists=Yes" flag. A warning is displayed that it might be better to set this flag and convert it to a specimen instead of creating a new specimen.

We also check if there are existing specimen items and make it possible to use them for copying data.

[Nicklas Nordborg]

In 6584:

References #1360: Updates to registration of specimen handled by external lab

Addad a check for duplicate Clarity ID in the database.