Collection Protocol

Short title of collection protocol(CP).

The default value is *, meaning any CP.

Lung Cancer

Visit Site

The collection site of visit.

The default value is *, meaning any visit site.

Arkansas Hospital

Lineage

All, Primary, Derived, and Aliquot

Specimen Types

Can select multiple values from the list of types and/or class

The default value is *, meaning any specimen type.

Example 1: All Fluid

Example 2: Frozen Tissue

1

Collection Protocol

Collection Protocol

CP Short Title

specimen_cp_short

Lung Cancer

2

Participant

Participant Protocol Identifier

PPID-Unique protocol-specific participant ID

specimen_ppid

ETP-9933

3

Participant

Master patient index

Participant unique ID

specimen_mpi

RTB18388

4

Visit

Visit Name

Visit name

visit_name

ETP-9933-S-01

5

Visit

Visit Date

The format of the date is as per locale in use.

visit_date

In US locale, 03-15-2016

Default: 15-03-2016

6

Visit

Specimen Requirement Code

Specimen requirement code, which is set in the CP.

specimen_requirement_code

EDTA, SST, GTT, P1

7

Specimen

Anatomic Site

Specimen anatomic site

specimen_anatomic_site

Abdomen, NOS

8

Specimen

Specimen Class

Specimen class value

specimen_class

Fluid, Molecular, Tissue, Cell

9

Specimen

Specimen Type

Type of specimen

specimen_type

Whole Blood, Serum, Cryopreserved Cells

10

Specimen

Created On

The date the specimen was created. The format of the date is as per locale in use.

specimen_created_on

In US locale, 03-15-2016

Default: 15-03-2016

11

Specimen

Primary Specimen

Primary specimen label at any level of child specimen under it. Useful for printing derivative or aliquot labels.

specimen_primary_label

Consider below lineage of specimens:

• Primary: ETP-9933-WB1

• Derivative: ETP-9933-P1 

• Aliquot: ETP-9933-P1.1, the token outputs ETP-9933-WB1 when the aliquot is printed

12

Specimen

Label

Specimen label

specimen_label

ETP-9933-S-01-P1

13

Specimen

Barcode

Specimen barcode

specimen_barcode

127182718

14

Specimen

Lineage

Specimen lineage

specimen_lineage

New, Aliquot, Derivative

15

Specimen

Location

Specimen storage location. The format is the Container Name (Row x Column).

specimen_location

Rosy0105 (3 x 4)

Rosy0105 is a container name. 3 is the row, and 4 is the column

16

Specimen

Pathological Status

Specimen pathological status.

specimen_pathology

Malignant, Metastatic

17

Specimen

Quantity

Specimen initial quantity

specimen_quantity

2.5, 7000000

18

Specimen

Concentration

Specimen concentration

specimen_concentration

10

19

Specimen

Specimen Collection Container

Collection container of specimen

specimen_collection_container

ACD Vacutainer

1

IRB ID

eval("IRB ID",#specimen.collectionProtocol.irbIdentifier)

Evaluates the collection protocol IRB ID

2

CP Code

eval("Code",#specimen.collectionProtocol.code)

Evaluates the collection protocol code

3

CP Principal Investigator's first name

eval("PI First Name",#specimen.collectionProtocol.principalInvestigator.firstName)

Gives the first name of the Principal Investigator of the CP

4

CP Principal Investigator's last name

eval("PI Last Name",#specimen.collectionProtocol.principalInvestigator.lastName)

Gives the Last name of the Principal Investigator of the CP

5

CP custom field

custom_field("Field Name",cp,field_name)

Prints CP custom fields

1

External Subject ID

eval("External Subject Id", #specimen.registration.externalSubjectId)

Evaluates participant’s External Subject Id.

2

First Name

eval("First_Name",#specimen.registration.participant.firstName)

Evaluates participant’s First Name.

3

Last Name

eval("Last_Name",#specimen.registration.participant.lastName)

Evaluates participant’s Last Name.

4

Birth Date

eval("DOB",#specimen.registration.participant.birthDate)

Evaluates participant’s Date of Birth.

5

Participant custom field

1. eval("Participant_Code",#specimen.registration.getExtension()?.getAttrValues()?.get("height"))

2. custom_field("Height",cpr,height)

Evaluates participant custom field height.

6

Participant Initials

First letter of First, middle, and last name

eval("FN",#specimen.registration.participant.firstName?.trim()?.length() > 0 ? #specimen.registration.participant.firstName.charAt(0) : ""),eval("MN",#specimen.registration.participant.middleName?.trim()?.length() > 0 ? #specimen.registration.participant.middleName.charAt(0) : ""),eval("LN",#specimen.registration.participant.lastName?.trim()?.length() > 0 ? #specimen.registration.participant.lastName.charAt(0) : "")

Gives the first character from the first name, middle name, and last name in the output.

7

Identifier

eval("Identifier",#specimen.registration.id)

Evaluate the participant identifier

1

Visit Name

eval("Vist name",#specimen.visit.name)

Evaluates the visit name

2

Visit Date

eval("Vist date",#specimen.visit.visitDate)

Evaluates the visit date

3

Visit custom field

1. eval("custom",#specimen.visit.getExtension()?.getAttrValues()?.get("additional_diagnosis"))

2. custom_field("Additional_Diagnosis",visit,additional_diagnosis)

Prints value for visit custom field additional_diagnosis.

4

Event Code

eval("Event_Code",#specimen.visit.cpEvent?.code)

Evaluates the event code of the CP corresponding to the specimen’s visit.

5

Event Label

eval("Event_Label",#specimen.visit.cpEvent?.eventLabel)

Evaluates the collection protocol event label corresponding to the specimen’s visit. E.g., ‘Baseline,’ 'Follow-up'

6

Surgical Pathology Number

#specimen.visit.surgicalPathologyNumber

Prints Surgical Pathology number documented at Visit level

1

Label

eval(“Label”, #specimen.label)

Evaluates the specimen label

2

Identifier

eval(“Identifier”, #specimen.id)

Evaluates the specimen identifier

3

Created On

eval("Created On", #formatDate(#specimen.createdOn, "MMM, yyyy"))

Expression to extract month and year from the created on the field in the specified format

4

Container name and position

eval("Storage",#specimen.position)

Evaluates container name with position in linear or two dimensions(row & column) as per box settings

5

Anatomic Site

eval("site",#specimen.tissueSite.value)

Evaluates the anatomic site

6

Specimen type abbreviation

eval("type",#specimen.specimenType.props['abbreviation'])

Evaluates the specimen type abbreviation

7

Specimen custom field

eval("Ext.Lab.Num",#specimen.getExtension()?.getAttrValues()?.get("ST21"))

From v10.2 onwards custom_field("Additive",specimen,additive)

Evaluates visit custom field ST21

From v10.2 onwards

Prints value for specimen custom field additive.

8

SR name

eval("SR Name",#specimen.specimenRequirement?.name)

Evaluates the specimen-requirement name.

9

Available Quantity

eval("Available_Qty",#specimen.availableQuantity)

Evaluates the available quantity of the specimen

10

Quantity Unit

eval("type",#specimen.specimenClass.props['quantity_unit'])

Evaluates the quantity unit based on the specimen class.

11

Concentration Unit

eval("Conc unit",#specimen.specimenClass.props['concentration_unit'])

Evaluates the concentration unit based on the specimen class.

12

Laterality

eval("side",#specimen.tissueSide.value)

Evaluates the laterality

13

Received Date

eval("RD",#specimen.receivedEvent.time)

Evaluates the received date

14

Parent SR code

eval("Parent SR Code",#specimen.parentSpecimen.specimenRequirement?.code)

Evaluates the parent specimen requirement code.

15

Collection date of primary specimen at aliquot level

eval("CD",#formatDate(#specimen.primarySpecimen.collectionEvent.time,"MMM, yyyy"))

Evaluates collection date of primary specimen at child level

16

Custom date field (server timezone)

eval("Collection date", #formatDate(T(java.util.Date).from(T(java.time.Instant).ofEpochMilli(T(Long).parseLong(#specimen.getExtension()?.getAttrValues()?.get("collection_date")))), "MM/dd/yyyy HH:mm"))

Evaluates the custom date field 'Collection Date'

17

Custom date field (specific timezone)

eval("Collection date", T(java.time.format.DateTimeFormatter).ofPattern("MM/dd/yyyy HH:mm").withZone(T(java.time.ZoneId).of("Asia/Kolkata")).format(T(java.time.Instant).ofEpochMilli(T(Long).parseLong(#specimen.getExtension()?.getAttrValues()?.get("collection_date")))))

Evaluates the custom date field 'Collection Date'

18

Ancestor Requirement Name

eval("Ancestor SR Name",#collFns.join(#specimen.getReqNames()))

Adds the ancestor requirement name on the child specimens as comma-seperated values.

This includes primary specimens and intermediate parent.

19

Ancestor Requirement Code

eval("Ancestor SR Code",#collFns.join(#specimen.getReqCodes()))

Adds the ancestor requirement code on the child specimens as comma-seperated values.

This includes primary specimens and intermediate parent.

20

Last character(s) of Specimen Label

eval("Last Char", #specimen.label.substring(#specimen.label.length - 1))

Gives last character from specimen label in the output.

You can replace -1 with any numbers E.g. -2 and it will give last 2 characters in the output

21

container position

eval("Storage Position",#specimen.position != null ? (#specimen.position.container.positionLabelingMode.name() == "TWO_D" ? (#specimen.position.posTwo + ", " + #specimen.position.posOne) : #specimen.position.container.positionLabelingMode.name() == "LINEAR" ? #specimen.position.getPosition() : "Not Applicable") : "Not Stored")

Gives container position i n4 scenarios - not stored, dimensionless, linear and 2 D layouts.

22

Additional Label

eval("Additional_Label",#specimen.additionalLabel)

Prints the value in the field ‘Additional Label’ from v10.x onwards

25

Concatenate multiple fields

eval("Participant identifier",#specimen.registration.getExtension()?.getAttrValues()?.get("UPN") + "_" + #specimen.registration.getExtension()?.getAttrValues()?.get("CPF-ID"))

It will concatenate values of registration custom fields ‘UPN’ and ‘CPF-ID’ in single column while generating print file

26

Parent Specimen Type

eval("Parent Type",#specimen.parentSpecimen.specimenType.value)

Generates the parent specimen type

27

Collection Event User

eval("CollectedUser",#specimen.primarySpecimen.collectionEvent.user.loginName)

Evaluates collection event user's 'login name'

28

Collection Event User

eval("CollectedUser",#specimen.primarySpecimen.collectionEvent.user.emailAddress)

Evaluates collection event user's 'Email Address'

caption

Field name to be displayed for the field

object_type

Level of the field

visit for Visit, cpr for participant

field

Field to be printed. Variable name in the form in case of custom fields

prop

Property of the field to be printed

abbreviation or concept_code

is_custom_field

To define whether the field is a custom field or not

true/false

Level

Field

Syntax

Description

Specimen

Collection Collection (Abbreviation)

pv_prop("Collection Container", collectionEvent.container, abbreviation)

Prints the abbreviation 'E' for the collection container value 'EDTA Vacutainer'

Specimen

Collection Collection (Concept Code)

pv_prop("Collection Container_code", collectionEvent.container, concept_code)

Prints the concept code 'EDTA' for the collection container value 'EDTA Vacutainer'

Specimen

Collection Procedure (Abbreviation)

pv_prop("Collection Procedure", collectionEvent.procedure, abbreviation)

Prints the abbreviation 'V' for the collection procedure value 'Venipuncture'

Specimen

Collection Procedure (Concept Code)

pv_prop("Collection Procedure_code", collectionEvent.procedure, concept_code)

Prints the concept code 'VEN' for the collection procedure value 'Venipuncture'

Specimen

Received Quality (Abbreviation)

pv_prop("Received Quality",receivedEvent.quality,abbreviation)

Prints the abbreviation 'A' for the received quality value 'Acceptable'

Specimen

Received Quality (Concept Code)

pv_prop("Received Quality_code",receivedEvent.quality,concept_code)

Prints the concept code 'ACC' for the received quality value 'Acceptable'

Specimen

Custom field (Abbreviation)

pv_prop("Analysis Type", analysis_type, abbreviation, true)

Prints the abbreviation 'G' for the custom field analysis type for value 'Genomics'

Specimen

Custom field (Concept Code)

pv_prop("Analysis Type_code", analysis_type, concept_code, true)

Prints the concept code 'GEN' for the custom field analysis type for value 'Genomics'

Visit

Cohort (Abbreviation)

pv_prop("Visit Cohort", visit, cohort, abbreviation)

Prints the abbreviation 'CHS' for the visit field cohort for value 'Coronary Heart Study'

Visit

Clinical Diagnosis Abbreviation

pv_prop("CD_Abbreviation",visit.clinicalDiagnoses[0],abbreviation)

Prints the abbreviation for the clinical diagnosis values

Visit

All Clinical Diagnosis Abbreviation

eval("CD_Abbreviation",#collFns.join(#specimen.visit.clinicalDiagnoses.![props['abbreviation']]))

Prints all the abbreviation values in one field as comma separated

Visit

Cohort (Concept Code)

pv_prop("Visit Cohort_code", visit, cohort, concept_code)

Prints the concept code 'COR' for the visit field cohort for value 'Coronary Heart Study'

Visit

Custom Field (Abbreviation)

pv_prop("Geo Region", visit, geo_region, abbreviation, true)

Prints the abbreviation 'Ala' for the visit custom field Geo Region for value 'Alabama'

Visit

Custom Field (Concept Code)

pv_prop("Geo Region_code", visit, geo_region,concept_code, true)

Prints the concept code 'ALA' for the visit custom field Geo Region for value 'Alabama'

Participant

Custom Field (Abbreviation)

pv_prop("City Of Birth", cpr, city_of_birth, abbreviation, true)

Prints the abbreviation 'N' for the participant custom field City of Birth for value 'Nashik'