Csv Order File: Documentation

Prima has the ability to accept CSV files at Accession to import orders, cases, etc. While the best way to integrate remains the REST API, simple tasks can be accomplished through the CSV importer that can reduce the amount of typing at Accession substantially. The following documentation lists what columns you can put into your file (header names) and valid values (where applicable).

Title
Anatomic Site
Description
The anatomic site of tissue contained in the sample.
Expected Value(s)
string
Column Name(s)
anatomic site,anatomicsite
Title
Animal Alternate Identifier
Description
String that provides an alternate identifier for the animal. Commonly used to provide the identifier in another system (e.g. in-life system).
Expected Value(s)
string
Column Name(s)
animal alternate id,animal alternate identifier,animal alt id,alt animal id,animalalternateid,animalalternateidentifier,animalaltid,altanimalid
Title
Breed
Description
The breed of animal from which the sample originated.
Expected Value(s)
string
Column Name(s)
breed
Title
Case Alternate Identifier
Description
String that provides an alternate identifier for the case. Commonly used to provide the identifier in another system(e.g.LIS).
Expected Value(s)
string
Column Name(s)
case alternate id,case alternate identifier,case alt id,alt case id,casealternateid,casealternateidentifier,casealtid,altcaseid
Title
Case Documents
Description
A semi-colon separated list of file paths that should be attached to the case as extraneous documents.
Expected Value(s)
Column Name(s)
casedocuments,case documents
Title
Case Serial Number
Description
Serial number for the case. If the entry is preceded by a '#', then these rows will use the same Prima generated case serial (e.g. #2 groups several items into case 0035). A number will tell Prima to not generate a serial (e.g. 35 will produce case 0035).
Expected Value(s)
Column Name(s)
case serial,case serial number,case number,caseserial,caseserialnumber,casenumber
Title
Case Year
Description
Created year for the case.
Expected Value(s)
Column Name(s)
case year,case created year,year,caseyear,casecreatedyear
Title
Cassette Part
Description
The part of the surgical identifier for the cassette or block (e.g. "3" in S22-0001:A-3).
Expected Value(s)
string
Column Name(s)
cassette part
Title
Cohort
Description
String title or identifier for the study cohort.
Expected Value(s)
string
Column Name(s)
cohort,arm
Title
Collection Date
Description
Date (and time) at which the sample was collected.
Expected Value(s)
Column Name(s)
collection date,collectiondate,date collected,datecollected
Title
Courier
Description
The courier that transfered the sample.
Expected Value(s)
string
Column Name(s)
courier
Title
Date Of Birth
Description
Birth Date (and time) of case subject.
Expected Value(s)
Column Name(s)
date of birth,birth date,DOB,dateofbirth,birthdate
Title
Date Of Death
Description
Death Date (and time) of case subject.
Expected Value(s)
Column Name(s)
date of death,death date,DOD,dateofdeath,deathdate
Title
Differential Diagnosis
Description
The differential diagnosis for the case to which the sample belongs.
Expected Value(s)
string
Column Name(s)
differential diagnosis,differentialdiagnosis
Title
Drug
Description
The drug or compound that is the focus of the study.
Expected Value(s)
string
Column Name(s)
drug
Title
Fixative
Description
The name of the fixative in which the sample arrived or should be placed.
Expected Value(s)
string
Column Name(s)
fixative
Title
Gender
Description
Gender or sex of case subject.
Expected Value(s)
Unknown
Hermaphrodite
Transgender
Female
Male
Column Name(s)
gender,sex
Title
Genotype
Description
The genotype of animal from which the sample originated.
Expected Value(s)
string
Column Name(s)
genotype
Title
Is Embed Only
Description
Specifies that no slides are to be generated as part of the order.
Expected Value(s)
true,t,yes,y,1,false,f,no,n,0,,
Column Name(s)
is embed only,embed only,isembedonly,embedonly
Title
Manner of Death
Description
The actual (planned or unplanned) manner in which the case subject died.
Expected Value(s)
string
Column Name(s)
manner of death
Title
Order Notes
Description
Notes or description to add on the order/work request.
Expected Value(s)
string
Column Name(s)
order notes
Title
Order Number
Description
The identifier for the order/work request.
Expected Value(s)
string
Column Name(s)
order number,ordernumber,order,case number,casenumber,work request #,workrequest#
Title
Origin
Description
Specifies the name of the origin of the shipment. Must exist as a location in Prima.
Expected Value(s)
string
Column Name(s)
origin
Title
Pathologist First Name
Description
The given name of the reviewing Pathologist.
Expected Value(s)
string
Column Name(s)
pathologist first name,pathologistfirstname
Title
Pathologist Last Name
Description
The surname of the reviewing Pathologist.
Expected Value(s)
string
Column Name(s)
pathologist last name,pathologistlastname
Title
Pathologist Middle Name
Description
The middle name of the reviewing Pathologist.
Expected Value(s)
string
Column Name(s)
pathologist middle name,pathologist mi,pathologistmiddlename,pathologistmi
Title
Pathologist Review
Description
Specifies that a Pathologist should review the case as part of this order.
Expected Value(s)
true,t,yes,y,1,false,f,no,n,0,,
Column Name(s)
professional review,review,professionalreview
Title
Principal Investigator First Name
Description
The given name of the principal investigator on the associated study.
Expected Value(s)
string
Column Name(s)
principal investigator first name,pi first name,principalinvestigatorfirstname,pifirstname
Title
Principal Investigator Last Name
Description
The surname of the principal investigator on the associated study.
Expected Value(s)
string
Column Name(s)
principal investigator last name,pi last name,principalinvestigatorlastname,pilastname
Title
Principal Investigator Middle Name
Description
The middle name of the principal investigator on the associated study.
Expected Value(s)
string
Column Name(s)
principal investigator mi,principal investigator middle name,pi mi,pi middle name,principalinvestigatormi,principalinvestigatormiddlename,pimi,pimiddlename
Title
Priority Level
Description
String title for the priority level of the order.
Expected Value(s)
string
Column Name(s)
priority,priority level,prioritylevel
Title
Protocol
Description
Specifies the protocol. Must exist as a protocol in Prima.
Expected Value(s)
string
Column Name(s)
protocol
Title
Request Digital Images
Description
Specifies that digital images are to be generated for all slides in the order.
Expected Value(s)
true,t,yes,y,1,false,f,no,n,0,,
Column Name(s)
requestdigitalimages,request digital images,request imaging,request images,digital images,digital imaging,slide images,slide imaging,requestimaging,requestimages,digitalimages,digitalimaging,slideimages,slideimaging
Title
Request Submitted Date
Description
The date/time the the original work order request was made/placed.
Expected Value(s)
Column Name(s)
request submitted date,requestsubmitteddate
Title
Requested By First Name
Description
The given name of the doctor or P.I. who has requested the work.
Expected Value(s)
string
Column Name(s)
requested by first name,requesting first name,requestedbyfirstname,requestingfirstname
Title
Requested By Last Name
Description
The surname of the doctor or P.I. who has requested the work.
Expected Value(s)
string
Column Name(s)
requested by last name,requesting last name
Title
Requested By Middle Name
Description
The middle name of the doctor or P.I. who has requested the work.
Expected Value(s)
string
Column Name(s)
requested by mi,requested by middle name,requesting mi,requesting middle name,requestedbymi,requestedbymiddlename,requestingmi,requestingmiddlename
Title
Requisition Forms
Description
A semi-colon separated list of file paths that should be attached to the case as requisition forms.
Expected Value(s)
Column Name(s)
requisitionforms,requisition forms
Title
Researcher First Name
Description
The given name of the researcher associated with the case or study.
Expected Value(s)
string
Column Name(s)
researcher first name,researcherfirstname
Title
Researcher Last Name
Description
The surname of the researcher associated with the case or study.
Expected Value(s)
string
Column Name(s)
researcher last name,researcherlastname
Title
Researcher Middle Name
Description
The middle name of the researcher associated with the case or study.
Expected Value(s)
string
Column Name(s)
researcher middle name,researcher mi,researchermiddlename,researchermi
Title
Results Recipient First Name
Description
The given name of the person to whom the results of the case or study should be sent.
Expected Value(s)
string
Column Name(s)
results person first name,resultspersonfirstname
Title
Results Recipient Last Name
Description
The surname of the person to whom the results of the case or study should be sent.
Expected Value(s)
string
Column Name(s)
results person last name,resultspersonlastname
Title
Results Recipient Middle Name
Description
The middle name of the person to whom the results of the case or study should be sent.
Expected Value(s)
string
Column Name(s)
results person mi,results person middle name,resultspersonmi,resultspersonmiddlename
Title
Sample Alternate Identifier
Description
String that provides an alternate identifier for the submitted sample. Commonly used to provide the identifier in another system (e.g. LIS).
Expected Value(s)
string
Column Name(s)
alternate id,alternate identifier,alt id,sample alternate identifier,sample alt id,sample alternate id,alt sample id,alternateid,alternateidentifier,altid,samplealternateidentifier,samplealtid,samplealternateid,altsampleid
Title
Sample Barcode
Description
String that specifies the barcode contents of an existing label on the submitted sample.
Expected Value(s)
string
Column Name(s)
barcode,sample barcode,barcode contents
Title
Sample Type
Description
Specifies what item the lab should expect to receive and the workflow to be applied.
Expected Value(s)
Cassette
Cassette containing fresh or fixed tissue that needs to undergo processing and embedding
Cell Pellet
Spun down cell suspension from a fluid specimen that is contained in a cassette or other container
Hematology Slide
Slide from a hematology source, such as a CBC or smear, that typically needs to be stained
Frozen Slide
Slide that was cut directly from a frozen section
Cytology Slide
Slide taken directly from a fluid specimen
Surgical Slide
Slide that was cut from a paraffin block
Paraffin Block
Paraffin block for cutting slides or re-embedding
Cassette Request
Request to have empty cassettes printed and barcoded for future submission
Processed Cassette
Cassette containing tissue that has undergone processing, but has not been embedded
Dead Animal
Dead animal provided for necropsy
Fluid Specimen
Specimen that is mostly fluid and must undergo cytology workflow
Frozen Section
Frozen specimen that must undergo work at the cryostat
Biopsy Specimen
Specimen that contains fresh or fixed tissue
Unknown
Unknown sample type
Live Animal
Live animal that must be killed before being processed
Frozen Block
A block that was cut from a frozen section elsewhere, but needs to be processed and embedded
Column Name(s)
sample type,sampletype,sample
Title
Send Out Blocks
Description
Specifies whether or not blocks should be returned to results recipient after lab work is completed.
Expected Value(s)
true,t,yes,y,1,false,f,no,n,0,,
Column Name(s)
return blocks,send out blocks,return cassettes,send out cassettes,returnblocks,sendoutblocks,returncassettes,sendoutcassettes
Title
Send Out Slides
Description
Specifies whether or not slides should be returned to results recipient after lab work is completed.
Expected Value(s)
true,t,yes,y,1,false,f,no,n,0,,
Column Name(s)
return slides,send out slides,returnslides,sendoutslides
Title
Send Out Specimens
Description
Specifies whether or not specimens should be returned to results recipient after lab work is completed.
Expected Value(s)
true,t,yes,y,1,false,f,no,n,0,,
Column Name(s)
return specimens,send out specimens,returnspecimens,sendoutspecimens
Title
Shipped Date
Description
The date that the shipment that contains the sample was shipped from the sample origin.
Expected Value(s)
Column Name(s)
date shipped,dateshipped,shipped,shipment date,shipmentdate
Title
Slide Part
Description
The part of the surgical identifier for the slide (e.g. "6" in S22-0001:A-3-6).
Expected Value(s)
string
Column Name(s)
slide part
Title
Species
Description
The species of animal from which the sample originated.
Expected Value(s)
string
Column Name(s)
species
Title
Specimen Part
Description
The part of the surgical identifier for the jar (e.g. "A" in S22-0001:A).
Expected Value(s)
string
Column Name(s)
specimen part
Title
Specimen Submission State
Description
The state of the specimen being submitted to the lab.
Expected Value(s)
Live,Fresh,Fixed,Frozen,Completed,Storage,Disposal
Column Name(s)
specimen submission state
Title
Stain Requests
Description
JSON array of slide data which will request that the provided slides and their stains will be created.
Expected Value(s)
Column Name(s)
requested stains,requested stain tests,requestedstains,requestedstainstests,stains,staintests
Title
Stain Test Panels
Description
List of comma separated stain test panels (names of panels that exist in Prima). All slides from the panels will be added to the order.
Expected Value(s)
Column Name(s)
stain test panels,stain panels,staintestpanels,stainpanels,optimizations,stain optimizations,stainoptimizations
Title
Strain
Description
The strain of animal from which the sample originated.
Expected Value(s)
string
Column Name(s)
strain
Title
Study Documents
Description
A semi-colon separated list of file paths that should be attached to the study.
Expected Value(s)
Column Name(s)
studydocuments,study documents
Title
Study Id
Description
String title or identifier for the corresponding study.
Expected Value(s)
string
Column Name(s)
study number,study,studynumber
Title
Study Phase
Description
The study phase.
Expected Value(s)
string
Column Name(s)
study phase,studyphase,time point,timepoint,time point/sample type,timepoint/sampletype
Title
Subject Id
Description
String identifier for the case subject.
Expected Value(s)
string
Column Name(s)
patient id,patientid,patient identifier,patientidentifier,patient,animal id,animalid,animal identifier,animalidentifier,animal
Title
Surgical Wheel
Description
The surgical wheel for the case (e.g. the 'S' in S19-0012).
Expected Value(s)
string
Column Name(s)
wheel,surgical wheel,surgicalwheel
Title
Tissue Type
Description
The tissues or tissue type(s) contained in the sample.
Expected Value(s)
string
Column Name(s)
tissue type,tissuetype
Title
Tracking Number
Description
The tracking number for the shipment in which the sample was received.
Expected Value(s)
string
Column Name(s)
tracking number,shipment tracking number,trackingnumber,shipmenttrackingnumber