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File Export, Import and Manager

Data can be exported from and imported into CoRA via the File Export/Import and File Manager system. Options for File Export and Import can be viewed under the left navigation bar. This capability is different from the Excel and PDF export that you will find on all data tables within CoRA such as with Search screens and Reports screens.

File Export

In order to export data from CoRA, navigate to Left Sidebar Menu -> File Export/Import-> File Export. Please note that users can only export data for the current project.

This will take you to the File Export page. This page lists the different types of files exports available in CoRA.

Export Types

The available type of exports and their descriptions are shown in the below table

Export Type Description
Base - All Base tables that hold descriptive data for CoRA
All Specimens and all its associations
DNA Specimens, DNA and all DNA associations
Measurements Specimens and all its measurements
Zones Specimens and all its zones
Associations Specimens and its pair, articualtion and refit associations
Pairs Specimens and all its pairs
Articulations Specimens and all its articulations
Refits Specimens and all its refits
Taphonomies Specimens and all its taphonomies
Pathology All Specimens and all its pathology, trauma and anomaly associations
Pathology Specimens and all its pathologies
Trauma Specimens and all its traumas
Anomaly Specimens and all its anomalies
Methods Specimens, its methods and method features
Missing Persons Missing Persons, and Genealogy
Instruments Instruments
Osteometric Sorting Bones and all its measurements

Export types options available to different role

Role Available Export Type
anthropologist Base - All, All, DNA, Measurements, Zones, Associations, Pairs, Articulations, Refits, Taphonomies,
Pathology All, Pathology, Trauma, Anomaly, Methods, Instruments, Osteometric Sorting
org administrator Base - All, All, DNA, Measurements, Zones, Associations, Pairs, Articulations, Refits, Taphonomies,
Pathology All, Pathology, Trauma, Anomaly, Methods, Missing Persons, Instruments, Osteometric Sorting
mp administrator Missing Persons

Osteometric Sorting

Osteometric sorting uses size and shape to separate bones from one another. Several statistical methods exist; some references for osteometric sorting are shown below.

References for osteometric sorting
  • Byrd, John E., and Bradley J. Adams. "Osteometric sorting of commingled human remains." Journal of forensic sciences 48.4 (2003): 717-724.
  • Lynch, Jeffrey James, John Byrd, and Carrie B. LeGarde. "The power of exclusion using automated osteometric sorting: pair‐matching." Journal of forensic sciences 63.2 (2018): 371-380.
  • Warnke‐Sommer, Julia D., et al. "Z‐transform method for pairwise osteometric pair‐matching." Journal of forensic sciences 64.1 (2019): 23-33.

CoRA produces a zip file of osteometric sorting bone measurement files for all long bones. Any osteometric sorting program used to process these files must accept the following fields.

Attribute Description
se_id The specimen or skeletal element id within CoRA
skeletal_element The composite key the specimen or skeletal element
accession_number The accession number for the specimen
provenance1 The provenance1 for the specimen
provenance2 The provenance2 for the specimen
designator The designator for the specimen
skeletal_bone The skeletal bone type
side The side: right, left, unsided
measurements Example measurement headers for the femur: Fem_01, Fem_02, Fem_03, Fem_04, Fem_05, Fem_06, Fem_07

Tip

Use the osteometric sorting export to download bone measurements formatted for input into the osteometric sorting tools.

CoRA creates a background job for the file export process. A notification will appear when the job has completed. You may need to refresh your screen to see the notification. The notification will indicate whether your export was successful or not. The exported records will appear in CoRA under File manager Section.

File Export Notification

Clicking on a file export button will not result in an immediate file(s) download. Instead, a request is made to CoRA to begin a file export job in the background. This may take several minutes depending on the number of records to be exported and the number of background jobs that are currently queued in CoRA. Once the file export job is competed a real-time notification will be seen under the notifications bell located on the top right header of the CoRA application.

To get rid of the notification, click on mark as read.

Advanced Exports Feature

The anthropologist and mp admin role can only see the export button option, which will export the entire column from that table. The org admin role had both the export and advanced button. The feature of the advanced button is that we can export specific columns from that table to export. Selecting the include timestamp check box, adds the four columns 'created_by, created_at, updated_by, updated_at, deleted_at' in the excel.

Click on 'Export Tables' to start the export for those particular tables and columns.

File Manager

All files exported and imported into CoRA can be accessed at a central location called the File Manager. The file(s) that you just exported will be located here after CoRA completes the file export job. To access the File Manager, navigate to Left Sidebar Menu -> File Export/Import-> File Manager.

The File Manager will list all the file export/import jobs that have been completed by CoRA with most recent export/import jobs listed first. To download a file export, click download. A file export does not become available on this page until the requested file export job has been completed by CoRA.

Click on the 'Download' button in green to download the particular files exported to CoRA.

File Import

In order to import a file, navigate to Left Sidebar Menu -> File Export/Import-> File Import

On the file import screen, select the import file type that you wish to upload. A template can be downloaded for the file type that you are importing. CoRA will not allow you to import a file unless the file import type is selected.

The pairs file type is shown as selected in the screenshot below. Click on browse to select a file to upload from your computer. Once selected, hit upload to upload the file to CoRA.

As with file export, CoRA creates a background job for the file import process. A notification will appear when the job has completed. You may need to refresh your screen to see the notification. The notification will indicate whether your import was successful or not. The imported records will appear in CoRA after a successful import. Click on 'view notification' to read the import information in detail.

Import Types

This section details the type of file import types available to the user. Templates can be downloaded for each import file type on the file import page. Following are the import types that are available to the user.

  1. Specimens
  2. Zones
  3. Measurements
  4. DNA sample
  5. Pairs (Results From Osteometric Sorting Tools)
  6. Articulations (Results From Osteometric Sorting Tools)
  7. DNA
  8. Isotopes
  9. Missing Persons
  10. Missing Persons-DCIPS
  11. External Systems - Specimens & DNA sample
  12. External Systems - Specimens
  13. External Systems - DNA sample

The file being imported must contain a specific word depending on the import type. The filename can contain other words and characters, but it must contain one of the following words.

Import Type Required Word
Specimens specimens
Zones zone
Measurements measurement
DNA dna
DNA Sample dna
Pairs pair
Articulations articulation
Missing Persons missing / dcips
Missing Persons - DCIPS dcips
Isotopes Isotope
External Systems - Specimen and DNA externalsystem
External Systems - Specimen externalse
External Systems - DNA externaldna

Import types options available to different role

Role Available Import Type
anthropologist Specimens,Zones,Measurements,DNA, DNA Sample, Isotopes, Pairs, Articulations,
External Systems - Specimens & DNA, External Systems - Specimens, External Systems - DNA
org administrator Specimens,Zones,Measurements,DNA,Pairs,Articulations,Missing Persons, Missing Persons-DCIPS,
External Systems - Specimens & DNA, External Systems - Specimens, External Systems - DNA
mp administrator Missing Persons, Missing Persons-DCIPS

File Upload

Click on browse to select a file to upload from your computer. Once selected, click upload to upload the file to CoRA. The upload button will be disabled until the import type selected and file is attached. Both are the mandatory input for the upload to get triggered.

Tip

CoRA validates that the type chosen and file name attached match, it will throws an error if they don't match.

File Upload - External Systems

Data can also be imported from external systems for DNA and Skeletal elements. The column names mapping from external systems to CoRA is shown below.

DNA

Data in a row is mapped to DNA if the value of the 'progname' column in the external systems is 'DNA Sample'.

External Systems DNA (CoRA)
org_id org_id
project_id project_id
afdil_case_no external_case_id
afdil_sample_no sample_number
priority priority
mito_sequence_number mito_sequence_number
mito_sequence_subgroup mito_sequence_subgroup
mito_sequence_similar mito_sequence_similar
mito_match_count mito_match_count
mito_total_count mito_total_count
mito_receive_date mito_receive_date
mito_haplogroup_id mito_haplogroup_id
analysis_type_id analysis_type_id
mito_results_confidence mito_results_confidence
mito_num_loci mito_num_loci
progname (checks conditions) sbId
austr_match_count austr_match_count
austr_total_count austr_total_count
austr_num_loci austr_num_loci
ystr_match_count ystr_match_count
ystr_total_count ystr_total_count
ystr_num_loci ystr_num_loci
ystr_haplogroup ystr_haplogroup
mito_mcc_date mito_mcc_date
priority_date priority_date
btb_request_date btb_request_date
btb_results_date btb_results_date
mito_request_date mito_request_date
austr_request_date austr_request_date
austr_receive_date austr_receive_date
austr_mcc_date austr_mcc_date
ystr_request_date ystr_request_date
ystr_receive_date ystr_receive_date
ystr_mcc_date ystr_mcc_date
mito_fasta_sequence mito_fasta_sequence
uuid uuid
mito_confirmed_regions mito_confirmed_regions
mito_base_pairs mito_base_pairs
locus locus
weight_sample_remaining weight_sample_remaining
notes notes
mito_method mito_method
external_sample_number external_sample_number
dispostion_of_evidence dispostion_of_evidence
disposition disposition
sample_condition sample_condition
mito_polymorphisms mito_polymorphisms
austr_method austr_method
austr_results_confidence austr_results_confidence
austr_sequence_number austr_sequence_number
austr_sequence_subgroup austr_sequence_subgroup
austr_sequence_similar austr_sequence_similar
austr_loci austr_loci
ystr_method ystr_method
ystr_results_confidence ystr_results_confidence
ystr_sequence_number ystr_sequence_number
ystr_sequence_subgroup ystr_sequence_subgroup
ystr_sequence_similar ystr_sequence_similar
ystr_loci ystr_loci
custom_field_1 custom_field_1
custom_field_2 custom_field_2
custom_field_3 custom_field_3
mito_haplosubgroup mito_haplosubgroup
ystr_haplosubgroup ystr_haplosubgroup
additional_testing additional_testing
resample_indicator resample_indicator
exhibitcreatedby created_by
exhibitcreatedby updated_by
Skeletal Elements

Data is mapped to skeletal elements if 'progname' column of external systems is not 'DNA Sample'.

External Systems DNA (CoRA)
casenumber accession_number
crimesceneid provenance 1
location_found provenance 2
exhibitno designator
user_id user_id
org_id org_id
project_id project_id
side side
progname (checks conditions) sb_id
inv_completeness completeness
measured measured
dna_sampled dna_sampled
ct_scanned ct_scanned
xray_scanned xray_scanned
clavicle_triage clavicle_triage
inventoried inventoried
reviewed reviewed
casenumber & exhibitno external_id
individual_number individual_number
inventoried_at inventoried_at
reviewed_at reviewed_at
consolidated_on consolidated_on
isotope_sampled isotope_sampled
count count
mass mass
bone_group_id bone_group_id
inventoried_by_id inventoried_by_id
remains_status remains_status
remains_release_date remains_release_date
identification_date identification_date
3D_scanned 3D_scanned
notes notes
uuid uuid
ct_scanned_date ct_scanned_date
xray_scanned_date xray_scanned_date
3D_scanned_date 3D_scanned_date
min_age min_age
max_age max_age
custom_field_1 custom_field_1
custom_field_2 custom_field_2
custom_field_3 custom_field_3
exhibitcreatedby created_by
exhibitcreatedby updated_by

File Import Notification

As with file export, CoRA creates a background job for the file import process. A notification will appear when the job has completed. You may need to refresh your screen to see the notification. The notification will indicate whether your import was successful or not. The imported records will appear in CoRA after a successful import. You can click the eye icon under the Action menu to see the detailed result of the import process. It explains how many records were successfully imported and if there were failures it will also provide the reason for the failure rows. Click the green bell sign in the top right corner to view and mark all notifications.

Osteometric Sorting

Pairs

A pairs file produced by an osteometric sorting program must have the following fields for upload to CoRA. Only pairs that were not excluded should be uploaded to CoRA.

Attribute Description
se_id The specimen or skeletal element id internal to CoRA.
pair_id The specimen or skeletal element id internal to CoRA for the paired element
se_skeletal_element The composite key for the specimen
se_accession_number The accession number for the specimen
se_provenance1 The provenance1 for the specimen
se_provenance2 The provenance2 for the specimen
se_designator The designator for the specimen
pair_skeletal_element The composite key for the paired specimen
pair_accession_number The accession number for the paired specimen
pair_provenance1 The provenance1 for the paired specimen
pair_provenance2 The provenance2 for the paired specimen
pair_designator The designator for the paired specimen
bonename The specimen bone type
compare_method The osteometric sorting method used
compare_method_settings Program settings
sample_size The size of the reference sample
pvalue The p-value of the statistical test
num_measurements Number of measurements used for the comparison
measurements_used The measurements that were used
measurement_means The means of the measurements in the reference population
measurement_sd The standard deviation of the measurements

Articulations

A articulations file produced by an osteometric sorting program must have the following fields for upload to CoRA. Only articulations that were not excluded should be uploaded to CoRA.

Attribute Description
se_id The specimen or skeletal element id internal to CoRA.
articulation_id The specimen or skeletal element id internal to CoRA for the articulated element
se_skeletal_element The composite key for the specimen
se_accession_number The accession number for the specimen
se_provenance1 The provenance1 for the specimen
se_provenance2 The provenance2 for the specimen
se_designator The designator for the specimen
articulation_skeletal_element The composite key for the articulated specimen
articulation_accession_number The accession number for the articulated specimen
articulation_provenance1 The provenance1 for the articulated specimen
articulation_provenance2 The provenance2 for the articulated specimen
articulation_designator The designator for the articulated specimen
bonename The specimen bone type
compare_method The osteometric sorting method used
compare_method_settings Program settings
sample_size The size of the reference sample
pvalue The p-value of the statistical test
num_measurements Number of measurements used for the comparison
measurements_used The measurements that were used
measurement_means The means of the measurements in the reference population
measurement_sd The standard deviation of the measurements

Missing Persons DCIPS Import

There is currently an issue affecting the Missing Persons DCIPS import. No more than 20,000 rows can be imported at one time, and the fields in the excel file generated by DCIPS are inaccurate.

Less than 20,000 rows at a time must be taken from the DCIPS excel file and pasted into the Missing Persons template. The import must then be run until all the fields have been imported. Currently, there are about 130,000 rows exported from DCIPS, and the import process requires seven separate files.

Another possible solution is to obtain a delta file containing only the changes from the last import. This approach has not yet been tested.


Last update: 2024-05-26
Created: 2023-12-23