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PathcoreFlow User Manual

Bulk Import

[BioPharma]

Metadata fields can be imported from a CSV file in bulk. Values imported from CSV can be mapped to new or existing metadata fields and attached to any file in the Repository.

When importing metadata from CSV, the entries in the first non-empty row will be treated as headers and the subsequent non-empty rows will be treated as metadata values. The values on each row will only be applied to a single file. The import process will attempt to identify the file in the Repository that matches each CSV row using the provided File Naming Scheme. Once a file is matched to a row in the CSV, the selected values from the row will be attached to the file according to the field mapping defined.

To import metadata from a CSV file

  1. Click on the Settings Settings button from the Navigation Menu

  2. Click on the Fields tab

  3. Click on the Import metadata button

  4. Click in the blue box to activate the CSV file selection dialog or simply drag a CSV file into the blue box

  5. Define the File Naming Scheme. See File Naming Scheme for details

  6. (Optional) From the Choose a Field dropdowns, select or create a field that corresponds to each column of the CSV file (column names are shown adjacent to each dropdown). If a column is not assigned in this way, the values from that column are not imported

  7. Click on the Preview Changes button to see the results

  8. Click Commit Changes if satisfied with the summary of results. Otherwise, click on CSV Mapping to reopen that section and adjust the import settings

Once the changes have been committed, they cannot be undone.

File Naming Scheme

The file naming scheme is used to associate rows of a CSV file with records in the Repository. It takes the form of a pattern used to assemble a file name from fixed text and column data from the CSV file. The file name computed for each row is matched against those in the database. If a single match is found, the specified metadata is applied to the record. If more than one record in the Repository would match, then this is considered a failed match and the metadata is not applied to any of them.

The first row of the CSV is assumed to be the header row and the remaining rows are assumed to be metadata that are imported. Headers that are enclosed in {} within the naming scheme are considered placeholders and are processed as defined above.

Use the green + button beside a field to add that header as a placeholder in the file naming scheme template.

Example

  1. Assuming the layout of an imported CSV file is:

    StudyAnimalDose GroupStain
    2021-365Dog5H&E
    2021-365Dog6H&E

  2. And the File Naming Scheme is: Image_{Study}_{Animal}_{Dose Group}.svs

  3. The import process would match the rows in the CSV file to the following items in the Repository:

    • Image_2021-365_Dog_5.svs
    • Image_2021-365_Dog_6.svs