Import and Export

Use Import and Export to connect Labii with external data.

If you have data created before using Labii, or if you want to migrate data from another platform to Labii ELN & LIMS, you can use Labii’s import function.

Import

External data can be imported into Labii. Labii supports *.tsv, *.xlsx files. Labii does not have any request on the number of columns. You will have options to match the headers with fields in Labii. Please use the first row as headers.

To import,

  1. Click Tables on the navbar

  2. Select a table from the menu list of options.

  3. Click the Menu button on the top bar and click Import.

  4. Choose which project to import from the drop-down list.

  5. Upload your *.tsv or *.xlsx file and click next.

  6. Choose the columns to match with each header for your records.

  7. Click Submit.

Mapping fields with columns

The title of the model shows the number of records to import. At this step, you can map all fields in your file with the defined columns in Labii.

  • Each field of form represents a column in your *.tsv or *.xlsx file.

  • The dropdown options are the table fields in Labii.

  • The value of the first row is displayed as the field description.

On default, Labii will create new records for all imported records. If you want to update an existing record, please include a "UID" column. If a unique ID is provided, the import function will update for that record.

Each field can only be matched for once, except for the metadata. If metadata is selected, the title will be treat as a metadata label and value will be treated as metadata value.

Prepare Import Table

Although Labii provides flexibilities in the number of columns. Certain data types have to be prepared in a proper way to import correctly.

We recommend you to prepare the data in an excel sheet or google sheets and then save the data as *.tsv or *.xlsx.

Here are some important notes to pay attention to:

  • First Row as Title - Always include the title at the first row

  • Use # at the beginning of a row to ignore. The whole row with # at the beginning will be excluded from importing.

  • The number of columns does not matter. You can ignore a column via not selecting a matched column.

  • The order of the column does not matter.

  • Use the Unique ID (UID) to match and update existing records. The UIDs that do not match to records in the database will be ignored and a new UID will be assigned. UID is mostly used to update an existing record.

  • For Select Use the exact value of your choice. use , to separate multiple values for MultiSelect.

  • For ForeignKey columns, use UID or name to match. use , to separate multiple UIDs or names for ForeignKeys.

  • For Boolean columns, Use true for true and false for false.

  • For Date columns, use YYYY-MMMM-DD

Export

We received a lot of requests to create all different kinds of exports, and here is the updated version. Labii's export function enables you to:

  • Have the flexibility to export any number of records. You are able to export one particular page or all records, you also can export the specific records.

  • Create any type of file. You can export the traditional text files like *.tsv, *.csv, *.txt. You can also export *.json and *.hl7. The *.hl7 is still under development.

  • Custom the columns. You can custom which columns to be included during the export.

  • Custom the column names. You can use metadata to change the column name during the export.

  • Join with other tables. You can now export the information from other tables via the ForeignKey widget. If a biospecimen is generated from a patient, you can include patient id/age/gender etc. when you are exporting the biospecimen table.

To export, go to the list view of a table, and then click the Menu -> Export.

Notes:

  • A preview of the data is provided at the bottom of the form.

  • Use Check all to select all columns

  • The title of the joined table column will be joined with :. For example source_protocol:name

Export selected

If you want to export certain records, you can do so via

  1. Select the records you want to export

  2. Click Menu -> Export selected

Export settings information

The data under settings can also be exported. Labii support two types of export for the setting data:

  • Export Current Page: Download the current page as a *.tsv file.

  • Export All Pages: Export all records as a *.json file.