Guidelines and Tips for Batch Sample Import
This topic provides guidelines and tips to help you compile a sample list, in Microsoft Excel format, for importing into BaseSpace Clarity LIMS.
Import up 3456 samples from a single sample list file. To import more than 3456 samples, divide the samples into multiple files.
If an error is detected in the spreadsheet, the import process aborts. No sample imports until the error condition is resolved. See Troubleshooting.
Column headers
Legend
An asterisk indicates a *mandatory field.
Regular font, without an asterisk, indicates an optional field. See Optional fields for details.
Text enclosed in angle brackets indicates a placeholder custom field name to replace with a value.
Italicized text indicates a group of fields that depend on each other. All headers in the group must be either all present or all absent.
The following column headers can be used in the sample list:
*Sample/Name—Specify the name of the sample. If the system has the unique sample name option enabled and there are duplicate sample names in the spreadsheet, expect an error message. The message provides information on this error condition. No sample is imported until duplicate names are resolved.
Sample/Volume—Specify the volume of the sample.
Container/Type—Specify the name of the container type to use for this sample. When specifying a value for this column, verify it exists in the system already. For instance, you can specify 100 well MALDI plate as a value, provided this container type is configured in the system.
Container/Name—Specify the name of the container to place this sample. If the name does not match a container already in the system, a new container by this name (and of the specified type) is created.
Sample/Well Location—Specify the well location for the sample. Values for this column are formatted like the following examples: A:1, B:12, or 1:10.
The import process validates this location against the container type specified. If the location is out of range, the process rejects it. If placing a sample into an existing container, the process checks if the well location is already occupied and rejects it if occupied.
Sample/Reagent Label—Specify the reagent label name to use for this sample. Values for this column are optional. They can exist in the system or, if the reagent label is not found, a new one is created. Only one reagent label is supported per sample via batch sample import.
Custom Field/<Name of Custom Field>—Add a custom field instance to the sample. The name of the custom field must exist in the system. If the custom field name specified is not in the system, an error message displays.
You can specify a value for this custom field in the remaining cells of this column. For example, if there is a custom field by the name Clinical Source, you may have a column header Custom Field/Clinical Source and a value of hospital for the sample. See Optional fields for details.
Container/Custom Field/<Name of Custom Field>—Add a custom field instance to container. This field functions in a similar way to the sample custom field previously described, except the values must be defined on each row (per container). If not, an error message displays.
Optional fields
Take Custom Field as an example. Its optional nature in the spreadsheet is contingent on whether a particular field is defined as optional or required in Clarity LIMS.
If there is a required custom field for a sample, there must be a column in the spreadsheet for this field. A value must be specified for it, before any sample can be imported.
Custom field values are validated against their type defined in Clarity LIMS, as follows.
Date type—For example, if there is a custom field type of Date and the name is Completion Date, the best practice method is to have a column header Custom Field/Completion Date. The remaining values for the cells in the file should be formatted using one of the Excel date formats.
Numeric type with a range defined—The value is first validated as a number. Then, the number is validated against the range defined in Clarity LIMS.
If the validation fails, error messages display.
No sample is imported until the value is validated.
Custom field with values defined in a group of defaults—If a custom field is configured to have one or more values defined in a group of defaults and is only allowed to have one of these defined values, Clarity LIMS validates the value entered against the defined values.
If the value in the spreadsheet does not match one of the default values, validation fails.
If the validation fails, an error message displays. No sample is imported.
Troubleshooting
If Clarity LIMS expects certain information to be provided and this information is not included in the sample list, the samples are not imported.
Consider the following examples:
If an option or field is mandatory, the sample list must contain a column to capture that information. The sample list must use the appropriate column title.
If the samples must contain unique names, the sample list must not contain duplicate names or the names of samples already recorded in Clarity LIMS.
Containers types referenced in the sample list must already be defined in Clarity LIMS. For example, 96-well plate or tube.
The sample list must not place a sample into a container well that is already populated with another sample.
Any custom fields referenced in the sample list must be defined in Clarity LIMS.
Last updated