For the most reliable method of importing data, first obtain a template for the data you are importing. You can then ensure that your data conforms to expectations before using either Add > Import from File or Edit > Update from File.
For Source Types, Sample Types, and Assay Results, click the category from the main menu. You'll see a Template button for each data structure defined.
You can also find the download template button on the overview page for each Sample Type, Source Type, Assay for downloading the template for that structure:
In case you did not already obtain a template, you can also download one from within the file import interface itself:
Use the downloaded template as a basis for your import file. It will include all possible columns and will exclude unnecessary ones. You may not need to populate every column of the template when you import data.
When import by file is large enough that it will take considerable time to complete, the import will automatically be done in the background. Files larger than 100kb will be imported asynchronously. This allows users to continue working within the app while the import completes.
Import larger files as usual. You will see a banner message indicating the background import in progress, and a icon alongside that sample type until it completes:
Any user in the application will see the spinner in the header bar. To see the status of all asynchronous imports in progress, choose Background Imports from the user menu.
Click a row for a page of details about that particular import, including a continuously updating log.
When the import is complete, you will receive an in-app notification via the menu.
Excel files containing formulas will take longer to upload than files without formulas.
The performance of importing data into any structure is related to the number of columns. If your sample type or assay design has more than 30 columns, you may encounter performance issues.
You can only delete 10,000 rows at a time. To delete larger sets of sample or assay data, select batches of rows to delete.
Data column headers should not include spaces or special characters like '///' slashes. Instead of spaces or special characters, try renaming data columns to use CamelCasing or '_' underscores as word separators. Displayed column headers will parse the internal caps and underscores to show spaces in the column names.
Once you've created a sample type or assay data structure following these guidelines, you can change the Label for the field (under Name and Linking Options in the field editor)) if desired. For example, if you want to show a column with units included, you could import the data with a column name of Platelets and then set the label to show "Platelets (per uL)" to the user.
You can also use Import Aliases to map a column name that contains spaces to a sample type or assay field that does not. Remember to use "double quotes" around names that include spaces.
For example, if your assay data includes a column named "Platelets (per uL)", you would define your assay with a field named "Platelets" and include "Platelets (per uL)" (including the quotes) in the Import Aliases box of the assay design definition.
Previewing data stored as a TSV or CSV file may be faster than previewing data imported as an Excel file, particularly when file sizes are large.
Previewing Excel files that include formulas will take longer to preview than similar Excel files without formulas.
There are a number of reserved field names used within the system for every data structure that will be populated internally when data is created or modified, or are otherwise reserved and cannot be redefined by the user:
If you infer a data structure from a file, and it contains any reserved fields, they will not be shown in the inferral but will be created for you. You will see a banner informing you that this has occurred:
If you import data that contains fields unrecognized by the system for that data structure (sample type, source type, or assay design), you will see a banner warning you that the field will be ignored:
If you expected the field to be recognized, you may need to check spelling or data type to make sure the data structure and import file match.
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