User guide

Viewing area

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The viewing area currently just gives a simple listing of the different objects in the database. The main feature of the viewing area is the ability to see a tree of all related objects with a sample of choice at the root. The listing of the objects is more limited than the admin area, so for browsing objects in the database it is still more user-friendly to use the admin area.

Admin area

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The admin area is where one actually inputs information into the database. Adding, editing, sorting and listing of objects is possible.

Bulk import

The Container and Sample tables have an option to bulk import multiple objects in one go with a csv, json or excel file. This is only recommended for advanced users, because you skip a lot of extra checks done that you would normally have when you fill in the forms. The importer’s error messages can be rather cryptic. That being said, here is how to do it.

Import a bunch of Samples in one go

  1. Go to the import page and download the csv template
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  1. Edit the csv template.
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The columns that link to other tables should contain the actual id. You can look them up in their corresponding tables. For instance for the sample_type you can look at the Sample types listing:

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and for collaborator in the Collaborator listing:

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The new ids for the samples don’t have to be filled in, since those will be generated by the system itself.

After the extra_columns_json you can add as many columns as you like. These will be stored in the extra_columns_json field in JSON format on import.

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3. Import the edited csv file. Make sure you saved the csv without added quotation marks around the values. Don’t mind the crossed out date part, this is a known bug in the importer.

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Bulk import a group of wells to store samples in one go

  1. Create a 384 Well Plate to connect the Wells to using the admin interface
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  1. Get the id for the new 384 Well Plate (51)
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  1. Determine the id for the container type you want to add (4)
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  1. Click on import in the Container listing
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  1. Change the given csv template. It uses the id from step 2 as the parent container and the sample type from step 3. You don’t have to specify an id for the new containers themselves because those will be automatically generated by the system. The content_type is an id that refers to the type of object that is stored, in this case 15 which represents the code for a Sample. This id might be different on your server though. You can look up the ids for other objects in the ContentTypes listing in the admin area. The object_id should contain the id of the object, in this example we used the ones from the previous step.
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  1. Import the csv file.
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Presentation

There’s also a presentation of the system available that incorporates several movies of how to use the system.

Issues

Check out the Issues section if you run into errors.