Importing Data

Indicia provides a general purpose importing tool which supports importing data of any type from CSV (comma separated values) files. The import tool is available for addition to any Indicia enabled Drupal site using a prebuilt form (under the Utilities form category, select the Importer form) or via the warehouse user interface using the upload functionality offered at the bottom of each data grid. It’s the same tool in both cases.

The best way to think of the import tool is to imagine the following steps:

  1. First, select some default values that will apply to every single record.

  2. Next, provide a mapping from the columns in your import CSV file to the attributes in the database.

  3. The importer will now work through the CSV file and posts each record to the same back-end process used when you enter data via the warehouse user interface. For example, if you are importing a term into a termlist then you will need to format your synonyms in the import data in exactly the same way you would if you were typing them into the user interface.

  4. Any record that fails a validation check is saved into a second errors CSV file on the server. At the end of the import, the invalid records are made available for download, so the user can correct the errors and re-import them.

Because the import is handled chunk by chunk, the only limits to the size of file you can upload are defined by the PHP upload limit settings of the server. If you need to upload larger files than this limit they will need to be split up into several smaller files.

Import Steps

For this example, we’re going to import some colour terms into a termlist as defined by the following table:









The import will be into the warehouse, though the steps are exactly the same if you import data using a client website configured with the Importer prebuilt form. Note that I’ve defined mauve as a synonym for purple (not being too technical at this point!) using the same formatting as we would use for defining term synonyms when inputting them into the warehouse’s user interface directly (as described on the data entry form itself). I’ve entered the data into a spreadsheet then saved the file as a colours.csv file. I’ve also created an empty termlist on the warehouse called Colours.

The Terms tab of the termlist’s details has an Upload CSV File button at the bottom:

The empty Colours termlist ready for uploading.

Next, I select the colours.csv file prepared earlier. Once selected, I click the Upload CSV File which takes me to the Import Settings step of the import.

The empty Colours termlist ready for uploading.

This step of the import process allows you to select default values for certain fields which will be applied to every imported record. For example in this case we are selecting to import all terms against the English language; we could include a language column in the import file with the language for each term instead, then not set a language at this step. The fields you can set a default are of course different for each type of data you might import.

The following step of the import process involves mapping columns in your import file to the available database fields. Fields available will depend on the database table you are importing into, but will include custom attributes as well as relevant associated tables. For example, we are importing into the termlists_terms table and the associated terms table. If importing occurrences data then we would also be able to map columns to fields in the samples table, occurrence_images table and any custom attributes available for these tables. The mapping step shows you a grid of the columns in your import file and the database attributes they map to. The drop down in the Maps to attribute column lets you pick from any of the available destination database fields. Note that the page shows you a list of tasks if there are any problems which prevent further progress, such as not mapping a mandatory field, or mapping the same field twice.

Mapping import columns to database fields.

Once all the columns are correctly mapped, clicking the Upload button kicks off the import process. This shows a progress bar during the import of larger files. Don’t forget that you are importing onto a web server so the import process can’t “hog” the entire machine unlike an import process running on your desktop. This means there is a limit to the optimisation that can be achieved in the code, therefore the import is not blisteringly quick. It does just chug on through the file without any intervention though.

Once you have completed the import, you will either receive a message that the import was successful, or that there were some errors. In the latter case you can download a file containing just a copy of the problem records with an additional column for the error message - so you can work through the errors then re-upload the error file to complete the import.

Remembered mappings

A significant part of the effort required to import a CSV file is the correct mapping of columns in the import file to database attributes. Version 0.9 and later of Indicia’s import code supports remembering of the mappings from a previous import so that, for example, if the user maps a “Place” import column to the Sample Location Name database attribute, future imports of the same import file template will remember the mapping so not require user input. In order for this to work when using the import from within Drupal, you need a field attached to the user account to store the remembered mappings in. So, you need to:

  1. Select Configuration on the admin toolbar, then select Account settings.

  2. Select the Manage fields tab in the top right.

  3. Drupal 7 - In the Add new field row, specify “Import Field Mappings” and make sure the field name is field_import_field_mappings. Field type should be set to Long text. Save the field and save the field settings in their default state. The Easy Login module will automatically hide this field from the user profile pages for you. In Drupal 8 - click Add field, then set the field type to Text (plain, long) and set the label to “Import Field Mappings”.

Additional tips

  1. When importing species, provide a column and map this to the Other Fields > Codes field. This can contain a list of codes to attach to the taxon, such as Bradley Fletcher numbers, GBIF numbers etc. The types of code must be first configured in the Taxon Code Types termlist. Provide the codes on separate lines, with the type followed by a | then the code itself. E.g.

    Bradley Fletcher|123
  2. Importing photos obviously can’t be achieved using a CSV file upload. However, if you are able to copy the images to the warehouse upload folder, you can then import a column with the image file name to link the image to the record.

  3. Boolean fields can be supplied using any of the values acceptable to the database.