Table of Contents
In some places the only way to get data into BASE is to import it from a file. This typically includes raw data, array design features, reporters and other things, which would be inconvenient to enter by hand due to the large number of data items. There is also convenience batch importers for importing other items such as biosources, samples, and extracts. The batch importers are described later in this chapter after the general import description.
Normally, a plug-in handles one type of items and may require a configuration, for example, the import plug-ins need some information about how to find headers and data lines in files. BASE ships with a number of export plug-ins as a part of the core plug-ins package, cf. Section B.3, “Core import plug-ins”. The core plug-in section links to configuration examples for some of the plugins. Go to → → to check which plug-ins are installed on your BASE server. When BASE finds a plug-in that supports import of a certain type of item an button is displayed in the toolbar on either the list view or the single-item view.
If the import button is missing from a page were you would expect to find them this usually means that:
Contact the server administrator or a similar user that has permission to administrate the plug-ins.
Starting a data import is done by a wizard-like interface. There are a number of step you have to go through:
Click on the auto detect option that lets you select a file and have BASE try to find a suitable plug-in/file format to use.button in the toolbar to start the import wizard. The first step is to select which plug-in and, if supported, which file format to use. There is also an
This is a combined list of plug-ins and their respective file format configurations. The list only includes combinations that the logged in user has permission to use. If you select an entry a short description of about the plug-in and configuration is displayed below the lists. More information about the plug-ins can be found under the menu choices→ → and → → .
|File format vs. Configuration|
A file format is the same thing as a plug-in configuration. It may be confusing that the interface sometimes use file format and sometimes use configuration, but for now, we'll have to live with it.
Proceed to the next step by clicking on thebutton.
The auto detect function lets you select a file and have BASE try to find a suitable plug-in and file format. This option is selected by default in the combined plug-in and file format list when there is at least one plug-in that supports auto detection.
|Support of auto detect|
Not all plug-ins support auto detection. The ones that do are marked in the list with ×.
Select the auto detect (all) option to search for a file format in all plug-ins that supports the feature, or select the auto detect (plugin) option to only search the file formats for a specific plug-in. Continue to the next step by clicking on the button.
You must now select a file to import from.
Displayes the selected plug-in or all if the auto-detection is used on all supporting plug-ins.
Enter the path and file name for the file you want to use. Use the Chapter 8, File management.button to browse after the file in BASE's file system. If the file does not exist in the file system you have the option to upload it. Read more about this in
The character set used in text files. If the selected file has been configured with a character set the correct option is automatically selected. In all cases, you have the option to override the default selection. Most files, typically use one of the UTF-8 or ISO-8859-1 character sets.
A list of files you have recently used for auto detection.
Click on thebutton to start the auto detection.
If the auto detection finds a exactly one plug-in and file format the next step is to configure any additional parameters needed by the plug-in. This is the same step as if you had selected the same plug-in and file format in the first step. If no plug-in can be found an error message is displayed.
|More then one compatible plug-in/file format|
If more than one matching plug-in or file format is used you will be taken back to the first step. This time the lists will only include the matching plug-ins/file formats and the auto detect option is not present.
When you have selected a plug-in and file format or used the auto detect function to find one, a form where you you can enter additional parameters for the plug-in is displayed.
The top of the window displays the names of the selected plug-in and configuration, a list with parameters to the left, an area for input fields to the right and buttons to proceed with at the bottom. Click on a parameter in the parameter list to show the form fields for entering values for the parameter to the right. Parameters with an X in front of their names already have a value. Parameters marked with a blue rectangle are required and must be given a value before it is possible to proceed.
The parameter list is very different from plug-in to plug-in. Common parameters for import plug-ins are:
The file to import data from. A value is already set if you used the auto detect function.
A section which contains different options how to handle errors when parsing the file. Normally you can select if the import should fail as a while or if the line with the error should be skipped.
Continue to the next step by clicking thebutton.
In this window should information about the job be filled in, like name and description. Where name is required and need to have valid string as a value. There are also two check boxes in this page.
Tick this check box if the job should send you a message when it is finished, otherwise untick it
If this check box is ticked, the job will be marked as removed when it is finished, on condition that it was finished successfully. This is only available for import- and export- plugins.
Clicking onwhen everything is set will end the job configuration and place the job in the job queue. A self-refreshing window appears with information about the job's status and execution time. How long time it takes before the job starts to run depends on which priority it and the other jobs in the queue have. The job does not depend on the status window to be able to run and the window can be closed without interrupting the execution.
|View job status|
A job's status can be viewed at any time by opening it from the job list page,→ .
There are in general several possibilities to import data into BASE. Bulk data such as reporter information and raw data imports are handled by plug-ins created for these tasks. For item types that are imported in more moderate quantities a suite of batch item importers available (Section B.3.1, “Core batch import plug-ins”). These importers allows the user to create new items in BASE and define item properties and associations between items using tab-separated (or equivalent) files.
The batch importers are available for most users and they may have been pre-configured but there is no requirement to configure the batch importer plug-ins. Here we assume that no plug-in configuration exists for the batch importers. Pre-configuration of the importers is really only needed for facilities that perform the same imports regularly whereas for occasional use the provided wizard is sufficient. Configuring the importers follows the route described in Section 22.4, “Plug-in configurations”.
The batch importers either creates new items or updates already existing items. In either mode the plugin can set values for
Simple properties, eg., string values, numeric values, dates, etc.
Single-item references, eg., protocol, label, software, owner, etc.
Multi-item references are references to several other items of the same type. The labeled extracts of a hybridization or pooled samples are two examples of items that refer to several other items; a hybridization may contain several labeled extracts and a sample may be a pool of several samples. In some cases a multi-item reference is bundled with simple values, eg., used quantity of a source biomaterial, the array index a labeled extract is used on, etc. Multi-item references are never removed by the importer, only added or updated. Removing an item from a multi-item reference is a manual procedure to be done using the web interface.
The batch importers do not set values for annotations since this is handled by the already existing annotation importer plug-in (Section 11.4.2, “Mass annotation import plug-in”). However, the annotation importer and batch item importers have similar behaviour and functionality to minimize the learning cost for users.
The importer only works one item type at each use and can be used in a dry-run mode where everything is performed as if a real import is taking place, but the work (transaction) is not committed to the database. The result of the test can be stored to a log file and the user can examine the output to see how an actual import would perform. Summary results such as the number of items imported and the number of failed items are reported after the import is finished, and in the case of non-recoverable failure the reason is reported.
For proper and efficient use of the batch importers users need to understand how the files to be imported should be formatted. For users who wishes to get a hands-on experience there is an OpenOffice spreadsheet with sample sheets that work with the batch importers available for download. This file can be used to import a set of data from the biosource level down to hybridizations with proper associations and properties simply by using the batch importers.
The input file must be organised into columns separated by a specified character such as a tab or comma character. The data header line contains the column headers which defines the contents of each column and defines the beginning of item data in the file. The item data block continues until the end of the file or to an optional data footer line defining the end of the data block.
When reading data for an item the plug-in must use some information for identifying items. Depending on item type there are two or three options to select the item identifier
Using the internal id. This is always unique for a specific BASE server.
Using the name. This may or may not be unique.
Some items have an externalId. This may or may not be unique.
Array slides may have a barcode which is similar to the externalId.
It is important that the identifier selected is unique in the file used, or if the file is used to update items already existing in BASE the identifier should also be unique in BASE for the user performing the update. The plug-in will check uniqueness when default parameters are used but the user may change the default behaviour.
Data for a single item may be split into multiple lines. The first line contains simple properties and single-item references, and the first multi-item reference. If there are more multi-item references they should be on the following lines with empty values in all other columns, except for the column holding the item identifier. The item identifier must have the same value on all lines associated with the item. Lines containing other data than multi-item references will be ignored or may be considered as an error depending on plug-in parameter settings. The reason for treating copied data entries as an error is to catch situations where two items is given the same item identifier by accident.
This section discuss specific parameters and features of the batch importers. The general use of the batch importers follow the description outlined in Section 19.1, “General import procedure” and the setting of column mapping parameters is assisted with the Test with file function described in Section 22.4.3, “The Test with file function”. The column headers are mapped to item properties at each use of the plug-in but, as pointed out above, they can also be predefined by saving settings as a plug-in configuration. The configuration also includes separator character and other information that is needed to parse files. The ability to save configurations depends on user credential and is by default only granted to administrators.
The plug-in parameter follows the standard BASE plug-in layout and shows help information for selected parameters. The list below comments on some of the parameters available.
Select the mode of the plug-in. The plug-in can create new items and/or update items already existing in BASE. This setting is available to allow the user to make a conscious choice of how to treat missing or already existing items. For example, if the user selects to only update items already existing the plug-in will complain if an item in the file does not exist in BASE (using default error condition treatment). This adds an extra layer of security and diagnostics for the user during import.
This parameter defines the method to use to find already existing items. The parameter can only be set to a set of item properties listed in the plug-in parameter dialog. The property selected by the user must be mapped to a column in the file. If it is not set there is obviously no way for the plug-in to identify if an item already exists .
Defines the set of items the plug-in should look in when it checks whether an item already exists. The options are the same that are available in list views and the actual set of parameters depends in user credentials.
When id is used as the Identification method, the plug-in looks for the item irrespective the setting of these parameters. Of course, the user still must have proper access to the item referenced.
Use the Test with file function described in Section 22.4.3, “The Test with file function” to set the column mapping parameters.
When creating pooled items, the pooled property is used to tell the plug-in that an item is pooled. Pooled in BASE language really means that the item parent is of the same type as the item itself. If an item is not pooled then the parent is of another type following a predefined hierarchy in BASE. In ascending order the BASE ordering of parent - child - grandchild - ... item relation is biosource - sample - extract - labeled extract.
The values accepted for pooled
empty (' '),
true. Any other string is
interpreted as the item is pooled. Sometimes all
items in a file to be imported are pooled but there
is no column that marks the pooled status. This can
be resolved by setting
the pooled mapping to a
'1' which make all items to be
treated as pooled in the import (no backslash '\'
character, compare with column header mapping
strings that contain backslash characters
After setting the parameters, select Next. Another parameter dialog will appear where error handling options can be set among with
Setting this parameter will turn on logging. The plug-in will give detailed information about how the file is parsed. This is useful for resolving file parsing issues.
Enable or disable test run of the plug-in. If enabled the plug-in will parse and simulate an import. When enabling this option you should set the Log file also. The dry run mode allows testing of large imports and updates by creating a log file that can be examined for inconsistencies before actually performing the action without a safety net.
During file parsing the plug-in will look for items referenced on each line. There are three outcomes of this item search
No item is found. Depending on parameter settings this may abort the plug-in, the plug-in may ignore the line, or a new item is created.
One item is found. This is the item that is going to be updated.
More than one item is found. Depending on parameter settings this may abort the plug-in or the plug-in may ignored the line.
The item batch importers are not designed to change or create annotations. There is another plug-in for this, see Section 11.4.2, “Mass annotation import plug-in” for an introduction to the annotation importer.
There is no need to map all columns when running the importer. When new items are created usually the only mandatory entry is Name, and when running the plug-in in update mode only the column defining the item identification property needs to be defined. This can be utilized when only one or a few properties needs to be updated; map only columns that should be changed and the plug-in will ignore the other properties and leave them as they are already stored in BASE. This also means that if one property should be deleted then that property must be mapped and the value must be empty in the file. Note, multi-item reference cannot be deleted with the batch importer, and deletion of multi-item references must be done using the web interface.
When parent and other relations are created using the plug-in the referenced items are properly linked and updated. This means that when a quantity that decreases a referenced item is used, the referenced item is updated accordingly. In consequence, if the relation is removed in a later update - maybe wrong parent was referenced - the referenced item is restored and any decrease of quantities are also reset.
A common mistake is to forget to make sure that some of the referenced items already exists in BASE, or at least are accessible for the user performing the import. Items such as protocols and labels must be added before referencing them. This is of course also true for other items but during batch import one usually follows the natural order of first importing biosources, samples, extracts, and so on. In this way the parents are always present and may be referenced without any issues.