Export

Export

Text format

To export data as a text file choose Data - Export … from the menu. A window as shown below will open. You have several options to adapt the format of the export. E.g. you may use a different style for the first author, specifiy the separator for the last author etc.

The colums that should be displayed can be specified in the list Displayed columns. A click on the Transfer to grid button to transfers the data into the data grid as shown below. The sequence of the columns can be changed by dragging a column in the position of your choice. After setting the correct sequence and formatting options (e.g. Format of year - see below) click on the Transfer to text button. Then the text ready for export will be shown in the textbox below. Click on the Save to file button to store the data in the specified file.

 

RIS format (Reference Manager)

To export data in the RIS format according to the commercial database Reference Manager use the RIS-Export function.

Choose Data → Export from the menu to start the export. A form will open.

Click on the Start export button to generate the RIS tagged format and on the Save button to store the result in the specified file.

Jan 14, 2025

Subsections of Export

Export CSV

Export CSV

Notes:

  • The Export CSV function provides a direct copy of selected database table as tabulator separated text file. If you want to generate flles that give a strutured overview of descriptors or description data, you should prefer the Export … Lists or the Export Wizard (coming soon).
  • The Export CSV function requires the “Bulk Copy” tool, which is part of a local Microsoft SQL Server installation. If “Bulk Copy” is not available on your computer, you will get an error message after opening the window.

To export the tables of the database in the a tabulator, comma or semicolon separated format, choose Data → Export → Export CSV … from the menu. A window as shown below will open where you can select the tables to be exported in sections Selection criteria and in the Tables for export.

To start the export click on the Start export button. By default the data will be exported into a directory <working directory>\Export\<database_name>. Click on the button to select a different target directory before starting export.

After export the tables are marked with green backgound, if table schema and data were exported successfully. If only the data were exported, this is marked with yellow background, if nothing was exported, the background is red. A detailled export report can be viewd by a click on the export result file name.  

May 16, 2024

Export Text

Export as text or RIS

To export data as a text file choose Data → Export → Export text or RIS … from the menu. A window as shown below will open. You have several options to adapt the format of the export. E.g. you may use a different style for the first author, specifiy the separator for the last author etc.

 

Text format

The first tab Export as text provides the plain text export. The colums that should be displayed can be specified in the list Displayed columns. A click on the Transfer to grid button to transfers the data into the data grid beneath the button. The sequence of the columns can be changed by dragging a column in the position of your choice. After setting the correct sequence and formatting options (e.g. Format of year - see below) click on the Transfer to text button. Then the text ready for export will be shown in the textbox below. Click on the Save to file button to store the data in the specified file.

If you select the option Generate tab separated  list and click on the Transfer to text button, the data as shown in the data grid will be inserted in a tabulator-separated text file and column titles will be inserted (see image below). Such a file could be edited with a spreadsheet application an re-imported using the Importwizard.

 

RIS format (Reference Manager)

The second tab RIS Export provides the export of data in the RIS format according to the commercial database ReferenceManager use the RIS-Export function.

Click on the Start export button to generate the RIS tagged format and on the Save button to store the result in the specified file.

Jan 14, 2025

Export Wizard

The export wizard provides a possibility to export the data selected in the main form. The data are exported as tab separated text file. The export may include transformations of the data as well as information provided by linked modules and webservices. Choose Data - Export - Export wizard from the menu and then select one of the export targets (Event, Specimen, ...). For a short introduction see the tutorial.  

Adding tables

There are the following ways to add tables:

  • One parallel table
  • Several parallel tables according to selected data
  • Dependent table

All options will include the depending tables as defined for the default table. The option for several tables will add as many tables as there are found in the data.

If you added parallel tables, you should set the sequence of the datasets within these tables: For the columns that should be used for sorting the data, set the ordering sequence to a value > 0 and choose if the ordering sequence should be ascending or descending .

Certain columns in the database may provide information linked to another table or a module resp. webservice . Click on the button to add a linked value.

Adding and editing file columns

To add columns to the exported file, use the buttons. In the textbox at the top of the file column, you can change the header for the column. To change the position of a file column use the resp. button. To fuse a column with the previous column, click in the gray bar on the left side of the column that will change to for fused columns. To remove a file column, use the button. Pre- and postfixes for the columns can directly be entered in the corresponding fields. To apply transformations on the data click on the button.  

Filter

To filter the exported data, use the filter function. Click on the button and enter the text for the filter. Only data matching the filter string will be exported. If a filter is set, the button will have a red background to remind you of the filter. The filter may be set for any number of columns you need for the restriction of the exported data.  

Rowfilter

This filter in contrast to the filter above strictly applies to the row according to the sequence of the data. For an explanation see a short tutorial Video starten.

 

Test

To test the export choose the Test tab, set the number of lines that should be included in the test and click on the Test export button. To inspect the result in a separate window, click on the button.

SQL

If you want to inspect the SQL commands created during the test check this option. To see the generated SQL click on the SQL button after the Test export. A window containing all commands including their corresponding tables will be shown.

 

Export

To export your data to a file, choose the Export tab. If you want to store the file in different place use the button to choose the directory and edit the name of the file if necessary. Check the include a schema option if you want to save a schema together with your export. To start the export, click on the Export data   button. To open the exported file, use the button.

 

Export to SQLite

To export your data into a SQLite database, choose the Export to SQLite tab. You may change the preset name of the database in order to keep previous exports. Otherwise you overwrite previous exports with the same filename. To start the export, click on the Export data   button. To view the exported data, use the button.

 

Schema

To handle the settings of your export, choose the Schema tab. To load a predefined schema, click on the button. To reset the settings to the default, click on the button. To save the current schema click on the button. With the button you can inspect the schema in a separate window.

Mar 26, 2024

Subsections of Export Wizard

Export Wizard Transformation

The exported data may be transformed e.g. to adapt them to a format demanded by the user. Click on the button to open a window as shown below. For an introduction see a short tutorial Video starten.

Here you can enter 6 types of transformation that should be applied to your data. Cut out parts,  Translate contents from the file, RegEx apply regular expressions or Replace text and apply Calculations Σ or Filters on the data from the file. All transformations will be applied in the sequence they had been entered. Finally, if a prefix and/or a postfix are defined, these will be added after the transformation. To remove a transformation, select it and click on the button.

 

Cut

With the cut transformation you can restrict the data taken from the file to a part of the text in the file. This is done by splitters and the position after splitting. In the example below, the month of a date should be extracted from the information. To achieve this, the splitter '.' is added and then the position set to 2. You can change the direction of the sequence with the button Seq starting at the first position and starting at the last position. Click on the button Test the transformation to see the result of your transformation.

With the Start at Pos. option the given splitters will be converted into space (' ') and the whole string starting with the given position will be used (see below).

 

Translate

The translate transformation translates values from the file into values entered by the user. In the example above, the values of the month should be translated from roman into numeric notation. To do this click on the button to add a translation transformation (see below). To list all different values present in the data, click on the button. A list as shown below will be created. You may as well use the and buttons to add or remove values from the list or the button to clear the list. Then enter the translations as shown below. Use the save button to save entries and the Test the transformation button to see the result. 

To load a predefined list for the transformation use the   button. A window as shown below will open. Choose the Encoding of the data in your translation source and indicate if the First line contains column definition. Click OK to use the values from the file for the translation.

 

Regular expression

The transformation using regular expressions will transform the values according to the entered Regular expression and Replace by values. For more details please see documentations about regular expressions.

 

Replacement

The replacement transformation replaces any text in the data by a text specified by the user. In the example shown below, the text "." is replaced by "-". 

 

Calculation 

The calculation transformation Σ performs a calculation on numeric value, dependent on an optional condition. In the example below, 2 calculations were applied to convert 2-digit values into 4 digit years.

 

Filter 

The filter transformation compares the values from the data with a value entered by the user. As a result you can either Export content into file or Export fixed value. To select another column that should be compared, click on the button and choose a column from the file in the window that will open. If the column that should be compared is not the column of the transformation, the number of the column will be shown instead of the symbol. To add further filter conditions use the button. For the combination of the conditions you can choose among AND and OR. 

 

 

 

 

 

 

Mar 26, 2024

Export Wizard Tutorial

This tutorial demonstrates the export of a small sample from the database. For an introduction see a short tutorial Video starten.

Choosing the data

In the main form, select the data that should be exported (only the data displayed in the query results are exported).

Exporting the data

Choose Data → Export → Wizard → Organism ... from the menu. A window as shown below will open where the available tables for export are listed in the upper left area. To show the data columns of a table, select this table in the list.

 

Adding additional tables

In this example, we want to add as many parallel identification tables as present in the data. To do this, click on the button of the Identification table. At the end of the list (depending on your data) the additional tables are added (see below).

 

Setting the sequence for the tables

To set the sequence of the Identifications, select the first table and for the column IdentificationSequence set sorting sequence to 1 and the direction for sorting to descending . 

 

Choosing data from linked modules

Some columns provide the possibility to add data from linked tables or modules. In this example we choose the column NameURI linking to the module DiversityTaxonNames (see below).

To provide linked values, click on the button. A window as shown below will open, where you can choose among the provided services.

After the service is selected, you will be asked for the value provided by the service (see below).

Now the selected link is added underneath the column as shown below. You can add as many links as you need for your export.

For some modules there are values that refer to other modules with a name like [Link to ...] as shown in the example below.

If you select one of theses values, you will be asked to select the service or database linked to this modul (see below)

... and then to select one of the provided columns (see below)

Within the form this linked values will be marked as shown below. If several results are retrieved these will be separated with by " | ".

 

Adding columns to the file

To add columns to the exported file, click on the buttons for the columns resp. linked values. In this example select all Family values and the TaxonomicName (see below).

 

Fusing columns

The families should appear as one column and as the sources can exist only once for each identification we can fuse these columns. To do so, click on the delimiters between these columns (see below).

 

Setting the headers

By default the headers for the exported data are set according to the names of the columns in the database. To change this, edit them as shown below where TaxonomicName has been changed to Taxon (see below). For fused columns only the header in the first column will be used.

 

Testing

To test the export, click on the Test export button. The result depends on the content in your data but should look similar as shown below.

 

Export

To finally export the data, choose the Export tab. By default the data will be exported into tab separated file in a directory in the application directory (see below). You can change the directory (click on the button). You can choose the Include schema option to create a schema that you may reuse in a later export.