Diversity Agents
Export
- Archive
- Export via Table editors as tab separated text file or SQLite database
- Export as CSV file via bcp
- Export via CacheDatabase in DiversityCollection and DiversityDescriptions
- Create a backup Backup
Subsections of Export
Diversity Agents
Backup
The chapter below refers to the module DiversityCollection but is valid for DiversityAgents as well
If you want to create a backup of your database, there are 2 options. You may either export the data as csv files to your local computer or you may create a backup on the server.
Export data as csv
To export your data as csv files to your local computer, choose Data
→ Export → 
CSV(bcp)
... from the menu. A window will open as shown below, where you can
select the tables that should be exported. Click on the Start Export
button to export your data. If you choose the option as shown below 2
files will be created for every table. The first file (*.csv) contains
the data while the second file (*.xml) contains the structure of the
table.
Create backup on the server
To create a backup of your database on the server, choose Data →
Backup database from the menu. This
will create a SQL-Server backup on the server where the database is
located. Ensure that there is enough space on the server.
Another option is to create a direct copy of the database files on the server. For this you have to use the functions provided by SQL-Server. However, you need administration rights for the database you want to create a backup of. Open the Enterprise Manager for SQL-Server, choose the database and detach it from the server as shown in the image below.
After detaching the database, you can save a copy of the ..._Data.MDF file to keep it as a backup.
After storing the backup you have to reattach the database.
A dialog will appear where you have to select the original database file in your directory.
Diversity Agents
Export CSV
The chapter below refers to the module DiversityCollection but is valid for DiversityAgents as well
To export the tables of the database in 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.
A prerequisite for this export is that the bcp program is installed on your computer. This has either been installed together with the installation of SQL-Server or you have to install the Microsoft Command Line Utilities for SQL Server.
To start the export click on the Start export 
button. By default the data will be exported into a directory
...\Export\<database_name> below your application directory. Click
on the 
button to select a
different target directory before starting export.
After export the tables are marked with green background, 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 detailed export report can be viewed by a click on the export result file name.
Diversity Agents
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 
.
Adding related values
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
.
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.
Subsections of Export Wizard
Diversity Agents
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
.
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.
Diversity Agents
Export Wizard Tutorial
This tutorial demonstrates the export of a small sample from the
database. For an introduction see a short tutorial
.
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.
