Diversity Scientific terms

Download

Upcoming version

4.2.1

• New table JsonCache containing the data related to a term as JSON. In the menu accessible via Administration → Json cache … or in the header click on the Show JsonCache button to see the json cache for the current term.

Current version

4.2 (2023-05-10)

Download

• Bugfixes in Workbench.dll
• Bugfix setting permissions
• Database documentation: Enumeration tables with specific title and generic table definition

Previous versions

4.1.21 (2023-02-22)

• Bugfix creating archive
• Bugfix linking to client software site
• Many order columns enabled
• New order columns Property, Section, Resource, Reference Ranking hierarchy included
• Docu: Bugfix retrieving column description for views

Database updates

• 01.00.15: New views View_TermProperty, View_SectionTerm, View_TermReference, View_TermResource, View_TermRankingHierarchy for query; Missing defaults for table TermDependency; Missing descriptions for tables, views, …; New function TerminologySize if missing; New column ArchiveProtocol in table Terminology including log table and trigger; Function TerminologyDataLastChanges; Missing grants for table TerminologyPropertyValue; Removing not used type - moved to table TermRepresentation;

Diversity Scientific terms

Installation

Resources

To run a module of the Diversity Workbench framework, you need access to a database and an installation of the respective client. The following instructions explain how to install the DiversityCollection client. All other modules are installed in the same way.

If you do not yet have an account for your institutional DWB platform, please contact your institution’s DWB administrator. If you wish to set up and use your own personal, institutional, domain-specific, or research-group-internal database environment, see Installation of a database for more information.

A German-language video demonstrates the installation using the DC client as an example. Please note that the initial steps in the video are outdated, as the downloads are now available via this manual, as described below. .

Download

All DiversityWorkbench modules can be downloaded free of charge. Within each module in the manual, you will find a Download menu item. There, you can download the latest version in the Current version section.

Installation of the client

The client is currently based on the .Net framework version 4.8 from Microsoft. If not already present, the software will prompt you to install it.

After downloading the client, unzip the .zip folder. The extracted setup folder contains two files: an .msi and a .bat file.

If you want to install the client on your computer, start the installation by double-clicking the .msi file.

If necessary, you can adjust the installation location in the next step.

Once the installation is complete, the software will be added to the program menu (see below) and a shortcut will be created on the desktop.

In the next chapter Database Login the login process is explained.

Run program without installer

There are several reasons why you might prefer to run DiversityCollection without installation. E.g. if you lack administrative permissions on your computer or if you want to use several different versions of DiversityCollection in parallel.

Therefore, the downloaded .zip file contains a .bat file. With this .bat file, a folder DiversityCollection_x_x_x is created on your desktop containing all relevant files to run the client DiversityCollection.

You have to unzip the downloaded .zip file to a local folder. The unzipped folder contains the .msi file and the .bat file. Within this unzipped! folder start the .bat file with a double-click. You might get a security warning, as shown in the section Windows protection warning.

The batch file unpacks the program files to a folder on your desktop named DiversityCollection_x_x_x, where "x_x_x" stands for the program version.

To start the DiversityCollection program, go to the folder and double-click on the file DiversityCollection.exe.

The login process is explained in the next chapter Database Login.

Technical notes and additional information

The software will be placed in the programs directory, as shown below.

Additionally, a folder is created in the user directory. This folder contains files and templates, for example, for label printing. It also contains hidden folders, such as Query. User input is saved there so that it can be loaded again the next time the program is started.

Windows protection warning

If you receive the following warning from Windows

please click on Weitere Informationen. A button Trotzdem ausführen will appear.

Please click on Trotzdem ausführen to install the software.

Diversity Scientific terms

Database login

To use a module from the DiversityWorkbench framework, such as “DiversityCollection”, you need access to a database. If you do not yet have an account for your institutional DWB platform, please contact your institution’s DWB administrator. If you wish to set up and use your own personal, institutional, domain-specific, or research-group-internal database environment, you will find instructions here.

Connect to a database

1. At the top left of the main window, go to Connection → Database … or click the Connect button . A dialog form “Connect to database” opens.

2. In the “Server” section, add the server name or the IP address and the port number.

3. In the “Login” section, choose an option:

   • Windows authentication: Using the Windows Login information.

     

   • SQL-Server authentication: User and password as defined in the database.

     

4. Click on the Connect to server button.

5. If the connection information is valid, you can Choose a database from the drop-down list at the bottom.

6. Choose the database you want to work with and click OK.

7. If you access a database for the first time, you will be asked to consent to the storage and processing of your personal data (see below) according to the General Data Protection Regulation. Without your consent the access is not possible.

Important The standard port number for SQL-Server is 1433 and is set as default. If the database server is configured to use a different port, you must change the port number in the port input field.

Previous connection

If you have been connected to a database in previous sessions, you can select one of these connections:

1. At the top of the “Connect to database” dialog form, click on the Previous connections button .
2. Select a connection from the drop-down list. This inserts the name or IP address and the port in the corresponding input fields in the server section.
3. To log into a database, proceed as described above starting from step 3.

Testing a connection

To test the connection, you can send a ping by clicking the button .

Switch between databases

1. At the top left, go to Connection → Database … or click on the Connect button .
2. If you are already connected to a server, you can select a database from the drop-down list Choose database at the bottom of the dialog box.

Reset and Cancel

Reset: If you are connected to a server, there is a Reset button below the “Login” section of the “Connect to database” dialogue box. Click the Reset button to change your server or login settings.

Cancel: If you do not want to change anything, click on Cancel.

Encryption

By default, the connection to the databases is encrypted. The icon next to the Connect to server button indicates an encrypted connection. By clicking on the icon, you can switch to an unencrypted connection, indicated by the icon .

Videos

• Login to a database: .

Diversity Scientific terms

Menu

Overview of the menu in DiversityScientificTerms

• Connection
  •  Database Choose one of the databases available on the server. Only those databases will be listed to which the user has access permission..png?class=inlineimg)
  •  Module connections … Edit the connections to the other modules within the DiversityWorkbench.
  •  Transfer previous settings Transfer the settings of a previous version.
  • Quit Quit the application and stop all processes started by the application.
• Data
  •   Table editors Edit data as selected in the query data directly in the data tables.
    •  Term … Edit data of the Term table.
    •  Representation … Edit data of the TermRepresentation table.
    •  Property … Edit data of the TermProperty table.
    •   Reference … Edit data of the TermReference table.
    •  Resource … Edit data of the TermResource table.
  •  Backup database … Backup of the whole database
  •  CSV (bcp) Export data of the whole database as csv files
• Administration
  •  Database Administration of the database
  •  Documentation … Documentation of the tables within the database
  •  Logins … Administration of the logins of the server their permissions in the databases
  •  Rename database Rename the current database
  •  Set published address Setting the address published for links by other modules
  •  Database tools … Creation of log tables, triggers etc. (only for dbo)
  •  Language … Enabling languages for the terms.
  •  Resources directory … Setting the directory for the resources.
  •  Terminologies … Administration of the terminologies.
• Help
  •  Manual Opens the online manual - Info Show the version and corresponding information
  •  Feedback … Opens a form for sending feedback
  •   Feedback history … Opens a window for browsing former feedback.
  •   Edit feedback … Opens a window for editing the feedbacks sent to the administrator (for admins only).
  •   Websites Websites related to DiversityScientificTerms
  • Download applications … Download DiversityScientificTerms from the website of the Diveristy Workbench project
  • Information model … Inspect the information model on the website of the Diveristy Workbench project
  •  Errorlog Inspect the errorlog of DiversityScientificTerms
• Update
  •  Update database … Update the database to the current version
  •  Update client … Download the current version of the client

Diversity Scientific terms

Query

Once you are connected to your database, you can search across all data. You have a wide range of options for this search.

Everything related to the query can be found on the left-hand side of the main window.

The upper part of the query section contains the list of all results “Query results”.

Below this you will find a section with all the buttons that are relevant for the search.

Under the query buttons you will find the “Query conditions”. You can enter all possible search criteria here.

Perform a query

Display the entire data set

To display the entire data set, start a search without specifying any criteria in the “Query conditions” section:

1. In the middle of the query section on the left side of the main window, click on the “filter” button.

2. A list of the results is displayed in the “Query results” section. The number of results is displayed above the list next to the “Query results” label.

Filter a search

Unter the query buttons, at the bottom of the query section, you will find the “Query conditions”.

1. Enter the filter criteria for your search. E.g. you can select a project from the dropdown list.
2. You can combine as many criteria as you want to limit your results.
3. Start the query by clicking on the filter button .
4. A list of the results is displayed in the “Query results” section. The number of results is displayed above the list next to the “Query results” label. If no result matches the query, the list is empty and the label “No match” is displayed.

Edit and customize query conditions

You can choose which query conditions are displayed in the main window. You can change this at any time.

1. At the top left above the query results list, click on the “checkbox” button .

2. Select any query conditions you want to use for your searches by selecting the respective checkboxes in the treeview.

Customize the interface

Hide/show the entire query section

In the main window go to the menu item Query → Show Query.

Hide the “Query conditions” section

On the left side of the “query buttons” in the middle of the query section, click on the “arrow” button .

Switch vertical/horizontal arrangement

You can change the arrangement of the query elements from vertical to horizontal and vice versa. To do this, click on the button below the main menu bar:

Edit the result list

Add results to the existing list

You can add new results with different query conditions to your current result list.

1. Enter the new filter criteria for your additional search.
2. Start and add these query results to the existing result list by clicking on the button .
3. The new results are appended to the existing list.

Remove result items from the list

You can remove entries from your current result list.

1. Select the entries you want to delete.
2. Click on the button .

Important This will not delete the data from the database. It only affects the current display in the results list.

Many result columns

The option to provide a result list with many columns is described in chapter Many result columns.

Query conditions

Remember the last query

By default the values you entered for the query will be remembered. Your query criteria will be pre-filled when the program starts. To change this behaviour, click on the button .

Query annotation

The query for annotations deviates from the standard query (see below). Additionally, you may specify a type of the annotation (Annotation , Problem , Reference ) and the linked table (see Annotation).

Duplicates

Certain query condition fields provide the option to add up to 3 duplicates of themselves. For adding a ‘duplicate’ search criteria, click on the green “Plus” button . Remove a ‘duplicate’ search condition with a click on the red “Minus” button . The restrictions can be combined with AND + and OR |. To change between the modes click on the + resp. | icon.

Query modules

In the “Query conditions” section, some values might be linked to other modules. E.g. within the “Identification” group the fields “Taxa” and “Terms” are linked to the “DiversityTaxonNames” and “DiversityScientificTerms” modules. You can also add “linked” values to your query condition.

1. Select the operator that determines how the entries are integrated into the search. See an explanation of all available operators in the table below.
2. To connect to the linked module, click on the “Ammonite” button at the right of the respective query field.

2. A query window for the linked module will open.
3. Search for values within the linked module and click ok.
4. If you want to see a list of the selected items, click on the magnifying glass button .

Info: There is also a detailed available, which explains all possible operators and how to use them.

Operator	Meaning	Example
∈	Search for entries with a list	Rosa | Rosa caninia \
∉	Search for entries not within a list	Rosa | Rosa caninia | ...
+H	search for entry including lower hierarchy	Picea | Picea abies | ...
+S	search for entry including synonyms	Picea abies | Pinus abies | ...
+HS	search for entry including lower hierarchy and synonyms	Picea | Picea abies | Pinus abies | ...
	Change filter mode between link and text	http://tnt.diversityworkbench.de/TaxonNames_Plants/4269 <> Picea abies L.

Query any fields

The query for any fields will search in several fields, e.g. withholding reasons in specimen, images etc. There are two versions: The first version (e.g. Notes) will search in all tables but not in collection event tables while the second version (e.g. Any notes) will search in any table (see image below).

Videos

• Introduction how to use the query conditions:
• How to use special query conditions:
• Tutorial on how to query modules:
• Tutorial on how to save a query: .

Wildcards in SQL

There are 4 different possibilities for wildcards in SQL:

Many colunns

The option to include several columns in the result list is only available for optimized queries . To display several columns in the result list, click on the button next to the order by column (see below). A window will open where you can select the next column for the sorting. Underneath the order by column the second column for the sorting will be added. To remove this sorting column you can click on the    button. By default the width for the columns is set to 10. You can change this according to content. To set the width to the maximal length of the current content, click on the button. To change the sorting of the added order column click on the button. The colums are separated via " | " as shown in the image below.

For an introduction see the videos:

• Mehrspaltige Suche:
• Sortierung:

Diversity Scientific terms

Editing the data

The main form of DiversityScientificTerms contains two main areas. On the left you find the query and the results of this query. On the right part the details of a dataset selected in the result list is shown. The upper part of the data area shows the position of the current term within the hierarchy. In the lower part you find the fields for the details of a term. At the base of the window the properties, references and resources of a term are listed. 

For every term one representation can be set the preferred one, indicated by the icon. To make a representation the preferred representation, simply click on this icon.

Display settings for charts etc.

For display in an interface used from other modules like DiversityCollection, e.g. via a chart, a term may have a display order, a color for the background and an image.

The display order will be applied within the terms of the same hierarchy level and works top down, so the term with the lowest display order will be presented at the top of the list.

To set the display color, click on the set color button. A window will open where you can either select an available color or define a new one. The color will e.g. be used as background in a chart. If depending terms should use a color of the same hue, click on the button to activate the inheritance for the color. The button will change to . See chapter chart for details.

To set the display image for a term, click on the button. A window will open where you can search for the image that should be presented. In a chart, the size of the image will be scaled down to a maximal width of 100. To remove an image, use the button next to the image.

After editing the data, click on the button to save your data. To see the description of the fields, just move the mouse into it. A small window will appear, showing the description. To see the description of all fields turn to the description of thedatabase.

Copy data

To create a new term click on the button above the query list. A form as shown below will open where you can enter some basic informations for the new term.

To create a copy of a term, choose an entry in the query list and click on the button besides the hierarchy. A form as shown below will open providing you with the possibility to create a synonym, an inferior dataset or a copy on the same level in the hierarchy as the original dataset.

To create a synonym of a term, choose an entry in the query list and click on the button besides the hierarchy. This will create a synonym to the original dataset.

To make a term a synonym to another term, choose the term in the hierarchy and click on the button besides the hierarchy. This will open a window, where you can select the term to which the current term should become a synonym to.

To delete a dataset, select it an click on the button.

Diversity Scientific terms

Import Export

The import wizard reachable in the menu Data -> Import can be used to import data into DiversityScientifcTerms. Currenlty there is no export wizard, but the data tables from DiversityScientificTerms can be exported using the Table editors, accessible via the menu -> Data -> Table Editors.

Diversity Scientific terms

Internals

For users that need more detailed information about the software including database design etc.