Diversity Exsiccatae

Clients for DiversityExsiccatae

There is 1 Client and 1 website available for editing resp. searching data in DiversityExsiccatae:

Index of Exsiccatae
DiversityExsiccatae.exe a generic editor.

Scope of DiversityExsiccatae within the Diversity Workbench

DiversityExsiccatae is the module for administration of exsiccatal series within the Diversity Workbench. The DiversityExsiccatae is requiered by the module DiversityCollection and on the other hand uses services provided by the modules like DiversityReferences and DiversityAgents.

The modules communicate with each other to provide their services for the other modules.

Data managment sectors of the application

Sector	Description
Evaluation	The evaluation of an exsiccatal series
Editors	The editors of an exsiccatal series
Publication span	The publication span of an exsiccatal series
References	The references related to an exsiccatal series
Examples	The examples for an exsiccatal series

Usage example

An exsiccatal series is administrated or published by several agents using a list of references and examples.

Main form of DiversityExsiccatae

To start the application double click on DiversityExsiccatae.exe.

The first time you start the application you have to configure the connection to the database (Connection, Server … ) you want to work with. The header of your form allways shows you, with which database you are working, the version of the client, the database server and your login.

To see the descriptions for the fields of the database, simply move your mouse over it. A tooltip will appear with an explanation of the field.

Where you have to choose items from lists, type the beginning of the item name in the field and then click on the drop down button . This will start a query in the database and list the result in the combobox. If contents can be linked to an other module, click on the button to start a query in this module.

Diversity exsiccatae

Download

Upcoming version

4.0.5 (2024-??-??)

Bugfix - Using new verion for database update

Current version

4.0.4 (2023-03-02)

Download

Several bugfixes
Several new order columns
Multicolumn resultlist enabled

Previous versions

4.0.3

Bugfix removing images of examples
Update for current Workbench
Optimized query enabled
Rember of Query enabled

Datebase updates

02.00.07: Adding PrivacyConsent columns in UserProxy;
02.00.08: Missing decriptions; Adding View_Coverage;

Diversity exsiccatae

Overview of the menu in DiversityExsiccatae

Connection
- Database …: Choose one of the databases available on the server. Only databases to which the user has access permission will be listed.
- Module connections…: Edit the connections to the other modules within the DiversityWorkbench.
- Transfer previous settings: Transfer the settings for IP-Address and port of the server, name of the database, login etc. of a previous version of the client to the current version.
- Current acivity on server …: List the processes on the database server.
- Quit: Quit the application and stop all processes started by the application.
Query
- Show query: Show or hide the query list.
- Predefined queries: All predefined queries will be listed.
Data
Administration
- Database: Administration of the database.
  - Descritption …: Administration of the descriptions and messages within the application.
  - Database tools …: Tools for the administration of the objects in the database - for experts only!.
  - Documentation …: Documentation of the structure of the database.
  - Logins …: Administration of the logins of the server and their permissions in the databases.
  - Queries …: Creating and editing predefined queries.
  - Rename database: Rename the current database.
  - Set published address: Setting the address published for links by other modules.
Help
- Manual: Opens the online manual.
- Feedback …: Opens a window 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).
- Info: Show the version of the program and corresponding information.
- Websites: Websites related to DiversityCollection.
ErrorLog …: Open the errorlog of the appliaction.
Update
- Update database …: Update the database to the current version.
- Update client …: Download the current version of the client.

Diversity exsiccatae

Editing the data

The main forms of all modules have a design as shown below

Main form

Status

In the status area you find

The name of the module,
The name of the database if different fron the module
The version of the software

The menu contains the options provided by the module

Commands

The commands area contains buttons for e.g. handling the data:

- To connect to a database click on the button.
- To save the changes in a dataset click on the button.
- To propagate the changes in a dataset to linked modules click on the button.
- To undo the changes a dataset click the button. This will recover the original data unless the changes had been saved or changes were done in certain tables or hierarchies were the data must be stored to display the hierarchy.
- To create a new entry in the database, click on the button below the search result listbox. This will create a entry with the specimen and show it in the list.
- To copy a specimen, choose it from the list and click on the button .
- To options a dataset click on the button .
- To change the arrangement of the query click on the button.

Create new exssicate

To create a new exssicate, click on the button above the search result listbox. You will be asked, if you are sure

Diversity exsiccatae

Editors

To add a new editor to the list click on the Button. To delete an selected editor from the list click on the Button.

To open the module DiversityAgents to get more infomation about an editor, click on the Button.

Diversity exsiccatae

Evaluation

In the evaluation part, further informations on the exsiccatal series are entered like the taxonomic coverage or the purpose of the exsiccatal series.

The geographcal regions covered in the exsiccatal series are in the corresponding area. To insert a new region, click on the Button and select a region offered by the module DiversityGazetteer. To delete a region, select it in the list and click on the button.

Diversity exsiccatae

Examples

The list of the examples is shown with their images in the list. If an example misses an image, this will be indicated with an entry in the list.

To add a new example to the list click on the Button. An window will open, where you can search for an image file. If you want to create an example without an image, just click OK without selecting any image. If you later want to add an image to you example click on the button and select an image file. A form will open, where you can search for an image.

Click OK to take the image in your example.

To delete an selected example from the list click on the Button. If you want to link to a collection specimen from the module DiversityCollection , click on the Button.To zoom a sector of the image, just drag the mouse over the image. A red square will indicate the zoomed area. To adapt the size of the image to the available space in the form click on the button. To change the orientation of the image use the appropriate buttons ( flip horizontal, flip vertical, rotate right, rotate left).

Only the file names are stored in the database. The directory for the file must be set in the menu under Adminstraton - Image folder … .

Diversity exsiccatae

Publication span

Details about the Publication span are entered in the area Publication span. The span of the numbers will be shown in the sequence overview.

Diversity exsiccatae

References

To add a new reference to the list click on the Button. To delete an selected reference from the list click on the Button.

To open the module DiversityReferences to get more infomation about an reference, click on the Button.

Diversity exsiccatae

Sequence

Details about the sequence are entered in the area “Title or author / editor changes”.

To enter a preceding exsiccatal series, click on the button. This will open a form where you can search for an exsiccatal series. If you want to remove the relation to a preceding exsiccatal series, click on the button. To change to a different exsiccatal series shown in the hierarchy, select it and click on the button.

If there happens to be a loop or a selfreference in the sequence the client will show you this by highlighting the hierarchy as shown below.

The button will be activated. You can change to the exsiccatal series that should be to topmost one in a sequence by using the button. Than click the button to remove the reference to the predecessor of this series.

Diversity exsiccatae

Table editors

For the data selected in the main window the table editors offer a direct access to the tables of the database. The menu Data - Table editors provide an editor for Exsiccata…, Editor… and Example…

A window with the content of the table will open. Columns with a gray background can not be edited here. Columns with a light gray background are linked to the contents of lookup tables that can be changed according to the contents of these tables. Columns containing an ID related to a lookuptable show the related value from the lookup table. To see the ID behind, click on the ID button.

Select Set timeout … from the menu to increase the default timeout from 5 seconds to a higher value, e.g. for greater amounts of data.

Editing

You can either edit the contents of the table directly or perform changes to any number of marked fields. To mark a whole column use the button. Once you have selected the contents to change, select one of the modes of change that appear in the upper left corner. The modes of change are:

Insert: Insert the given value at the beginning of the content
Append: Append the given value at the end of the content
Replace: Replace a string in the content with the given value
Clear: Remove the content

After selecting the change mode, enter the text in the field where necessary and click on the corresponding button to perform the changes

Filtering

To filter the content of the table, click in the column that should be used for filtering. Then choose the mode of comparision:

= : The content must be exactly like the given value
~ : The content must contain the given value
≠ : The content must be different to the given value

If you want the filtering to be case sensitive, choose the a<>A option. After all parameters are set, click on the button. To undo the filtering, click on the button. This will reset the data to the last saved version. If you want your changes to be saved, click the button before you reset the filtering. If you close the window all changes so far will be saved automatically. So if you do not want to save your changes, click on the button before closing the window.

Export

To export the data as a tab separated text file, click on the button. The file will be automatically saved in the client-folder.

Log data

To see the log data of the table, you can click on the button. The content of the log table can not be changed, but is read only.

Diversity exsiccatae

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.

Troubleshooting

If you don’t have sufficient permissions on your computer to install anything, you can use the client by following the instructions Run the program without an installer. If you receive a warning from Windows that this computer is protected, follow the instructions Windows protection warning.

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 exsiccatae

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

At the top left of the main window, go to Connection → Database … or click the Connect button . A dialog form “Connect to database” opens.
In the “Server” section, add the server name or the IP address and the port number.
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.
Click on the Connect to server button.
If the connection information is valid, you can Choose a database from the drop-down list at the bottom.
Choose the database you want to work with and click OK.
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:

At the top of the “Connect to database” dialog form, click on the Previous connections button .
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.
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

At the top left, go to Connection → Database … or click on the Connect button .
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

Diversity exsiccatae

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:

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

Enter the filter criteria for your search. E.g. you can select a project from the dropdown list.
You can combine as many criteria as you want to limit your results.
Start the query by clicking on the filter button .
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.

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

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.

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

Remove result items from the list

You can remove entries from your current result list.

Select the entries you want to delete.
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.

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

A query window for the linked module will open.
Search for values within the linked module and click ok.
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:

Operator	Description	Example	Result
%	any string consisting of no, one or many characters	Pinus %	will find anything like Pinus, Pinus sylvestris, Pinus strobus etc.
*	same effect as % (see above)
_	a single character	Pinus s_lvestris	will find Pinus sylvestris and Pinus silvestris etc.
[…]	any character out of a given range like [abcde] or [a-e]	Pinus s[iy]lvestris	will find Pinus sylvestris and Pinus silvestris
[^…]	any character not in a given range like [^abcde] or [^a-e]	Pinus s[^i]lvestris	will find Pinus sylvestris but not Pinus silvestris

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 exsiccatae

Internals

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

Diversity exsiccatae

Database

Organisation of the data

The main data are kept in the table Exsiccata. Editors are listed in the table ExsiccataEditor, examples in the table ExsiccataExample and geographicla regions in the table ExsiccataRegion.

Descriptions of tables and columns

Diversity Exsiccatae

TABLES, VIEWS, FUNCTIONS, PROCEDURES, ROLES

The following objects are not included:

Logging tables

Enumeration tables

System objects

Objects marked as obsolete

Previous versions of objects

TABLES

Table Exsiccata

An Exsiccata is a series of specimen issued in a publication like form.

Column	Data type	Description	Nullable	Relation
ExsiccataID	int	ID of the exsiccata (primary key)	NO	-
Version	int	The version of the datasetDefault value: (1)	YES	-
ExsAbbreviation	nvarchar (255)	Std. abbreviation (authors/editors, std. abbrev. of title)	NO	-
ExsTitle	nvarchar (255)	Exact title (create a new entry if title spelling changed considerably, link entries using PrecededBy/SupersededBy)	NO	-
EditingInstitution	nvarchar (255)	Issuing/Editing institution (If no editors are known, at least this must be entered)	YES	-
EditingLocationOri	nvarchar (255)	Original spelling of city/country where the exsiccata has been issued	YES	-
EditingLocationCurrent	nvarchar (255)	Current spelling of city/country where the exsiccata has been issued	YES	-
EditingLocationEnglish	nvarchar (255)	Current English spelling of city/country where the exsiccata has been issued	YES	-
PrecededBy	int	An earlier exsiccata publication appeared under different title or editors (Reference to entry in this database)	YES	Refers to table Exsiccata
ExsNumberFirst	nvarchar (20)	If known: number of the first exsiccata that was issued by the current editors under the current title	YES	-
ExsNumberLast	nvarchar (20)	If known: number of the last exssiccata that was issued by the current editors under the current title	YES	-
ExsPublYearFirst	nvarchar (20)	If known: publication year of the first exsiccata that was issued by the current editors under the current title	YES	-
ExsPublYearLast	nvarchar (80)	If known: publication year of the last exsiccata that was issued by the current editors under the current title	YES	-
Notes	nvarchar (2000)	Annotation, please add your name and a date for each annotation	YES	-
Problems	nvarchar (MAX)	Please explain here if you have a problem, this field will later be checked	YES	-
Fungi	smallint	check if exsiccata covers fungal species (default) 1 or -1= Yes it does, 0=No it does not, Null/empty = don’t know	YES	-
Algae	smallint	check if exsiccata covers Algae/Cyanophyta	YES	-
Bryophytes	smallint	check if exsiccata covers mosses/bryophytes	YES	-
Pteridophytes	smallint	check if exsiccata covers pteridophytes	YES	-
HigherPlants	smallint	check if exsiccata covers higher plants	YES	-
Zoocecidia	smallint	check if exsiccata covers galls on plants caused by animals	YES	-
Educational	smallint	Educational purpose of the exsiccata, 1 or -1= Yes, 0=No, Null/empty = don’t know	YES	-
Scientific	smallint	Scientific purpose of the exsiccata, 1 or -1= Yes, 0=No, Null/empty = don’t know	YES	-
GroupSpecific	smallint	Exsiccata is restricted to a taxonomic entity or ecologically delimited group, e.g. family or lichens on leaves, 1 or -1= Yes, 0=No, Null/empty = don’t know	YES	-
LogUpdatedWhen	datetime	The last time when this dataset was updatedDefault value: getdate()	YES	-
LogUpdatedBy	nvarchar (50)	ID of the person to update this data set lastDefault value: [dbo].UserID	YES	-
Bacteria	smallint	check if exsiccata covers pteridophytes	YES	-

trgInsExsiccata

set last changes in ProjectProxy

Table ExsiccataEditor

The editors that published an exsiccatal series.

Column	Data type	Description	Nullable	Relation
ExsiccataID	int	Reference to ExsiccataID in Exsiccata (foreign Key)	NO	Refers to table Exsiccata
Name	nvarchar (255)	Enter as last name, comma, first names, use blanks after comma and period	NO	-
EditorAgentURI	varchar (255)	The URI of the Agent, e.g. as stored within the module DiversityAgents	YES	-
Sequence	datetime	(automatically set during entry, to maintain the sequence of editors)Default value: getdate()	NO	-
LogUpdatedWhen	datetime	The last time when this dataset was updatedDefault value: getdate()	YES	-
LogUpdatedBy	nvarchar (50)	ID of the person to update this data set lastDefault value: [dbo].UserID	YES	-

Depending on:

Exsiccata

trgInsExsiccataEditor

setting the version in the main table

Table ExsiccataExamples

Examples for an exsiccatal series.

Column	Data type	Description	Nullable	Relation
ExsiccataID	int	Reference to ExsiccataID in Exsiccata (foreign Key)	NO	Refers to table Exsiccata
ExampleID	int	A number that defines the sequence in which the examples have been added.	NO	-
ImageFile	nvarchar (255)	Example: Path and file name for an image of the label of the exsiccata example issue	YES	-
ResourceURI	varchar (255)	Optionally: The URI under which the image is recoded in e.g. DiversityResources.	YES	-
PublishedName	nvarchar (255)	Example: Published taxon name of example issue	YES	-
CollectionName	nvarchar (255)	Example: Name or Acronym of collection where the example issue is available. Default is M for München	YES	-
Number	nvarchar (50)	Example: Number of example issue within the exsiccata series	YES	-
StorageLocation	nvarchar (255)	Example: Deposited under (scientific name indicating a storage location)	YES	-
CollectionSpecimen	varchar (255)	Optionally: The Display text of the example specimen as recorded in e.g. DiversityCollection	YES	-
CollectionSpecimenURI	varchar (255)	Optionally: The URI under which the example specimen is recorded in e.g. DiversityCollection	YES	-
LogUpdatedWhen	datetime	The last time when this dataset was updatedDefault value: getdate()	YES	-
LogUpdatedBy	nvarchar (50)	ID of the person to update this data set lastDefault value: [dbo].UserID	YES	-

Depending on:

Exsiccata

trgInsExsiccataExamples

setting the version in the main table

Table ExsiccataReference

The references where an exsiccatal series is listed.

Column	Data type	Description	Nullable	Relation
ExsiccataID	int	Reference to ExsiccataID in Exsiccata (foreign Key)	NO	Refers to table Exsiccata
ReferenceTitle	nvarchar (255)	The title of the publication where information on the exiccata was published. Note this is only a cached value where ReferenceURI is present	NO	-
ReferenceURI	varchar (255)	URI (e.g. LSID) of reference where information on the exsiccata was published, e.g. referring to the module DiversityReferences	YES	-
LogUpdatedWhen	datetime	The last time when this dataset was updatedDefault value: getdate()	YES	-
LogUpdatedBy	nvarchar (50)	ID of the person to update this data set lastDefault value: [dbo].UserID	YES	-

Depending on:

Exsiccata

trgInsExsiccataReference

setting the version in the main table

Table ExsiccataRegion

The geographic regions that are covered by the specimen within an exsiccatal series.

Column	Data type	Description	Nullable	Relation
ExsiccataID	int	Reference to ExsiccataID in Exsiccata (foreign Key)	NO	Refers to table Exsiccata
Region	nvarchar (50)	A region where the specimens within the exsiccata were collected.	NO	-
LogUpdatedWhen	datetime	The last time when this dataset was updatedDefault value: getdate()	YES	-
LogUpdatedBy	nvarchar (50)	ID of the person to update this data set lastDefault value: [dbo].UserID	YES	-

Depending on:

Exsiccata

trgInsExsiccataRegion

setting the version in the main table

VIEWS

View View_Coverage

Coverage and purpose columns of table Exsiccata

Column	Data type	Description	Nullable
ExsiccataID	int	ID of the exsiccata (primary key)	NO
Coverage	varchar (27)	Combined coverage columns of table Exsiccata	NO
Purpose	varchar (11)	Combined Purpose columns of table Exsiccata	NO

Depending on:

Exsiccata

View ViewBaseURL

Content of function BaseURL() for linked server

Column	Data type	Description	Nullable
BaseURL	varchar (255)	Content of function BaseURL()	YES

Depending on:

BaseURL

View ViewDiversityWorkbenchModule

Content of function DiversityWorkbenchModule() for linked server

Column	Data type	Description	Nullable
DiversityWorkbenchModule	nvarchar (50)	Content of function DiversityWorkbenchModule()	YES

Depending on:

DiversityWorkbenchModule

FUNCTIONS

Function BaseURL

Returns the basic URL for the database

DataType: varchar (255)

Function DiversityWorkbenchModule

Name of the module

DataType: nvarchar (50)

Function PrivacyConsentInfo

Provides a link to common information about the DiversityWorkbench

DataType: varchar (900)

Function StableIdentifier

The stable identifier published for a exsiccata

DataType: varchar (500)

Parameter	DataType	Description
@ExsiccataID	int	ID of the exsiccata

Depending on:

Exsiccata
StableIdentifierBase

Function StableIdentifierBase

DataType: varchar (255)

Function UserID

ID of the User as stored in table UserProxy

DataType: int

Depending on:

UserProxy

Function UserName

Name of the User as stored in table UserProxy

DataType: nvarchar (50)

Parameter	DataType	Description
@ID	varchar (10)	The ID of the user, Primary key

Depending on:

UserProxy

Function Version

Version of the database

DataType: nvarchar (8)

Function VersionClient

Minimal version of the client compatible with the database

DataType: nvarchar (11)

PROCEDURES

Procedure procCopyExsiccata

Copy a exsiccata

Parameter	DataType	Description
@ExsiccataID	int	ID of the new exsiccata
@OriginalExsiccataID	int	ID of the original exsiccata
@ExsTitle	nvarchar (255)	Title of the new exsiccata
@ExsAbbreviation	nvarchar (255)	Abbreviation of the new exsiccata

Depending on:

Exsiccata
ExsiccataEditor
ExsiccataExamples
ExsiccataReference
ExsiccataRegion

Procedure procSetVersionExsiccata

Setting the version of a dataset

Parameter	DataType	Description
@ID	int	ID of the exsiccata

Depending on:

Exsiccata
ProjectProxy
UserProxy

ROLES

Role DiversityWorkbenchEditor

Role with permission to edit the data

Permissions	INSERT	UPDATE	DELETE	EXECUTE	Type
Exsiccata	•	•			TABLE
Exsiccata_log					TABLE
ExsiccataEditor	•	•	•		TABLE
ExsiccataEditor_log					TABLE
ExsiccataExamples	•	•	•		TABLE
ExsiccataExamples_log					TABLE
ExsiccataReference	•	•	•		TABLE
ExsiccataReference_log					TABLE
ExsiccataRegion	•	•	•		TABLE
ExsiccataRegion_log					TABLE
View_Coverage					VIEW
ViewBaseURL					VIEW
ViewDiversityWorkbenchModule					VIEW
BaseURL					FUNCTION
DiversityWorkbenchModule					FUNCTION
PrivacyConsentInfo					FUNCTION
StableIdentifier					FUNCTION
StableIdentifierBase					FUNCTION
UserID					FUNCTION
UserName					FUNCTION
Version					FUNCTION
VersionClient					FUNCTION
procCopyExsiccata				•	PROCEDURE
procSetVersionExsiccata				•	PROCEDURE

Role DiversityWorkbenchUser

Role restricted to ReadOnly

Permissions	SELECT	EXECUTE	Type
Exsiccata	•		TABLE
Exsiccata_log			TABLE
ExsiccataEditor	•		TABLE
ExsiccataEditor_log			TABLE
ExsiccataExamples	•		TABLE
ExsiccataExamples_log			TABLE
ExsiccataReference	•		TABLE
ExsiccataReference_log			TABLE
ExsiccataRegion	•		TABLE
ExsiccataRegion_log			TABLE
View_Coverage	•		VIEW
ViewBaseURL	•		VIEW
ViewDiversityWorkbenchModule	•		VIEW
BaseURL		•	FUNCTION
DiversityWorkbenchModule		•	FUNCTION
PrivacyConsentInfo		•	FUNCTION
StableIdentifier		•	FUNCTION
StableIdentifierBase		•	FUNCTION
UserID		•	FUNCTION
UserName		•	FUNCTION
Version		•	FUNCTION
VersionClient		•	FUNCTION
procCopyExsiccata			PROCEDURE
procSetVersionExsiccata			PROCEDURE

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Version

For information about the version of the client application choose Help, Info…

The current version in the example above is 4.0.0 for the client and 2.1.13 for the database

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License

This manual is copyrighted work licensed under a Creative Commons License.

All material in this manual is the property of the contributing authors and fully copyrighted. By choosing this way of publication, the contributing authors have agreed to license the work under a Creative Commons License permitting reproduction, distribution, and derivative works, requiring attribution, notice, and share-alike, and prohibiting commercial use.

For information about the license of the client software choose Help, Info…

The client software is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation.

The client software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License (GPL) for more details.

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Data Access

Access to the data

To get access to the data, you have to fulfill several requirements. In DiversityCollection, you must be a member of one of the user groups. You can only access data, which is listed in the projects you have access to. For external users data may be blocked by entries in the data withholding reasons or due to a data embargo.

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To administrate the logins on the database server, their permissions and roles respectively as well as access to projects choose Administration - Database - Logins ... from the menu. A window will open as shown below.

To set the website where information about details concerning the General Data Protection Regulation are shown, click on the button.

To see the current activity on the server click on the button. A window as shown below will open listing all user related processes on the server.

To administrate the linked servers, click on the button.

To send a feedback click on the button.

Statistics

To see the activity of a login click on the button. A window will open as shown below listing all databases and tables together with the time span (From - To) and the number of data sets where any activity of the current login has been found.

To create a new login click on the button. A window will open as shown below. A login that should be able to create new logins must to be a System administrator.

Here you can enter the name of the new login, the password and the information about the user which will be stored in a DiversityAgents database. You may either create a new entry in this database or select an existing one: Click on the button to search for a name in the database (see below).

To copy a login including all permissions etc. into a new login, select the original login in the list and click on the button.

To edit the access for a login on the server select the login in the list. If a login should be disabled , uncheck the enabled checkbox (see below).

All databases on the server will be listed with the current database showing a yellow background. The databases where the login has [no access] will be listed in [gray] while the databases accessible for a login are black.

To allow the access to a database select the database from the list and choose database as shown below.

The state and date of the privacy consent according to the General Data Protection Regulation is shown in dependence of the selected database.

Use the > and < buttons to add or remove roles for the login in the database (see below).

To see the detailed permissions of a role, select it in the list of [Available] roles and click on the button. A window as shown below will open listing all objects in the database the role has permissions for (see below).

As a database owner you can edit the permissions and role memberships with the and buttons. Please keep in mind that any change of the permissions may cause serious troubles and should only be used for testing and bug fixing. The final setting of the permissions should be performed by a proper update script of the database. For every action you will get the code that is to be included in an update script (see below).

Depending on the database you can edit the list of projects accessible for a login (see below). Projects are related to the module DiversityProjects. To get additional information about a project select it in the list and click on the button.

Starting with database version 02.05.35 next to the projects with full access, a second list provides projects with [Read Only] access (see image below). Use the and buttons to move projects between Accessible and Read Only. If a project is set on [Read Only] a user can still add annotations. Starting with version 4.3.219 a project as a whole can be locked with the restriction of access to read only. For more details see chapter Project administration.

To load additional projects click on the Load projects button. A window will open as shown below. Projects already in the database will be listed in green, missing projects in red (see below). Check all projects you need in your database and click the Start download button.

To see an overview of the users within a project select one of the project in either list and click on the corresponding button . A window as shown below will open listing all users and their roles with access to the selected project.

To add or remove a role for a login, select the corresponding field and choose or from the context menu (see below).

Depending on the database you can edit the settings of a login as shown below.

If you wish to use settings already defined for another login, click on the Search template button. A window (see below) will open where you can choose among the settings defined for logins in the database.

If you want to see an overview of all permissions and project for a login, click on the button. A window as shown below will open. It lists all modules and their databases, the roles, accessible projects and read only projects for a login.

To copy the permissions and projects of the current login to another login, select the login where the settings should be copied to from the list at the base of the window and click on the button to copy the settings for all databases or the button to copy the settings of the selected database into this login.

Overview for a database

If you see an overview of all user and roles in a database, click on the button. A window a shown below will open. It lists all user, roles and projects in the database.

To remove a user, select it in the list and click on the button.

Correction of logins

If you select one of the databases, at the base a button may appear. This indicates that there are windows logins listed where the name of the login does not match the logins of the server. This may happen if e.g. a database was moved from one server to another. To correct this, click on the button. A list of deviating logins will be shown, that can be corrected automatically.

If logins with the same name but different server are found, one of them has to be deleted to make the correction possible. You will get a list where you can select those that should be removed.

Select the duplicate logins that should be removed and click OK.

To find users within the database that have no valid login, click on the button. A window as shown below will open, listing the users without a login. Select those that should be removed and click OK. This will include a removal from the collection managers.

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History

To inspect the history of a dataset click on the button. A form will open, showing all former states of the data in the tables with the current dataset at the top. The version is shown in the header of the main.

The version will be set automatically. If a dataset is changed the version will be increased if the last changes where done by a different user or the last change is more than 24 hours ago (for further details see topic Logging ).

For analysis of the succession of changes the log tables contain additional columns:

Kind of change: This column is set by the trigger inserting data into the log table
- current version: This is the current state of the data in the table
- UPDATE: This is the state of the data before an update happened
- DELETE: This is the state of the data when the data have been deleted
Date of change: The date and time of the changes. This column has the default value getdate() that means the current date an time is set when any data are inserted into the log table
Responsible: The user reponsible for the changes. This column has the default value suser_sname() that means the current user is set when any data are inserted into the log table
LogID: A unique ID of the logtable. This column is an identity that means it is set by the database when any data are inserted into the log table

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Update

Update of database and client

If either the database or the client needs to be updated, the menu will show an additional entry: Update.

Database update

To update the database, choose Update → Update database … from the menu. See chapter Database update for details.

Client update

To update the client, choose Update → Update client … and download the lastest version of the client. ee chapter Update client for details.

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Update Client

Replace the files and folders of your installation of DiversityCollection with the files you received by e-mail or downloaded from the DiversityWorkbench portal. The database will not be influenced by this replacement. After starting the new software you need to transfer the settings of the previous version. When you start the program and connect to a database, the program will check if it is compatible with the database or if the database needs an update. In any of these cases an update entry in the menu will appear. If a new version of the client is available, this menu will contain an update client … entry. Click on it to open the webpage where you may download the client as shown below.

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Update Database

Update database to current version

If you are the owner of the database (Database role = dbo) and the database needs to be updated, the menu will contain an update database … entry. Select this entry to open a window as shown below to run the provided update scripts, delivered with the client software. These scripts need to run consecutively, so e.g. to update from version 2.5.1 to 2.5.4 you either have to run the script DiversityCollectionUpdate_020501_To_020504 or the scripts DiversityCollectionUpdate_020501_To_020502, DiversityCollectionUpdate_020502_To_020503 and DiversityCollectionUpdate_020503_To_020504. The program will guide you through these steps and check for the scripts. All you need to do is click the Start update button.

Update of all databases on a server

If you are database owner and have a windows login to the database server (user=dbo), you have the option to update all DiversityCollection databases on this server by starting the application with command line parameters. Open a command line window, navigate to the program directory and start DiversityCollection with the keyword “UpdateDatebase”, the server name (or IP address) and the port number:

DiversityCollection.exe UpdateDatabase 127.0.0.1 5432

The program will connect to the server and update all available databases to the current version. If you want to exclude dedicated databases from update, create a text file named “ExcludeDb.txt” that contains the excluded database names - each name in a separate line - and locate it in the resources directory. The update will be done in the background without opening a program window. When the update processing is finished, an overview of the performed actions will be written into the protocol file “Updatereport.log” in directory resources/Updates.

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Errorlog

If any error messages show up while working with the application, you can find further details concerning the part of the application where the error occurred and the parameters involved in the file e.g. DiversityCollectionError.log in the Module DiversityCollection located in your resources directory.

To open the errorlog, choose Help - ErrorLog from the menu. A window will open showing the content of the errolog. By default the errorlog will be reset at program start. You can keep the errorlog if needed by chossing Help - Errorlog - Keep error log from the menu. A button will appear that allows you to clear the error log manually: Help - Clear ErrorLog.

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Module connections

Connections between the modules of the Diversity Workbench

The DiversityWorkbench is a set of components for building and managing biodiversity information, each of which focuses on a particular domain. DiversityAgents is referred by several modules. To scan for references from these modules on data in DiversityAgents choose Data - Scan modules - from the menu (see image below).

With these options the program will scan all sources of the selected module as listed in the connections for references to the current agent. After selecting an agent in the tree, the sources of the selected modules together with the linked data will be listed as shown below.

Select a link to see a summary of the linked data (see below).

To get further information about an item click on the button. If so far the path to the respective application has not been set, you will get a corresponding message (see below).

Click on the button to set the path to the application (see below).

By default the path to the application is C:\Program Files (x86)\DiversityWorkbench\Diversity...\Diversity.…exe as shown.

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Resources

The resources directory is set via the menu (Administration - Resources).

There are 3 possibilities for the resources directory:

Select any directory you have read/write access (User defined)
Select the "Home" directory of the user
Select the "My Documents" directory of the user

The default is set to Home. This directory will contain all files the user needs access to (see image below as an example for the module DiversityAgents).

Certain directories are hidden (Query) and are handled by the software i.e. the content should not be changed by the user. The other folders are generated by the software if missing, e.g. Export for any exports (see below).

Optional copy

By default all files the software needs from the application directory will be copied into the selected resources directory of the user. You can change this behaviour to one of the options listed below:

Copy files at program start
Add missing files at program start
Do not copy

With the next start of the program the software will act according to the selected behaviour. If you change from the Do not copy option to one of the other options the software will act at once according to the new option and e.g. copy missing directories and files into the user directory.

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Settings

The settings for the software are stored in a directory created by the application, e.g. C:\Users\[LoginName]\AppData\Local\DiversityWorkbench\[DiversityWorkbenchModule].exe_Url_0he1anjeninqrrxpdywiwnwxaqvlezn3\4.4.13.0 where [LoginName] is the name of the user and [DiversityWorkbenchModule] the name of the Diversity Workbench module e.g. DiversityCollection. This directory contains the file user.config where all settings are stored in xml format. An example for the content in the module DiversityCollection is shown below:

<?xml version="1.0" encoding="utf-8"?>
<configuration>
    <configSections>
        <sectionGroup name="userSettings">
            <section name="DiversityWorkbench.WorkbenchSettings" type="System.Configuration.ClientSettingsSection, System, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089" allowExeDefinition="MachineToLocalUser" requirePermission="false" />
        </sectionGroup>
    </configSections>
    <userSettings>
        <DiversityWorkbench.WorkbenchSettings>
            <setting name="ModuleName" serializeAs="String">
                <value>DiversityCollection</value>
            </setting>
            <setting name="GenerateTraceFile" serializeAs="String">
                <value>False</value>
            </setting>
            <setting name="DatabaseServer" serializeAs="String">
                <value>zsm.diversityworkbench.de</value>
            </setting>
            <setting name="IsTrustedConnection" serializeAs="String">
                <value>True</value>
            </setting>
            <setting name="DatabaseName" serializeAs="String">
                <value>DiversityCollection</value>
            </setting>
            <setting name="QueryMaxResults" serializeAs="String">
                <value>100</value>
            </setting>
            <setting name="DatabasePort" serializeAs="String">
                <value>5432</value>
            </setting>
            <setting name="DatabaseUser" serializeAs="String">
                <value>User</value>
            </setting>
            <setting name="ResourcesDirectory" serializeAs="String">
                <value>Home</value>
            </setting>
            <setting name="HowToCopyAppToUserDirectory" serializeAs="String">
                <value>Missing</value>
            </setting>
        </DiversityWorkbench.WorkbenchSettings>
        <DiversityCollection.Forms.FormCollectionSpecimenSettings>
            <setting name="SplitContainerData_SplitterDistance" serializeAs="String">
                <value>270</value>
            </setting>
            <setting name="QueryConditionVisibility" serializeAs="String">
                <value>10000100011000010000000000001000000001100000000000000000000000000001110000110110000000000000000000000000000000000000000000000000000000000000000000000000011100001000000000000000010000000000000000001000000000000000000000000001000000000000000000000000000000000000000000000000000000000000000</value>
            </setting>
            <setting name="ImageDisplay" serializeAs="String">
                <value>Hidden</value>
            </setting>
            <setting name="AskOnExit" serializeAs="String">
                <value>True</value>
            </setting>
        </DiversityCollection.Forms.FormCollectionSpecimenSettings>
    </userSettings>
</configuration>

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Clients for DiversityExsiccatae

Scope of DiversityExsiccatae within the Diversity Workbench

Data managment sectors of the application

Usage example

Main form of DiversityExsiccatae

Subsections of Exsiccatae

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Download

Upcoming version

4.0.5 (2024-??-??)

Current version

4.0.4 (2023-03-02)

Previous versions

4.0.3

Datebase updates

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Menu

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Editing the data

Status

Menu

Commands

Create new exssicate

Subsections of Editing

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Editors

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Evaluation

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Examples

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Publication span

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References

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Sequence

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Table editors

Editing

Filtering

Export

Log data

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Installation

Resources

Download

Installation of the client

Run program without installer

Technical notes and additional information

Windows protection warning

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Database login

Connect to a database

Previous connection

Testing a connection

Switch between databases

Reset and Cancel

Encryption

Videos

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Query

Perform a query

Display the entire data set

Filter a search

Edit and customize query conditions

Customize the interface

Edit the result list

Add results to the existing list

Remove result items from the list

Many result columns

Query conditions

Remember the last query

Query annotation

Duplicates

Query modules

Query any fields

Videos

Wildcards in SQL

Many colunns