ABCD2Mapping - Revision history

JoergHoletschek: /* Initial Testing of the Data Source */

2018-10-01T09:03:14Z

Initial Testing of the Data Source

← Older revision		Revision as of 11:03, 1 October 2018
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	Into the text box below you can enter the request XML text. Because it would be cumbersome to enter the whole BioCASe request, you can use the links below the box to load templates. For now, click on <small>ABCD2 Search</small> to fill the box with a BioCASe Search request for documents in the ABCD2 format (the one you’ve just mapped):		Into the text box below you can enter the request XML text. Because it would be cumbersome to enter the whole BioCASe request, you can use the links below the box to load templates. For now, click on <small>ABCD2 Search</small> to fill the box with a BioCASe Search request for documents in the ABCD2 format (the one you’ve just mapped):

	<syntaxhighlight>		<syntaxhighlight lang="XML">
	<?xml version='1.0' encoding='UTF-8'?>		<?xml version='1.0' encoding='UTF-8'?>
	<request xmlns='http://www.biocase.org/schemas/protocol/1.3'>		<request xmlns='http://www.biocase.org/schemas/protocol/1.3'>

JoergHoletschek: /* Adding additional ABCD Elements */

2018-10-01T08:57:22Z

Adding additional ABCD Elements

← Older revision		Revision as of 10:57, 1 October 2018
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	[[File:abcdMappingEditorSearch.png\|500px]]		[[File:abcdMappingEditorSearch.png\|500px]]

	Continue the sequence mapping new elements/testing until you’ve mapped all information you want to publish. You can have a look at the list of recommend and commonly used ABCD elements on the [[CommonABCD2Concepts\|Common ABCD2 Concepts]] and [ABCD2Concepts] pages. The full ABCD documentation can be found in the [http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki].		Continue the sequence mapping new elements/testing until you’ve mapped all information you want to publish. You can have a look at the list of recommend and commonly used ABCD elements on the [[CommonABCD2Concepts\|Common ABCD2 Concepts]] and [[ABCD2Concepts]] pages. The full ABCD documentation can be found in the [http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki].

	The following page will show you a sample response ABCD document for a web service with 77 concepts mapped. Of course your documents will look different, because you will probably use different ABCD elements, but still it’s good to get an idea: [[SampleABCDDocument]].		The following page will show you a sample response ABCD document for a web service with 77 concepts mapped. Of course your documents will look different, because you will probably use different ABCD elements, but still it’s good to get an idea: [[SampleABCDDocument]].

JoergHoletschek: /* Adding additional ABCD Elements */

2018-10-01T08:56:40Z

Adding additional ABCD Elements

← Older revision		Revision as of 10:56, 1 October 2018
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	[[File:abcdMappingEditorSearch.png\|500px]]		[[File:abcdMappingEditorSearch.png\|500px]]

	Continue the sequence mapping new elements/testing until you’ve mapped all information you want to publish. You can have a look at the list of recommend and commonly used ABCD elements on the [[CommonABCD2Concepts\|Common ABCD2 Concepts]] ~~page~~. The full ABCD documentation can be found in the [http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki].		Continue the sequence mapping new elements/testing until you’ve mapped all information you want to publish. You can have a look at the list of recommend and commonly used ABCD elements on the [[CommonABCD2Concepts\|Common ABCD2 Concepts]] and [ABCD2Concepts] pages. The full ABCD documentation can be found in the [http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki].

	The following page will show you a sample response ABCD document for a web service with 77 concepts mapped. Of course your documents will look different, because you will probably use different ABCD elements, but still it’s good to get an idea: [[SampleABCDDocument]].		The following page will show you a sample response ABCD document for a web service with 77 concepts mapped. Of course your documents will look different, because you will probably use different ABCD elements, but still it’s good to get an idea: [[SampleABCDDocument]].

JoergHoletschek: /* Access to Biological Collection Data Schema (ABCD) */

2018-10-01T08:54:37Z

Access to Biological Collection Data Schema (ABCD)

← Older revision		Revision as of 10:54, 1 October 2018
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	ABCD in its current version 2.06 is the data schema typically used in conjunction with BioCASe. It is a highly complex XML data schema with about 1,000 elements that is able to store almost every piece of information that can be found in a natural history specimen collection or an observation database. The complexity is due to the fact that it can be used for a wide range of collections/databases – for living and preserved specimens, observations and culture collections, for zoological, botanical, bacterial and viral collections, marine or terrestrial, for herbaria, botanic and zoological gardens. For each of these special types, ABCD features special sections where information specific for this type can be stored. Other sections of ABCD will be shared by all these types, for example for gathering site, identifier or metadata.		ABCD in its current version 2.06 is the data schema typically used in conjunction with BioCASe. It is a highly complex XML data schema with about 1,000 elements that is able to store almost every piece of information that can be found in a natural history specimen collection or an observation database. The complexity is due to the fact that it can be used for a wide range of collections/databases – for living and preserved specimens, observations and culture collections, for zoological, botanical, bacterial and viral collections, marine or terrestrial, for herbaria, botanic and zoological gardens. For each of these special types, ABCD features special sections where information specific for this type can be stored. Other sections of ABCD will be shared by all these types, for example for gathering site, identifier or metadata.

	The full ABCD documentation can be found in the http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki], a list of commonly used ABCD elements on the Wiki page [[CommonABCD2Concepts\|Common ABCD2 Concepts]].		The full ABCD documentation can be found in the http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki], a list of commonly used ABCD elements on the Wiki page [[CommonABCD2Concepts\|Common ABCD2 Concepts]] and a comprehensive list of example values on the page [[ABCD2Concepts]].

	== Creating an ABCD Mapping for a Data Source ==		== Creating an ABCD Mapping for a Data Source ==

JoergHoletschek: /* Adding additional ABCD Elements */

2016-09-12T08:49:41Z

Adding additional ABCD Elements

← Older revision		Revision as of 10:49, 12 September 2016
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	[[File:abcdMappingEditorSearch.png\|500px]]		[[File:abcdMappingEditorSearch.png\|500px]]

	Continue the sequence mapping new elements/testing until you’ve mapped all information you want to publish. You can have a look at the list of recommend and commonly used ABCD elements on the [[CommonABCD2Concepts\|Common ABCD2 Concepts]] page. The full ABCD documentation can be found in the [http://~~wiki~~.tdwg.org/~~ABCD~~ ABCD Wiki].		Continue the sequence mapping new elements/testing until you’ve mapped all information you want to publish. You can have a look at the list of recommend and commonly used ABCD elements on the [[CommonABCD2Concepts\|Common ABCD2 Concepts]] page. The full ABCD documentation can be found in the [http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki].

	The following page will show you a sample response ABCD document for a web service with 77 concepts mapped. Of course your documents will look different, because you will probably use different ABCD elements, but still it’s good to get an idea: [[SampleABCDDocument]].		The following page will show you a sample response ABCD document for a web service with 77 concepts mapped. Of course your documents will look different, because you will probably use different ABCD elements, but still it’s good to get an idea: [[SampleABCDDocument]].

JoergHoletschek: /* Access to Biological Collection Data Schema (ABCD) */

2016-09-12T08:49:14Z

Access to Biological Collection Data Schema (ABCD)

← Older revision		Revision as of 10:49, 12 September 2016
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	ABCD in its current version 2.06 is the data schema typically used in conjunction with BioCASe. It is a highly complex XML data schema with about 1,000 elements that is able to store almost every piece of information that can be found in a natural history specimen collection or an observation database. The complexity is due to the fact that it can be used for a wide range of collections/databases – for living and preserved specimens, observations and culture collections, for zoological, botanical, bacterial and viral collections, marine or terrestrial, for herbaria, botanic and zoological gardens. For each of these special types, ABCD features special sections where information specific for this type can be stored. Other sections of ABCD will be shared by all these types, for example for gathering site, identifier or metadata.		ABCD in its current version 2.06 is the data schema typically used in conjunction with BioCASe. It is a highly complex XML data schema with about 1,000 elements that is able to store almost every piece of information that can be found in a natural history specimen collection or an observation database. The complexity is due to the fact that it can be used for a wide range of collections/databases – for living and preserved specimens, observations and culture collections, for zoological, botanical, bacterial and viral collections, marine or terrestrial, for herbaria, botanic and zoological gardens. For each of these special types, ABCD features special sections where information specific for this type can be stored. Other sections of ABCD will be shared by all these types, for example for gathering site, identifier or metadata.

	The full ABCD documentation can be found in the [http://~~wiki~~.tdwg.org/~~ABCD~~ ABCD Wiki], a list of commonly used ABCD elements on the Wiki page [[CommonABCD2Concepts\|Common ABCD2 Concepts]].		The full ABCD documentation can be found in the http://terms.tdwg.org/wiki/ABCD_2 ABCD Wiki], a list of commonly used ABCD elements on the Wiki page [[CommonABCD2Concepts\|Common ABCD2 Concepts]].

	== Creating an ABCD Mapping for a Data Source ==		== Creating an ABCD Mapping for a Data Source ==

JoergHoletschek: /* The Mapping Editor */

2012-02-15T15:50:31Z

The Mapping Editor

← Older revision		Revision as of 17:50, 15 February 2012
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	If your metadata table holds just one record (because all occurrences published share the same metadata) and if it is not linked to the root table by a foreign key, you can specify this table in the drop-down box <small>Static table Alias</small>. The Provider Software will use a natural join to connect the metadata record stored in this table to all occurrences published. If your metadata table is referenced by a foreign key in the root able, you must not declare the metadata table as a static table! So either join the metadata table using a foreign key OR declare it as a static table.		If your metadata table holds just one record (because all occurrences published share the same metadata) and if it is not linked to the root table by a foreign key, you can specify this table in the drop-down box <small>Static table Alias</small>. The Provider Software will use a natural join to connect the metadata record stored in this table to all occurrences published. If your metadata table is referenced by a foreign key in the root able, you must not declare the metadata table as a static table! So either join the metadata table using a foreign key OR declare it as a static table.

			'''Note:''' If you're using Access, you cannot use a static table, because Access doesn't support that. So when using Access, you always have to reference the metadata table with a foreign key.

	When you’ve set the root table (and static table, if you use that), press <small>Save</small>. As with the DB structure setup, this will write your changes to the configuration files, closing the tab without saving will discard your changes! Also, in case you messed something up, you can use the <small>Revert</small> button to restore the state when you’ve saved for the last time.		When you’ve set the root table (and static table, if you use that), press <small>Save</small>. As with the DB structure setup, this will write your changes to the configuration files, closing the tab without saving will discard your changes! Also, in case you messed something up, you can use the <small>Revert</small> button to restore the state when you’ve saved for the last time.

JoergHoletschek: /* Adding Mandatory ABCD Elements */

2012-02-01T18:03:35Z

Adding Mandatory ABCD Elements

← Older revision		Revision as of 20:03, 1 February 2012
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	The second reason is even more important: Using literals for an element will result in this element to become not searchable, which means it cannot be used in a filter of a Search or a Scan request. Even though this behaviour is discoverable with a Capabilities request (by evaluating the ''searchable'' flag), a potential user of your web service might just not think of that, so it’s a good idea to avoid that in first place. Please use literals sparsely!		The second reason is even more important: Using literals for an element will result in this element to become not searchable, which means it cannot be used in a filter of a Search or a Scan request. Even though this behaviour is discoverable with a Capabilities request (by evaluating the ''searchable'' flag), a potential user of your web service might just not think of that, so it’s a good idea to avoid that in first place. Please use literals sparsely!

	In the mapping editor window, you can select several source columns and several literals, even a combination of both. The Provider Software will simply concatenate the values retrieved from the database and the literals specified (in the order they’re given). But ~~again~~: ~~Keep in mind that this~~ will make the element not searchable. A better solution is to do ~~any concatenation operations~~ in a database view.		In the mapping editor window, you can select several source columns and several literals, even a combination of both. The Provider Software will simply concatenate the values retrieved from the database and the literals specified (in the order they’re given). But be careful: any use of concatenation or literals will make the element not searchable. A better solution is to do such manipulations earlier, in a database view, and direct the mapping editor to a single resulting database field.

	Use the mapping editor window to add mappings for all eight mandatory fields: Click on the <strong>+</strong> symbol next to the element, choose table/column name and the correct data type, then press <small>Save</small>. When you’re done, the page should look similar to the following image. Press <small>Save</small> in the main window to write your changes to the configuration files.		Use the mapping editor window to add mappings for all eight mandatory fields: Click on the <strong>+</strong> symbol next to the element, choose table/column name and the correct data type, then press <small>Save</small>. When you’re done, the page should look similar to the following image. Press <small>Save</small> in the main window to write your changes to the configuration files.

JoergHoletschek: /* Initial Testing of the Data Source */

2011-08-18T13:43:12Z

Initial Testing of the Data Source

← Older revision		Revision as of 15:43, 18 August 2011
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	Once you’ve mapped all mandatory elements, you can do the first test of your BioCASe web service. Even though you haven’t mapped any real information yet, it is a good idea to check the service and solve any problems hitherto before continuing with the mapping. Click on <small>Test mapping!</small> to open the Query Form that can be used for this purpose:		Once you’ve mapped all mandatory elements, you can do the first test of your BioCASe web service. Even though you haven’t mapped any real information yet, it is a good idea to check the service and solve any problems hitherto before continuing with the mapping. Click on <small>Test mapping!</small> to open the Query Form that can be used for this purpose:

	[[File:abcdQueryFormEmpty.png]]		[[File:abcdQueryFormEmpty.png\|border]]

	With the Query Form you can send a BioCASe request to your web service; it will wait for the reply of the web service and display the response document. On top of the page you can see the URL of your web service. In this case it is ''<nowiki>http://localhost/biocase/pywrapper.cgi?dsa=flora</nowiki>'', ''flora'' being the name of the datasource. Make sure this is correct for your installation!		With the Query Form you can send a BioCASe request to your web service; it will wait for the reply of the web service and display the response document. On top of the page you can see the URL of your web service. In this case it is ''<nowiki>http://localhost/biocase/pywrapper.cgi?dsa=flora</nowiki>'', ''flora'' being the name of the datasource. Make sure this is correct for your installation!
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	As you can see, there is a filter set on the ''ScientificName'' element. Since we haven’t mapped this element yet, this won’t work. So let’s remove the filter (all lines between <filter> and </filter>, including the ''filter'' tags), leaving the text box like this:		As you can see, there is a filter set on the ''ScientificName'' element. Since we haven’t mapped this element yet, this won’t work. So let’s remove the filter (all lines between <filter> and </filter>, including the ''filter'' tags), leaving the text box like this:

	[[File:abcdQueryFormFilled.png]]		[[File:abcdQueryFormFilled.png\|border]]

	Pressing <small>Submit</small> will send the request to the web service and – hopefully – display the response document with the correct ABCD records. For the mapping we’ve just created, it should look similar to the following (use the "–" symbol next to the trees TechnicalContact, ContentContact and Metadata to collapse them):		Pressing <small>Submit</small> will send the request to the web service and – hopefully – display the response document with the correct ABCD records. For the mapping we’ve just created, it should look similar to the following (use the "–" symbol next to the trees TechnicalContact, ContentContact and Metadata to collapse them):

	[[File:abcdResponseMandatoryElements.png]]		[[File:abcdResponseMandatoryElements.png\|border]]

	If you get an error, please check out the [[Debugging]] tutorial on how to debug a web service. You should continue the mapping process only after your web service returns results for the basal mapping we’ve just created.		If you get an error, please check out the [[Debugging]] tutorial on how to debug a web service. You should continue the mapping process only after your web service returns results for the basal mapping we’ve just created.

JoergHoletschek: /* Creating an ABCD Mapping for a Data Source */

2011-08-18T13:42:32Z

Creating an ABCD Mapping for a Data Source

← Older revision		Revision as of 15:42, 18 August 2011
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	If you created a data source from a template (e.g. ''abcdmetadata''), a schema mapping for ABCD will be already existent. In this case, you can directly jump to the next section. If you created an empty data source, the section <small>Schemas</small> in the data source configuration overview will be empty:		If you created a data source from a template (e.g. ''abcdmetadata''), a schema mapping for ABCD will be already existent. In this case, you can directly jump to the next section. If you created an empty data source, the section <small>Schemas</small> in the data source configuration overview will be empty:

	[[File:abcdSchemaMappings.png]]		[[File:abcdSchemaMappings.png\|border]]

	In order to create a new schema mapping, select the desired schema from the list and click <small>Create</small>. For ABCD, choose <small>ABCD_2.06.xml</small> (be careful not to hit one of the ABCD extensions, they look quite similar). After clicking <small>Create</small>, you will be directed to the mapping editor, which will allow you to edit the mappings.		In order to create a new schema mapping, select the desired schema from the list and click <small>Create</small>. For ABCD, choose <small>ABCD_2.06.xml</small> (be careful not to hit one of the ABCD extensions, they look quite similar). After clicking <small>Create</small>, you will be directed to the mapping editor, which will allow you to edit the mappings.