Edit the parser, index new elements - Revision history

PatriciaKelbert: /* Add a new data standard */

2016-03-01T10:15:21Z

Add a new data standard

← Older revision		Revision as of 12:15, 1 March 2016
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	And get inspired from the closest existing standard already known by B-HIT.		And get inspired from the closest existing standard already known by B-HIT.


			If you have a new namespace, add it to the namespaceMap in src/org/binhum/gbif/util/ABCDProcessor.java.

PatriciaKelbert: /* Add a new data standard */

2016-02-03T09:21:52Z

Add a new data standard

← Older revision		Revision as of 11:21, 3 February 2016
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	=Add a new data standard=		=Add a new data standard=
			A) Add it in the database, in the standardschema table. <br/>
			B) Document the changes<br/>
			C) Add a new method in the Unit.java class, that will be called from the function public int parse(String accesspoint).<br/>
			For example:<br/>
			<pre>
			if (getStandard().equalsIgnoreCase("abcd3")) {
			parseABCD3(utils,tripleIDStore);
			}
			....

			private void parseABCD3(XMLutil utils, TripleIDStore tripleIDStore) {.....
			</pre>

			And get inspired from the closest existing standard already known by B-HIT.

PatriciaKelbert: /* Add an simple element (ie. it can be added to an existing table in the database) */

2016-02-03T09:18:10Z

Add an simple element (ie. it can be added to an existing table in the database)

← Older revision		Revision as of 11:18, 3 February 2016
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	=Add an simple element (ie. it can be added to an existing table in the database)=		=Add an simple element (ie. it can be added to an existing table in the database)=
	#Choose where you want to save it		A) Choose where you want to save it<br/>
			B) Add a new column in the table from the concept that will have a this new element.<br/>
			C) Document the file with the "SQL changes".<br/>
			D) Edit the Java code!<br/>
			<br/><br/>
			For example, if you want to add an element linked to the gathering group, you will have to create a new String or Int value in the Gathering.java class, create the corresponding getters and setters, and extract the value from your document (ABCD, Darwin etc..). You will also have to edit the create and update queries for the corresponding concept (add the field name in the insert statement, add the value in the prepared statement, and check the query has the same number of fields than values!)

	=Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)=		=Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)=

PatriciaKelbert: /* Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database) */

2016-02-03T09:12:19Z

Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)

← Older revision		Revision as of 11:12, 3 February 2016
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	These new fields also have to be deleted by the next update : at the ~~end of~~ the ~~public ArrayList<Integer> cleanOccurrences~~(~~String dataset, String elementType, int fk_datasourceid~~) ~~method in the OccurrenceDaoImpl, make a call~~ to a ~~new~~ function~~/SQL query that will delete all~~ references ~~that are not used (except~~ the ~~ID 1) (for example, look at the function deleteFromSecundaryBasedOnTripleidstoreid)~~.		These new fields also have to be deleted by the next update : add the query statement in the processDeletionBasedOnOccurrenceid or in the processDeletionBasedOnTripleidstoreid method (depending on what it's based).
			You also might have to write a similar function to the cleanAssociation to remove the unused references from the database.

	=Add a new data standard=		=Add a new data standard=

PatriciaKelbert: /* Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database) */

2016-02-02T10:46:05Z

Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)

← Older revision		Revision as of 12:46, 2 February 2016
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	These new fields also have to be deleted by the next update : at the end of the ~~private void processDeletion(final~~ ArrayList<Integer> ~~deletedIDs~~) method in the OccurrenceDaoImpl, make a call to a new function that will delete all references that are not used (except the ID 1).		These new fields also have to be deleted by the next update : at the end of the public ArrayList<Integer> cleanOccurrences(String dataset, String elementType, int fk_datasourceid) method in the OccurrenceDaoImpl, make a call to a new function/SQL query that will delete all references that are not used (except the ID 1) (for example, look at the function deleteFromSecundaryBasedOnTripleidstoreid).

	=Add a new data standard=		=Add a new data standard=

PatriciaKelbert: /* Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database) */

2016-02-02T10:36:53Z

Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)

← Older revision		Revision as of 12:36, 2 February 2016
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	*createOrUpdatePreparation : add ps.setInt(6, prepa.getReferenceid()); and change ps.setInt(6, prepa.getId()); to ps.setInt(7, prepa.getId());		*createOrUpdatePreparation : add ps.setInt(6, prepa.getReferenceid()); and change ps.setInt(6, prepa.getId()); to ps.setInt(7, prepa.getId());
	</pre>		</pre>
	!! Check the field order and the number of fields/columns !!		!! Check the field order and the number of fields/columns !!<br/><br/>


			Now it will be stored with the next harvesting. If you want to force the indexation of the new field (the original data might have not changed since the last indexing), you will have to delete the old records from the database (use the Management tab for it). <br/>

	*delete ~~by updates!~~
			These new fields also have to be deleted by the next update : at the end of the private void processDeletion(final ArrayList<Integer> deletedIDs) method in the OccurrenceDaoImpl, make a call to a new function that will delete all references that are not used (except the ID 1).

	=Add a new data standard=		=Add a new data standard=

PatriciaKelbert: /* Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database) */

2016-02-02T10:10:36Z

Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)

← Older revision		Revision as of 12:10, 2 February 2016
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	A Reference is made of 3 elements: TitleCitation, CitationDetail and URI. As a Reference can be linked to several ABCD concepts, it might make more sense to link the Reference(s) to the concept than to the whole Unit		A Reference is made of 3 elements: TitleCitation, CitationDetail and URI. As a Reference can be linked to several ABCD concepts, it might make more sense to link the Reference(s) to the concept than to the whole Unit

	A) Create a new table in the database for the references, with an auto-incrementation ID. Put a new empty line (referenceID 1, titleCitation null, citationDetail null, URI null) because you will need a foreign key to make the rest easier.		A) Create a new table in the database for the references, with an auto-incrementation ID. Put a new empty line (referenceID 1, titleCitation null, citationDetail null, URI null) because you will need a foreign key to make the rest easier.<br/>
	B) Add a new column in the table from the concept that will have a Reference (ie. fk_referenceID), and configure it as a foreign-Key with the default value 1 for all the old records)		B) Add a new column in the table from the concept that will have a Reference (ie. fk_referenceID), and configure it as a foreign-Key with the default value 1 for all the old records)<br/>
	C) Document the file with the "SQL changes".		C) Document the file with the "SQL changes".<br/>
	D) Edit the Java code!		D) Edit the Java code!<br/><br/>
	*Have a look at the src/org/binhum/abcd/Multimedia.java class. The new class could look like this:		*Have a look at the src/org/binhum/abcd/Multimedia.java class. The new class could look like this:
	<pre>		<pre>
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	savePreparation(prepa);		savePreparation(prepa);
	</pre>		</pre>
	-> You will have to create the method setReferenceid and getReferenceid in the class Preparation.java.		-> Do it for each standard (get them from the public int parse(String accesspoint) method in Unit.java)<br/>
	!! For each concept, reset the referenceID first to 1, or you might have the reference from a previous element attached to the current concept !!		-> You will have to create the method setReferenceid and getReferenceid in the class Preparation.java.<br/>
	Also, you have to update the savePreparation method (ie. occurrenceDao.createOrUpdatePreparation(prepa); ie. you will have to edit in the OccurrenceDaoImpl.java class following elements:		!! For each concept, reset the referenceID first to 1, or you might have the reference from a previous element attached to the current concept !!<br/>
			Also, you have to update the savePreparation method (ie. occurrenceDao.createOrUpdatePreparation(prepa); ie. you will have to edit in the OccurrenceDaoImpl.java class following elements:<br/>
	<pre>		<pre>
	*createPreparation : add a ps.setInt(6, prepa.getReferenceid());		*createPreparation : add a ps.setInt(6, prepa.getReferenceid());

PatriciaKelbert: /* Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database) */

2016-02-02T10:06:24Z

Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)

← Older revision		Revision as of 12:06, 2 February 2016
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	savePreparation(prepa);		savePreparation(prepa);
	</pre>		</pre>
			-> You will have to create the method setReferenceid and getReferenceid in the class Preparation.java.
	!! For each concept, reset the referenceID first to 1, or you might have the reference from a previous element attached to the current concept !!		!! For each concept, reset the referenceID first to 1, or you might have the reference from a previous element attached to the current concept !!
			Also, you have to update the savePreparation method (ie. occurrenceDao.createOrUpdatePreparation(prepa); ie. you will have to edit in the OccurrenceDaoImpl.java class following elements:
			<pre>
			*createPreparation : add a ps.setInt(6, prepa.getReferenceid());
			*CREATE_PREPA_SQL : add the table column and a question mark for the SQL statement
			*UPDATE_PREPA_SQL : add the table column with the question mark for the SQL statement
			*createOrUpdatePreparation : add ps.setInt(6, prepa.getReferenceid()); and change ps.setInt(6, prepa.getId()); to ps.setInt(7, prepa.getId());
			</pre>
			!! Check the field order and the number of fields/columns !!

PatriciaKelbert at 10:01, 2 February 2016

2016-02-02T10:01:16Z

← Older revision		Revision as of 12:01, 2 February 2016
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	=Add an simple element (ie. it can be added to an existing table in the database)=		=Add an simple element (ie. it can be added to an existing table in the database)=
	#Choose where you want to save it		#Choose where you want to save it

	#

	=Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)=		=Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)=
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	}		}
	</pre>		</pre>
	*Have a look at the class of concept you want to link it to		*Save the new Reference and get it ID (ie. referenceid= occurrenceDao.createOrUpdateReference(referenceObj);
	~~#The reference will have~~ to ~~be saved in the DB before~~ the concept it ~~belongs~~ to! ~~(because of~~ the ~~foreign key)~~		--> create the createOrUpdateReference method in org/binhum/harvest/util/jdbc/dao/OccurrenceDao.java (abstract) and org/binhum/harvest/util/jdbc/dao/OccurrenceDaoImpl.java
			*Have a look at the class of concept you want to link it to.
			*Add this ID to the concept you want to link it to, usually in the Unit.java class (for example:
			<pre>
			Preparation prepa = new Preparation();
			prepa.setTripleidstoreid(triplestoreid);
			prepa.setPreparationDate(extractionDate);
			prepa.setPreparationStaff(extractionStaff);
			prepa.setPreparationMaterials(extractionMethod);
			prepa.setPreparationType(preparationType);
			prepa.setReferenceid(referenceid);
			savePreparation(prepa);
			</pre>
			!! For each concept, reset the referenceID first to 1, or you might have the reference from a previous element attached to the current concept !!

PatriciaKelbert: /* Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database) */

2016-02-02T09:53:27Z

Add a repeatable or a more complex element or group of elements (ie. it will need a new table in the database)

@@ Line 10: / Line 10: @@
 .Choose where you want to save it
 Example: add a reference group (ABCD2.06) http://www.bgbm.org/tdwg/codata/schema/ABCD_2.06/HTML/ABCD_2.06.html#complexType_Reference_Link031A69A8
-A Reference is made of 3 elements: TitleCitation, CitationDetail and URI.
+A Reference is made of 3 elements: TitleCitation, CitationDetail and URI. As a Reference can be linked to several ABCD concepts, it might make more sense to link the Reference(s) to the concept than to the whole Unit
 =Add a new data standard=