XBio:D Data Management - Revision history

Nfj at 16:10, 18 September 2015

2015-09-18T16:10:12Z

Nfj at 15:51, 18 September 2015

2015-09-18T15:51:20Z

Jcora at 19:59, 7 August 2015

2015-08-07T19:59:59Z

Jcora at 21:44, 27 July 2015

2015-07-27T21:44:11Z

Jcora at 17:04, 21 July 2015

2015-07-21T17:04:49Z

Jcora: Protected "XBio:D Data Management" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

2015-07-21T15:57:59Z

Protected "XBio:D Data Management" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

Jcora: Created page with "---- '''xBio:D Data Management''' This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. ..."

2015-07-21T15:56:38Z

Created page with "---- '''xBio:D Data Management''' This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. ..."

New page

----

'''xBio:D Data Management'''

This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. These tasks are not available through web applications and must either be performed by running a script or a database procedure.

== Change Occurrence Record (Specimen) CUID ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC updateSpmID(old_cuid, new_cuid);</code>. The procedure will only produce output when a problem occurred.

== Merged/Remove Locality Name ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC change_locality(obsolete_loc_name, valid_loc_name);</code>. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter ''coll_date'', which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.

[[Category:OSUC Private]]

@@ Line 34: / Line 34: @@
 ## Scroll to the bottom to ''Create New Resource'', specify a short name and resource type, then upload the previously exported file and create resource
 ## Fill in the metadata section of the resource with the appropriate values for provider, owner, etc.
-# Log into the hymfiles server (''osuc.biosci.ohio-state.edu'') via Remote Desktop and open IPT DwC-A import script, ''populate_ipt.py''. The Python script is located in ''C:\backup_scripts''.
+# Log into the hymfiles server (''hymfiles.biosci.ohio-state.edu'') via Remote Desktop and open IPT DwC-A import script, ''populate_ipt.py''. The Python script is located in ''C:\backup_scripts''.
 # Go to the ''handlePopulateIPT'' function and add the taxon or collection you would like to export.
 ## The numeric identifiers are the same as defined in the ''export'' step above

@@ Line 31: / Line 31: @@
 ## Taxon checklist example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_tax_195000.zip''
 # Create project in xBio:D IPT for the data you will be disseminating.
-## Log into IPT and go to ''Manage Resources''
+## Log into IPT at (''xbiod.osu.edu/ipt/'') and go to ''Manage Resources''
 ## Scroll to the bottom to ''Create New Resource'', specify a short name and resource type, then upload the previously exported file and create resource
 ## Fill in the metadata section of the resource with the appropriate values for provider, owner, etc.

← Older revision		Revision as of 19:59, 7 August 2015
Line 39:		Line 39:
	## The second parameter for the populate script is the resource short name specified above.		## The second parameter for the populate script is the resource short name specified above.
	# Register and publish the new project. The resource will now be available on GBIF and can be shared with other data aggregators like iDigBio, VertNet, etc.		# Register and publish the new project. The resource will now be available on GBIF and can be shared with other data aggregators like iDigBio, VertNet, etc.
		+
		+
		+	== Specialized Scripts for DB processing Tasks ==
		+	These scripts include DOI lookup for xBio:D publication, processing the gender of people, and uploading of PDFs into Zenodo. The scripts are located in ''/scripts'' on the Database server.

@@ Line 7: / Line 7: @@
-== Change Occurrence Record (Specimen) CUID ==
+== Change Occurrence (Specimen) Record CUID ==
 In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC updateSpmID(old_cuid, new_cuid);</code>. The procedure will only produce output when a problem occurred.
 == Merged/Remove Locality Name ==
 In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC change_locality(obsolete_loc_name, valid_loc_name);</code>. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter ''coll_date'', which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.

← Older revision	Revision as of 15:57, 21 July 2015
(No difference)