From da690ebf9d0bd63e799eceee54e4d9f0b09d8aac Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 15:25:27 -0500 Subject: [PATCH 1/5] VIVO-434 restoring "documentation for" --- rdf/tbox/filegraph/object-properties.owl | 62 +++++++++----------- rdf/tbox/filegraph/research-resource.owl | 13 ++++ rdf/tbox/firsttime/initialTBoxAnnotations.n3 | 5 ++ 3 files changed, 46 insertions(+), 34 deletions(-) diff --git a/rdf/tbox/filegraph/object-properties.owl b/rdf/tbox/filegraph/object-properties.owl index 4c95312e..1f06a387 100644 --- a/rdf/tbox/filegraph/object-properties.owl +++ b/rdf/tbox/filegraph/object-properties.owl @@ -201,7 +201,6 @@ - @@ -317,7 +316,6 @@ - @@ -497,7 +495,6 @@ - @@ -575,7 +572,6 @@ - @@ -593,8 +589,6 @@ PERSON: Melissa Haendel PERSON: Melissa Haendel used to study - - @@ -914,14 +908,7 @@ there is a measurement process p that has specified output m, a measurement datu http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) is_manufactured_by - - - - - - - - + @@ -1671,7 +1658,8 @@ there is a measurement process p that has specified output m, a measurement datu - + + @@ -1679,7 +1667,21 @@ there is a measurement process p that has specified output m, a measurement datu - + + + + + + + + + + + + + + + @@ -1687,7 +1689,16 @@ there is a measurement process p that has specified output m, a measurement datu - + + + + + + + + + + @@ -1704,7 +1715,6 @@ there is a measurement process p that has specified output m, a measurement datu - @@ -1717,22 +1727,6 @@ there is a measurement process p that has specified output m, a measurement datu - - - - - - - - - - - - - - - - diff --git a/rdf/tbox/filegraph/research-resource.owl b/rdf/tbox/filegraph/research-resource.owl index dccf8f43..795cdeb9 100644 --- a/rdf/tbox/filegraph/research-resource.owl +++ b/rdf/tbox/filegraph/research-resource.owl @@ -507,5 +507,18 @@ + + + + + OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) + PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice. + PlanAndPlannedProcess Branch + Protocol + a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. + protocol + + + diff --git a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 index cef6df9c..44a3d725 100644 --- a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 +++ b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 @@ -407,6 +407,9 @@ foaf:Person obo:OBI_0000643 rdfs:label "has grain"@en-US . +obo:OBI_0000272 + rdfs:label "protocol"@en-US . + vcard:Identification rdfs:label "Identification"@en-US . @@ -6173,6 +6176,8 @@ obo:ERO_0001716 vitro:prohibitedFromUpdateBelowRoleLevelAnnot ; vitro:selectFromExistingAnnot + "true"^^xsd:boolean ; + vitro:offerCreateNewOptionAnnot "true"^^xsd:boolean . vcard:hasRelated From 8d8df54219a76f8da3222ac91de6999c10beee4e Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 15:26:07 -0500 Subject: [PATCH 2/5] fixes a vcard bug --- .../update/sparqlConstructs/additions/vcard1-0c.sparql | 3 ++- .../update/sparqlConstructs/additions/vcard2d.sparql | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql index 03405d95..7443d28a 100644 --- a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql +++ b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard1-0c.sparql @@ -8,7 +8,8 @@ CONSTRUCT { _:vcard arg:ARG_2000029 ?s . _:vcard a v:Individual . } WHERE { - ?s vivo:middleName ?middleName + ?s vivo:middleName ?middleName . + ?s a foaf:Person FILTER NOT EXISTS { ?s arg:ARG_2000028 ?vcard } diff --git a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql index a065a9fe..cb32f1b9 100644 --- a/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql +++ b/productMods/WEB-INF/ontologies/update/sparqlConstructs/additions/vcard2d.sparql @@ -8,6 +8,7 @@ CONSTRUCT { ?name vivo:middleName ?middleName . } WHERE { ?s vivo:middleName ?middleName . + ?s a foaf:Person . ?s arg:ARG_2000028 ?vcard . ?vcard v:hasName ?name } From 5adf4a587f6c7079a7013db34438fdf7d475c600 Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 15:50:11 -0500 Subject: [PATCH 3/5] object property cleanup --- rdf/tbox/filegraph/object-properties.owl | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/rdf/tbox/filegraph/object-properties.owl b/rdf/tbox/filegraph/object-properties.owl index 1f06a387..f61d226f 100644 --- a/rdf/tbox/filegraph/object-properties.owl +++ b/rdf/tbox/filegraph/object-properties.owl @@ -558,24 +558,6 @@ related technique - - - - - - - - - - - - - - - - - - From ef3ac5008d150351a503498fe70c881b9a5ca4bb Mon Sep 17 00:00:00 2001 From: brianjlowe Date: Tue, 5 Nov 2013 16:08:22 -0500 Subject: [PATCH 4/5] VIVO-494 hiding "realizes" --- rdf/tbox/firsttime/initialTBoxAnnotations.n3 | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 index 44a3d725..672d3388 100644 --- a/rdf/tbox/firsttime/initialTBoxAnnotations.n3 +++ b/rdf/tbox/firsttime/initialTBoxAnnotations.n3 @@ -5983,7 +5983,11 @@ vcard:Name rdfs:label "Name"@en-US . obo:BFO_0000055 - rdfs:label "realizes"@en-US . + rdfs:label "realizes"@en-US ; + vitro:hiddenFromDisplayBelowRoleLevelAnnot + ; + vitro:prohibitedFromUpdateBelowRoleLevelAnnot + . geo:nationalityAR rdfs:label "nationalityAR"@en-US ; From 6940771720a08f2532c066a20ac37234ac188824 Mon Sep 17 00:00:00 2001 From: j2blake Date: Tue, 5 Nov 2013 17:51:09 -0500 Subject: [PATCH 5/5] VIVO-448 Correct the installation instructions for ORNG. The change from deploy.properties to build/runtime.properties wasn't handled correctly. --- doc/install.html | 39 +++++++++++++++++++-------------------- doc/setting_up_orng.html | 16 ++++++++-------- 2 files changed, 27 insertions(+), 28 deletions(-) diff --git a/doc/install.html b/doc/install.html index 00c033cd..c30b768e 100644 --- a/doc/install.html +++ b/doc/install.html @@ -339,6 +339,25 @@ issuing SPARQL queries that read data, and its URI for issuing SPARQL UPDATE com es_MX + + + These values are used when deploying VIVO as an OpenSocial container + and integrating with OpenSocial gadgets + (see Step 13, below). If you are creating + a VIVO installation that does not use OpenSocial gadgets, these values are omitted. + + + + + OpenSocial.shindigURL
+ OpenSocial.tokenService
+ OpenSocial.tokenKeyFile
+ OpenSocial.sandbox + + +   + + @@ -938,26 +957,6 @@ issuing SPARQL queries that read data, and its URI for issuing SPARQL UPDATE com - - - These values are used when deploying VIVO as an OpenSocial container - and integrating with OpenSocial gadgets - (see Step 13, below). If you are creating - a VIVO installation that does not use OpenSocial gadgets, these values are omitted. - - - - - OpenSocial.shindigURL
- OpenSocial.tokenService
- OpenSocial.tokenKeyFile
- OpenSocial.sandbox - - -   - - - diff --git a/doc/setting_up_orng.html b/doc/setting_up_orng.html index 9f7e59a6..9eb99459 100644 --- a/doc/setting_up_orng.html +++ b/doc/setting_up_orng.html @@ -188,7 +188,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle

I.iv Configure VIVO

- In the VIVO home directory, the file called runtime.properties + In the VIVO distribution directory, the file called build.properties contains configuration options for the VIVO application. You must set some additional parameters so VIVO will be able to communicate with Shindig-ORNG.

@@ -333,7 +333,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
  • VIVO was not re-deployed with ant deploy after the OpenSocial - values were set in runtime.properties + values were set in build.properties
@@ -405,7 +405,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
  • - OpenSocial.tokenKeyFile is not set in runtime.properties, + OpenSocial.tokenKeyFile is not set in build.properties, or the file does not exist at the specified location.
@@ -449,7 +449,7 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle
  • - In runtime.properties, OpenSocial.tokenService is not set correctly. + In build.properties, OpenSocial.tokenService is not set correctly.
@@ -692,11 +692,11 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle

III.i. Re-running the deployment script

- The OpenSocial framework relies on several of the settings in the runtime.properties file, + The OpenSocial framework relies on several of the settings in the build.properties and runtime.properties files, in addition to the ones that are explicitly linked to it.

- Each time you change the settings in runtime.properties, you should re-deploy + Each time you change the settings in build.properties or runtime.properties, you should re-deploy the framework with 

          ant orng

@@ -750,12 +750,12 @@ set CATALINA_OPTS=-Dshindig.host=localhost -Dshindig.port=8080 -Djava.awt.headle Disabling the gadgets, as above, will remove essentially all of the OpenSocial processing within VIVO. To remove the remainder of it, you can disable the connection between VIVO and the OpenSocial service. Do this by removing or commenting - the OpenSocial properties in runtime.properties + the OpenSocial properties in build.properties (see section I.iv. Configure VIVO).

- Restart Tomcat to make this change take effect. + To make this change take effect, re-deploy VIVO and restart Tomcat.

Remove the OpenSocial webapp from Tomcat