Fix invalid displayIds

tcmitchell · tcmitchell · commit b865bd19158f · 2020-08-27T15:26:00.000-04:00
The spec says that if the identity of an entity is a URL then the
displayId must match the last element in the URL's path.
diff --git a/SBOL3/multicellular/multicellular.jsonld b/SBOL3/multicellular/multicellular.jsonld
@@ -242,7 +242,7 @@
     "@id" : "GFP_protein",
     "@type" : "sbol:Component",
     "description" : "GFP",
-    "displayId" : "GFP",
+    "displayId" : "GFP_protein",
     "name" : "GFP",
     "type" : "SBO:0000252"
   }, {
diff --git a/SBOL3/multicellular/multicellular.nt b/SBOL3/multicellular/multicellular.nt
@@ -300,7 +300,7 @@
 <https://sbolstandard.org/examples/AHL_producer/subcomponent_2> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#SubComponent> .
 <https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
 <https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#name> "GFP" .
-<https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#displayId> "GFP" .
+<https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#displayId> "GFP_protein" .
 <https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#description> "GFP" .
 <https://sbolstandard.org/examples/GFP_protein> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
 <https://sbolstandard.org/examples/luxI> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> .
diff --git a/SBOL3/multicellular/multicellular.rdf b/SBOL3/multicellular/multicellular.rdf
@@ -86,7 +86,7 @@
    <sbol:Component rdf:about="GFP_protein">
       <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
       <sbol:name>GFP</sbol:name>
-      <sbol:displayId>GFP</sbol:displayId>
+      <sbol:displayId>GFP_protein</sbol:displayId>
       <sbol:description>GFP</sbol:description>
    </sbol:Component>
    <sbol:Component rdf:about="LuxR_AHL">
diff --git a/SBOL3/multicellular/multicellular.rj b/SBOL3/multicellular/multicellular.rj
@@ -1353,7 +1353,7 @@
   "https://sbolstandard.org/examples/GFP_protein" : { 
     "http://sbols.org/v3#displayId" : [ { 
       "type" : "literal" ,
-      "value" : "GFP"
+      "value" : "GFP_protein"
     }
      ] ,
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
diff --git a/SBOL3/multicellular/multicellular.ttl b/SBOL3/multicellular/multicellular.ttl
@@ -374,7 +374,7 @@
 
 :GFP_protein  a           sbol:Component ;
         sbol:description  "GFP" ;
-        sbol:displayId    "GFP" ;
+        sbol:displayId    "GFP_protein" ;
         sbol:name         "GFP" ;
         sbol:type         SBO:0000252 .
 
diff --git a/SBOL3/provenance_entity/activity/activity.jsonld b/SBOL3/provenance_entity/activity/activity.jsonld
@@ -60,7 +60,7 @@
     "@id" : "toggle_switch_optimised",
     "@type" : "sbol:Component",
     "description" : "Toggle Switch genetic circuit - codon optimised",
-    "displayId" : "toggle_switch optimised",
+    "displayId" : "toggle_switch_optimised",
     "name" : "Toggle Switch Optimised",
     "type" : "SBO:0000241",
     "wasDerivedFrom" : "toggle_switch",
diff --git a/SBOL3/provenance_entity/activity/activity.nt b/SBOL3/provenance_entity/activity/activity.nt
@@ -1,7 +1,7 @@
 <https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/ns/prov#wasDerivedFrom> <https://sbolstandard.org/examples/toggle_switch> .
 <https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/ns/prov#wasGeneratedBy> <https://sbolstandard.org/examples/codon_optimization_activity> .
 <https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#description> "Toggle Switch genetic circuit - codon optimised" .
-<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#displayId> "toggle_switch optimised" .
+<https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#displayId> "toggle_switch_optimised" .
 <https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000241> .
 <https://sbolstandard.org/examples/toggle_switch_optimised> <http://sbols.org/v3#name> "Toggle Switch Optimised" .
 <https://sbolstandard.org/examples/toggle_switch_optimised> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
diff --git a/SBOL3/provenance_entity/activity/activity.rdf b/SBOL3/provenance_entity/activity/activity.rdf
@@ -22,7 +22,7 @@
          <prov:Activity rdf:about="codon_optimization_activity"/>
       </prov:wasGeneratedBy>
       <sbol:description>Toggle Switch genetic circuit - codon optimised</sbol:description>
-      <sbol:displayId>toggle_switch optimised</sbol:displayId>
+      <sbol:displayId>toggle_switch_optimised</sbol:displayId>
       <sbol:type rdf:resource="https://identifiers.org/SBO:0000241"/>
       <sbol:name>Toggle Switch Optimised</sbol:name>
    </sbol:Component>
diff --git a/SBOL3/provenance_entity/activity/activity.rj b/SBOL3/provenance_entity/activity/activity.rj
@@ -212,7 +212,7 @@
   "https://sbolstandard.org/examples/toggle_switch_optimised" : { 
     "http://sbols.org/v3#displayId" : [ { 
       "type" : "literal" ,
-      "value" : "toggle_switch optimised"
+      "value" : "toggle_switch_optimised"
     }
      ] ,
     "http://www.w3.org/ns/prov#wasGeneratedBy" : [ { 
diff --git a/SBOL3/provenance_entity/activity/activity.ttl b/SBOL3/provenance_entity/activity/activity.ttl
@@ -12,7 +12,7 @@
 :toggle_switch_optimised
         a                    sbol:Component ;
         sbol:description     "Toggle Switch genetic circuit - codon optimised" ;
-        sbol:displayId       "toggle_switch optimised" ;
+        sbol:displayId       "toggle_switch_optimised" ;
         sbol:name            "Toggle Switch Optimised" ;
         sbol:type            SBO:0000241 ;
         prov:wasDerivedFrom  :toggle_switch ;
diff --git a/SBOL3/toggle_switch/toggle_switch.jsonld b/SBOL3/toggle_switch/toggle_switch.jsonld
@@ -3,7 +3,7 @@
     "@id" : "GFP_protein",
     "@type" : "sbol:Component",
     "description" : "GFP",
-    "displayId" : "GFP",
+    "displayId" : "GFP_protein",
     "name" : "GFP",
     "type" : "SBO:0000252"
   }, {
diff --git a/SBOL3/toggle_switch/toggle_switch.nt b/SBOL3/toggle_switch/toggle_switch.nt
@@ -309,7 +309,7 @@
 <https://sbolstandard.org/examples/TetR_producer/interaction_1> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Interaction> .
 <https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
 <https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#name> "GFP" .
-<https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#displayId> "GFP" .
+<https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#displayId> "GFP_protein" .
 <https://sbolstandard.org/examples/GFP_protein> <http://sbols.org/v3#description> "GFP" .
 <https://sbolstandard.org/examples/GFP_protein> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
 <https://sbolstandard.org/examples/toggle_switch/constraint_1> <http://sbols.org/v3#subject> <https://sbolstandard.org/examples/toggle_switch/componentreference_1> .
diff --git a/SBOL3/toggle_switch/toggle_switch.rdf b/SBOL3/toggle_switch/toggle_switch.rdf
@@ -34,7 +34,7 @@
    <sbol:Component rdf:about="GFP_protein">
       <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
       <sbol:name>GFP</sbol:name>
-      <sbol:displayId>GFP</sbol:displayId>
+      <sbol:displayId>GFP_protein</sbol:displayId>
       <sbol:description>GFP</sbol:description>
    </sbol:Component>
    <sbol:Component rdf:about="ter_lacI">
diff --git a/SBOL3/toggle_switch/toggle_switch.rj b/SBOL3/toggle_switch/toggle_switch.rj
@@ -1206,7 +1206,7 @@
   "https://sbolstandard.org/examples/GFP_protein" : { 
     "http://sbols.org/v3#displayId" : [ { 
       "type" : "literal" ,
-      "value" : "GFP"
+      "value" : "GFP_protein"
     }
      ] ,
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
diff --git a/SBOL3/toggle_switch/toggle_switch.ttl b/SBOL3/toggle_switch/toggle_switch.ttl
@@ -381,7 +381,7 @@
 
 :GFP_protein  a           sbol:Component ;
         sbol:description  "GFP" ;
-        sbol:displayId    "GFP" ;
+        sbol:displayId    "GFP_protein" ;
         sbol:name         "GFP" ;
         sbol:type         SBO:0000252 .
 

Original file line number	Diff line number	Diff line change
`@@ -1353,7 +1353,7 @@`
`1353`	`1353`	`"https://sbolstandard.org/examples/GFP_protein" : {`
`1354`	`1354`	`"http://sbols.org/v3#displayId" : [ {`
`1355`	`1355`	`"type" : "literal" ,`
`1356`		`- "value" : "GFP"`
	`1356`	`+ "value" : "GFP_protein"`
`1357`	`1357`	`}`
`1358`	`1358`	`] ,`
`1359`	`1359`	`"http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ {`
Original file line number	Diff line number	Diff line change
`@@ -212,7 +212,7 @@`
`212`	`212`	`"https://sbolstandard.org/examples/toggle_switch_optimised" : {`
`213`	`213`	`"http://sbols.org/v3#displayId" : [ {`
`214`	`214`	`"type" : "literal" ,`
`215`		`- "value" : "toggle_switch optimised"`
	`215`	`+ "value" : "toggle_switch_optimised"`
`216`	`216`	`}`
`217`	`217`	`] ,`
`218`	`218`	`"http://www.w3.org/ns/prov#wasGeneratedBy" : [ {`