Added test methodas to test get and set methods and reading back from…

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goksel · Sep 20, 2020 · 5ac5705 · 5ac5705
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diff --git a/libSBOLj3/output/entity/annotation/annotation.jsonld b/libSBOLj3/output/entity/annotation/annotation.jsonld
@@ -4,12 +4,16 @@
     "@type" : [ "sbol:TopLevel", "igem:Repository" ],
     "website" : "http://parts.igem.org/Main_Page",
     "description" : "Registry of Standard Biological Parts",
-    "displayId" : "parts.igem.org",
     "name" : "iGEM Registry"
+  }, {
+    "@id" : "http://synbiohub.org#about",
+    "@type" : [ "sbol:TopLevel", "igem:Repository" ],
+    "displayId" : "about",
+    "name" : "SynBioHub"
   }, {
     "@id" : "BBa_J23119",
     "@type" : "sbol:Component",
-    "belongsTo" : "http://parts.igem.org",
+    "belongsTo" : [ "http://parts.igem.org", "http://synbiohub.org#about" ],
     "experienceURL" : "igem:Part:BBa_J23119:Experience",
     "group" : "iGEM2006_Berkeley",
     "hasInformation" : "BBa_J23119/information1",
@@ -46,15 +50,15 @@
     "name" : "BBa_J23119_usage"
   } ],
   "@context" : {
+    "name" : {
+      "@id" : "http://sbols.org/v3#name"
+    },
     "displayId" : {
       "@id" : "http://sbols.org/v3#displayId"
     },
     "registryStar" : {
       "@id" : "http://parts.igem.org/registryStar"
     },
-    "name" : {
-      "@id" : "http://sbols.org/v3#name"
-    },
     "uses" : {
       "@id" : "http://parts.igem.org/uses"
     },

diff --git a/libSBOLj3/output/entity/annotation/annotation.nt b/libSBOLj3/output/entity/annotation/annotation.nt
@@ -1,3 +1,7 @@
+<http://synbiohub.org#about> <http://sbols.org/v3#name> "SynBioHub" .
+<http://synbiohub.org#about> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
+<http://synbiohub.org#about> <http://sbols.org/v3#displayId> "about" .
+<http://synbiohub.org#about> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://parts.igem.org/Repository> .
 <https://sbolstandard.org/examples/BBa_J23119/usage1> <http://sbols.org/v3#displayId> "usage1" .
 <https://sbolstandard.org/examples/BBa_J23119/usage1> <http://parts.igem.org/registryStar> "1" .
 <https://sbolstandard.org/examples/BBa_J23119/usage1> <http://sbols.org/v3#name> "BBa_J23119_usage" .
@@ -16,6 +20,7 @@
 <https://sbolstandard.org/examples/BBa_J23119> <http://parts.igem.org/hasInformation> <https://sbolstandard.org/examples/BBa_J23119/information1> .
 <https://sbolstandard.org/examples/BBa_J23119> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000251> .
 <https://sbolstandard.org/examples/BBa_J23119> <http://parts.igem.org/hasUsage> <https://sbolstandard.org/examples/BBa_J23119/usage1> .
+<https://sbolstandard.org/examples/BBa_J23119> <http://parts.igem.org/belongsTo> <http://synbiohub.org#about> .
 <https://sbolstandard.org/examples/BBa_J23119> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
 <https://sbolstandard.org/examples/BBa_J23119> <http://parts.igem.org/experienceURL> <http://parts.igem.org/Part:BBa_J23119:Experience> .
 <https://sbolstandard.org/examples/BBa_J23119> <http://parts.igem.org/group> "iGEM2006_Berkeley" .
@@ -30,7 +35,6 @@
 <http://parts.igem.org> <http://sbols.org/v3#description> "Registry of Standard Biological Parts" .
 <http://parts.igem.org> <http://sbols.org/v3#name> "iGEM Registry" .
 <http://parts.igem.org> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#TopLevel> .
-<http://parts.igem.org> <http://sbols.org/v3#displayId> "parts.igem.org" .
 <http://parts.igem.org> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://parts.igem.org/Repository> .
 <https://sbolstandard.org/examples/BBa_J23119/information1> <http://parts.igem.org/regulation> "//regulation/second_regulation" .
 <https://sbolstandard.org/examples/BBa_J23119/information1> <http://parts.igem.org/regulation> "//regulation/constitutive" .

diff --git a/libSBOLj3/output/entity/annotation/annotation.rdf b/libSBOLj3/output/entity/annotation/annotation.rdf
@@ -13,13 +13,7 @@
    xml:base="https://sbolstandard.org/examples/">
    <sbol:Component rdf:about="BBa_J23119">
       <igem:belongsTo>
-         <sbol:TopLevel rdf:about="http://parts.igem.org">
-            <igem:website>http://parts.igem.org/Main_Page</igem:website>
-            <sbol:description>Registry of Standard Biological Parts</sbol:description>
-            <sbol:name>iGEM Registry</sbol:name>
-            <sbol:displayId>parts.igem.org</sbol:displayId>
-            <rdf:type rdf:resource="http://parts.igem.org/Repository"/>
-         </sbol:TopLevel>
+         <sbol:TopLevel rdf:about="http://parts.igem.org"/>
       </igem:belongsTo>
       <sbol:role rdf:resource="https://identifiers.org/SO:0000167"/>
       <sbol:displayId>BBa_J23119 part</sbol:displayId>
@@ -59,7 +53,21 @@
             <igem:inStock>true</igem:inStock>
          </sbol:Identified>
       </igem:hasUsage>
+      <igem:belongsTo>
+         <sbol:TopLevel rdf:about="http://synbiohub.org#about"/>
+      </igem:belongsTo>
       <igem:experienceURL rdf:resource="http://parts.igem.org/Part:BBa_J23119:Experience"/>
       <igem:group>iGEM2006_Berkeley</igem:group>
    </sbol:Component>
+   <sbol:TopLevel rdf:about="http://parts.igem.org">
+      <igem:website>http://parts.igem.org/Main_Page</igem:website>
+      <sbol:description>Registry of Standard Biological Parts</sbol:description>
+      <sbol:name>iGEM Registry</sbol:name>
+      <rdf:type rdf:resource="http://parts.igem.org/Repository"/>
+   </sbol:TopLevel>
+   <sbol:TopLevel rdf:about="http://synbiohub.org#about">
+      <sbol:name>SynBioHub</sbol:name>
+      <sbol:displayId>about</sbol:displayId>
+      <rdf:type rdf:resource="http://parts.igem.org/Repository"/>
+   </sbol:TopLevel>
 </rdf:RDF>
diff --git a/libSBOLj3/output/entity/annotation/annotation.rj b/libSBOLj3/output/entity/annotation/annotation.rj
@@ -128,11 +128,6 @@
   }
    ,
   "http://parts.igem.org" : { 
-    "http://sbols.org/v3#displayId" : [ { 
-      "type" : "literal" ,
-      "value" : "parts.igem.org"
-    }
-     ] ,
     "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
       "type" : "uri" ,
       "value" : "http://parts.igem.org/Repository"
@@ -159,6 +154,28 @@
      ]
   }
    ,
+  "http://synbiohub.org#about" : { 
+    "http://sbols.org/v3#displayId" : [ { 
+      "type" : "literal" ,
+      "value" : "about"
+    }
+     ] ,
+    "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
+      "type" : "uri" ,
+      "value" : "http://parts.igem.org/Repository"
+    }
+    , { 
+      "type" : "uri" ,
+      "value" : "http://sbols.org/v3#TopLevel"
+    }
+     ] ,
+    "http://sbols.org/v3#name" : [ { 
+      "type" : "literal" ,
+      "value" : "SynBioHub"
+    }
+     ]
+  }
+   ,
   "https://sbolstandard.org/examples/BBa_J23119" : { 
     "http://sbols.org/v3#displayId" : [ { 
       "type" : "literal" ,
@@ -193,6 +210,10 @@
     "http://parts.igem.org/belongsTo" : [ { 
       "type" : "uri" ,
       "value" : "http://parts.igem.org"
+    }
+    , { 
+      "type" : "uri" ,
+      "value" : "http://synbiohub.org#about"
     }
      ] ,
     "http://sbols.org/v3#name" : [ { 

diff --git a/libSBOLj3/output/entity/annotation/annotation.ttl b/libSBOLj3/output/entity/annotation/annotation.ttl
@@ -10,6 +10,11 @@
 @prefix prov:  <http://www.w3.org/ns/prov#> .
 @prefix om:    <http://www.ontology-of-units-of-measure.org/resource/om-2/> .
 
+<http://synbiohub.org#about>
+        a               sbol:TopLevel , igem:Repository ;
+        sbol:displayId  "about" ;
+        sbol:name       "SynBioHub" .
+
 <BBa_J23119/usage1>  a     sbol:Identified , igem:IGEMUsage ;
         igem:inStock       "true" ;
         igem:registryStar  "1" ;
@@ -21,7 +26,7 @@
         sbol:name          "BBa_J23119_usage" .
 
 :BBa_J23119  a               sbol:Component ;
-        igem:belongsTo       <http://parts.igem.org> ;
+        igem:belongsTo       <http://parts.igem.org> , <http://synbiohub.org#about> ;
         igem:experienceURL   igem:Part:BBa_J23119:Experience ;
         igem:group           "iGEM2006_Berkeley" ;
         igem:hasInformation  <BBa_J23119/information1> ;
@@ -42,7 +47,6 @@
         a                 sbol:TopLevel , igem:Repository ;
         igem:website      "http://parts.igem.org/Main_Page" ;
         sbol:description  "Registry of Standard Biological Parts" ;
-        sbol:displayId    "parts.igem.org" ;
         sbol:name         "iGEM Registry" .
 
 <BBa_J23119/information1>

diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.jsonld
@@ -0,0 +1,24 @@
+{
+  "@id" : "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122",
+  "@type" : "sbol:Component",
+  "name" : "TetR",
+  "type" : "SBO:0000252",
+  "@context" : {
+    "name" : {
+      "@id" : "http://sbols.org/v3#name"
+    },
+    "type" : {
+      "@id" : "http://sbols.org/v3#type",
+      "@type" : "@id"
+    },
+    "@vocab" : "https://sbolstandard.org/examples/",
+    "SBO" : "https://identifiers.org/SBO:",
+    "CHEBI" : "https://identifiers.org/CHEBI:",
+    "GO" : "https://identifiers.org/GO:",
+    "sbol" : "http://sbols.org/v3#",
+    "EDAM" : "https://identifiers.org/edam:",
+    "SO" : "https://identifiers.org/SO:",
+    "prov" : "http://www.w3.org/ns/prov#",
+    "om" : "http://www.ontology-of-units-of-measure.org/resource/om-2/"
+  }
+}
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.nt
@@ -0,0 +1,3 @@
+<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://sbols.org/v3#name> "TetR" .
+<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://sbols.org/v3#type> <https://identifiers.org/SBO:0000252> .
+<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://sbols.org/v3#Component> .
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rdf
@@ -0,0 +1,17 @@
+<rdf:RDF
+    xmlns:SO="https://identifiers.org/SO:"
+    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+    xmlns:EDAM="https://identifiers.org/edam:"
+    xmlns:sbol="http://sbols.org/v3#"
+    xmlns:CHEBI="https://identifiers.org/CHEBI:"
+    xmlns:prov="http://www.w3.org/ns/prov#"
+    xmlns:SBO="https://identifiers.org/SBO:"
+    xmlns:GO="https://identifiers.org/GO:"
+    xmlns="https://sbolstandard.org/examples/"
+    xmlns:om="http://www.ontology-of-units-of-measure.org/resource/om-2/"
+   xml:base="https://sbolstandard.org/examples/">
+   <sbol:Component rdf:about="urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122">
+      <sbol:name>TetR</sbol:name>
+      <sbol:type rdf:resource="https://identifiers.org/SBO:0000252"/>
+   </sbol:Component>
+</rdf:RDF>
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.rj
@@ -0,0 +1,19 @@
+{ 
+  "urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122" : { 
+    "http://www.w3.org/1999/02/22-rdf-syntax-ns#type" : [ { 
+      "type" : "uri" ,
+      "value" : "http://sbols.org/v3#Component"
+    }
+     ] ,
+    "http://sbols.org/v3#name" : [ { 
+      "type" : "literal" ,
+      "value" : "TetR"
+    }
+     ] ,
+    "http://sbols.org/v3#type" : [ { 
+      "type" : "uri" ,
+      "value" : "https://identifiers.org/SBO:0000252"
+    }
+     ]
+  }
+}
diff --git a/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl b/libSBOLj3/output/entity/component_urn_uri/component_urn_uri.ttl
@@ -0,0 +1,15 @@
+@base          <https://sbolstandard.org/examples/> .
+@prefix :      <https://sbolstandard.org/examples/> .
+@prefix SBO:   <https://identifiers.org/SBO:> .
+@prefix CHEBI: <https://identifiers.org/CHEBI:> .
+@prefix GO:    <https://identifiers.org/GO:> .
+@prefix sbol:  <http://sbols.org/v3#> .
+@prefix EDAM:  <https://identifiers.org/edam:> .
+@prefix SO:    <https://identifiers.org/SO:> .
+@prefix prov:  <http://www.w3.org/ns/prov#> .
+@prefix om:    <http://www.ontology-of-units-of-measure.org/resource/om-2/> .
+
+<urn:uuid:d0accf73-2c60-11b2-80d9-acde48001122>
+        a          sbol:Component ;
+        sbol:name  "TetR" ;
+        sbol:type  SBO:0000252 .
diff --git a/libSBOLj3/output/measurement_entity/measurement/catalog-v001.xml b/libSBOLj3/output/measurement_entity/measurement/catalog-v001.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
     <group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base="">
-        <uri id="Automatically generated entry, Timestamp=1598819660337" name="https://sbolstandard.org/examples/" uri="measurement.rdf"/>
+        <uri id="Automatically generated entry, Timestamp=1599474822429" name="https://sbolstandard.org/examples/" uri="measurement.rdf"/>
     </group>
 </catalog>
diff --git a/libSBOLj3/output/measurement_entity/measurement/measurement.jsonld b/libSBOLj3/output/measurement_entity/measurement/measurement.jsonld
@@ -28,21 +28,24 @@
     "name" : "cubicMeter",
     "hasBase" : "meter",
     "hasExponent" : "3",
-    "label" : "cubicMeter"
+    "label" : "cubicMeter",
+    "symbol" : "m3"
   }, {
     "@id" : "kelvin",
     "@type" : "om:SingularUnit",
     "displayId" : "kelvin",
     "name" : "kelvin",
-    "label" : "kelvin"
+    "label" : "kelvin",
+    "symbol" : "kelvin"
   }, {
     "@id" : "kelvinMole",
     "@type" : "om:UnitMultiplication",
     "displayId" : "kelvinMole",
     "name" : "kelvinMole",
     "hasTerm1" : "kelvin",
     "hasTerm2" : "mole",
-    "label" : "kelvinMole"
+    "label" : "kelvinMole",
+    "symbol" : "K mol"
   }, {
     "@id" : "litre",
     "@type" : "om:SingularUnit",
@@ -54,13 +57,15 @@
     "comment" : "The litre is a unit of volume defined as 1.0e-3 cubic metre.",
     "hasFactor" : "0.001",
     "label" : "liter",
-    "longcomment" : "This is an example long comment."
+    "longcomment" : "This is an example long comment.",
+    "symbol" : "l"
   }, {
     "@id" : "meter",
     "@type" : "om:SingularUnit",
     "displayId" : "meter",
     "name" : "meter",
-    "label" : "meter"
+    "label" : "meter",
+    "symbol" : "m"
   }, {
     "@id" : "milli",
     "@type" : "om:SIPrefix",
@@ -72,29 +77,33 @@
     "comment" : "Comment for the milli prefix.",
     "hasFactor" : "0.001",
     "label" : "milli",
-    "longcomment" : "This is an example long comment for the milli prefix."
+    "longcomment" : "This is an example long comment for the milli prefix.",
+    "symbol" : "m"
   }, {
     "@id" : "millimole",
     "@type" : "om:PrefixedUnit",
     "displayId" : "millimole",
     "name" : "millimole",
     "hasPrefix" : "milli",
     "hasUnit" : "mole",
-    "label" : "millimole"
+    "label" : "millimole",
+    "symbol" : "mmol"
   }, {
     "@id" : "millimolePerLitre",
     "@type" : "om:UnitDivision",
     "displayId" : "millimolePerLitre",
     "name" : "millimolar",
     "hasDenominator" : "litre",
     "hasNumerator" : "millimole",
-    "label" : "millimolar"
+    "label" : "millimolar",
+    "symbol" : "mmol/l"
   }, {
     "@id" : "mole",
     "@type" : "om:SingularUnit",
     "displayId" : "mole",
     "name" : "mole",
-    "label" : "mole"
+    "label" : "mole",
+    "symbol" : "mol"
   } ],
   "@context" : {
     "description" : {
@@ -109,6 +118,9 @@
     "displayId" : {
       "@id" : "http://sbols.org/v3#displayId"
     },
+    "symbol" : {
+      "@id" : "http://www.ontology-of-units-of-measure.org/resource/om-2/symbol"
+    },
     "comment" : {
       "@id" : "http://www.ontology-of-units-of-measure.org/resource/om-2/comment"
     },