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Fix GFF3 issue
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@cjmyers
cjmyers committed Dec 2, 2024
1 parent 6d69488 commit 464bc81
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Showing 11 changed files with 283 additions and 1,473 deletions.
6 changes: 3 additions & 3 deletions java/src/main/java/org/synbiohub/ConvertToGenBankJob.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,7 @@ public void execute() throws Exception
{
ByteArrayOutputStream logOutputStream = new ByteArrayOutputStream();
ByteArrayOutputStream errorOutputStream = new ByteArrayOutputStream();

System.err.println("GFF3="+gff3Out);


SBOLDocument doc = SBOLValidate.validate(
new PrintStream(logOutputStream),
new PrintStream(errorOutputStream),
Expand All @@ -45,9 +43,11 @@ public void execute() throws Exception
false,
false,
gff3Out,
false,
"",
false,
false,
false,
false);

String log = new String(logOutputStream.toByteArray(), StandardCharsets.UTF_8);
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689 changes: 47 additions & 642 deletions tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml
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Binary file modified tests/previousresults/get_file_public-:collectionId-:displayId-:version-omex_.xml
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80 changes: 40 additions & 40 deletions tests/previousresults/get_file_public-:collectionId-:displayId-:version-sbol_.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -88,46 +88,46 @@
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_R0040/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012"/>
<sbol:displayId>BBa_C0012</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_R0040/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0012/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_J61101/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_J61101"/>
<sbol:displayId>BBa_J61101</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/ECK120029600/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/ECK120029600"/>
<sbol:displayId>ECK120029600</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61101/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/ECK120029600/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_C0012"/>
<sbol:displayId>BBa_C0012</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_R0040/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_R0040"/>
<sbol:displayId>BBa_R0040</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0012/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_R0040/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/ECK120029600/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/ECK120029600"/>
<sbol:displayId>ECK120029600</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_J61101/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/BBa_J61101"/>
<sbol:displayId>BBa_J61101</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKELeftCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/ECK120029600/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61101/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
Expand Down Expand Up @@ -231,68 +231,68 @@
<sbol:type rdf:resource="http://www.biopax.org/release/biopax-level3.owl#DnaRegion"/>
<sbol:role rdf:resource="http://identifiers.org/so/SO:0000280"/>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736"/>
<sbol:displayId>ECK120033736</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120"/>
<sbol:displayId>BBa_J61120</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/ECK120033736/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61120/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010"/>
<sbol:displayId>BBa_R0010</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040"/>
<sbol:displayId>BBa_E0040</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_R0010/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_E0040/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130"/>
<sbol:displayId>BBa_J61130</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040"/>
<sbol:displayId>BBa_C0040</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61130/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0040/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61120"/>
<sbol:displayId>BBa_J61120</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/ECK120033736"/>
<sbol:displayId>ECK120033736</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61120/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/ECK120033736/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_E0040"/>
<sbol:displayId>BBa_E0040</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_R0010"/>
<sbol:displayId>BBa_R0010</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_E0040/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_R0010/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
<sbol:component>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_C0040"/>
<sbol:displayId>BBa_C0040</sbol:displayId>
<sbol:Component rdf:about="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130/1">
<sbol:persistentIdentity rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/BBa_J61130"/>
<sbol:displayId>BBa_J61130</sbol:displayId>
<sbol:version>1</sbol:version>
<sbh:topLevel rdf:resource="http://localhost:7777/public/testid1/part_pIKERightCassette_1/1"/>
<sbh:ownedBy rdf:resource="http://localhost:7777/user/testuser"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_C0040/1"/>
<sbol:definition rdf:resource="http://localhost:7777/public/testid1/BBa_J61130/1"/>
<sbol:access rdf:resource="http://sbols.org/v2#public"/>
</sbol:Component>
</sbol:component>
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