From 464bc8111debd37a4c60e299e83791c635518f26 Mon Sep 17 00:00:00 2001 From: Chris Myers Date: Sun, 1 Dec 2024 20:35:12 -0700 Subject: [PATCH] Fix GFF3 issue --- .../org/synbiohub/ConvertToGenBankJob.java | 6 +- ...:collectionId-:displayId-:version-gff_.xml | 689 ++---------------- ...collectionId-:displayId-:version-omex_.xml | Bin 7702 -> 7606 bytes ...collectionId-:displayId-:version-sbol_.xml | 80 +- ..._public-:collectionId-:displayId-sbol_.xml | 80 +- ...ublic-:collectionId-:displayId-sbolnr_.xml | 80 +- ...:collectionId-:displayId-:version-gff_.xml | 689 ++---------------- ...collectionId-:displayId-:version-omex_.xml | Bin 7536 -> 7583 bytes ...collectionId-:displayId-:version-sbol_.xml | 44 +- ...:userId-:collectionId-:displayId-sbol_.xml | 44 +- ...serId-:collectionId-:displayId-sbolnr_.xml | 44 +- 11 files changed, 283 insertions(+), 1473 deletions(-) diff --git a/java/src/main/java/org/synbiohub/ConvertToGenBankJob.java b/java/src/main/java/org/synbiohub/ConvertToGenBankJob.java index 779ef29f3..89f180ee9 100644 --- a/java/src/main/java/org/synbiohub/ConvertToGenBankJob.java +++ b/java/src/main/java/org/synbiohub/ConvertToGenBankJob.java @@ -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), @@ -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); diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml index 2d25d7d09..dc44833ee 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-:version-gff_.xml @@ -1,642 +1,47 @@ - - - - - BBa_R0040 - 1 - pTetR - pTet promoter - - - - - - - - - ECK120029600 - 1 - ECK120029600 - Terminator1 - - - - - - - - - BBa_E0040 - 1 - gfp - gfp coding sequence - - - - - - - - - BBa_C0012 - 1 - lacI - lacI coding sequence - - - - - - - - - part_pIKERightCassette_1 - 1 - LacI Inverter - LacI Inverter - - - - - - - - BBa_C0040 - 1 - - - - - - - - - - BBa_R0010 - 1 - - - - - - - - - - BBa_J61130 - 1 - - - - - - - - - - BBa_E0040 - 1 - - - - - - - - - - BBa_J61120 - 1 - - - - - - - - - - ECK120033736 - 1 - - - - - - - - - - anno6 - 1 - - - - - - location6 - 1 - - - 1464 - 1554 - - - - - - - - - - anno3 - 1 - - - - - - location3 - 1 - - - 69 - 729 - - - - - - - - - - anno4 - 1 - - - - - - location4 - 1 - - - 730 - 742 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 56 - 68 - - - - - - - - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 55 - - - - - - - - - - anno5 - 1 - - - - - - location5 - 1 - - - 743 - 1463 - - - - - - - - - - ECK120033736 - 1 - ECK120033736 - Terminator2 - - - - - - - - - BBa_C0040 - 1 - tetR - tetR coding sequence - - - - - - - - - part_pIKELeftCassette_1 - 1 - TetR Inverter - TetR Inverter - - - - - - - - BBa_R0040 - 1 - - - - - - - - - - ECK120029600 - 1 - - - - - - - - - - BBa_J61101 - 1 - - - - - - - - - - BBa_C0012 - 1 - - - - - - - - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 55 - - - - - - - - - - anno3 - 1 - - - - - - location3 - 1 - - - 69 - 1197 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 56 - 68 - - - - - - - - - - anno4 - 1 - - - - - - location4 - 1 - - - 1198 - 1288 - - - - - - - - - - BBa_J61130 - 1 - BBa_J61101 RBS - RBS2 - - - - - - - - - BBa_J61120 - 1 - BBa_J61101 RBS - RBS2 - - - - - - - - - BBa_J61101 - 1 - BBa_J61101 RBS - RBS1 - - - - - - - - - part_pIKE_Toggle_1 - 1 - LacI/TetR Toggle Switch - LacI/TetR Toggle Switch - - - - - - - - pIKELeftCassette_1 - 1 - - - - - - - - - - pIKERightCassette_1 - 1 - - - - - - - - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 1285 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 1286 - 2834 - - - - - - - - - - BBa_R0010 - 1 - pLacI - pLacI promoter - - - - - - - - - part_BBa_E0040 - 1 - - - atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa - - - - - part_BBa_R0010 - 1 - - - tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac - - - - - part_BBa_J61101 - 1 - - - aaagacaggacc - - - - - part_BBa_J61130 - 1 - - - aaagaaacgaca - - - - - part_BBa_C0012 - 1 - - - atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa - - - - - part_BBa_C0040 - 1 - - - atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa - - - - - part_BBa_J61120 - 1 - - - aaagacaggacc - - - - - part_ECK120033736 - 1 - - - ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa - - - - - part_BBa_R0040 - 1 - - - tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac - - - - - part_ECK120029600 - 1 - - - ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa - - - +Test Synbiohub

Error

Error: java.lang.NullPointerException + at org.sbolstandard.core2.GFF3.write(GFF3.java:66) + at org.sbolstandard.core2.SBOLWriter.write(SBOLWriter.java:229) + at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:2848) + at org.synbiohub.ConvertToGenBankJob.execute(ConvertToGenBankJob.java:25) + at org.synbiohub.Main$1.run(Main.java:30) + at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) + at java.util.concurrent.FutureTask.run(FutureTask.java:266) + at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) + at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) + at java.lang.Thread.run(Thread.java:748) + + at responseCallbacks.(anonymous function) (/synbiohub/lib/java.js:69:16) + at DestroyableTransform.javaProcess.stdout.pipe.on (/synbiohub/lib/java.js:40:3) + at DestroyableTransform.emit (events.js:182:13) + at addChunk (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_readable.js:291:12) + at readableAddChunk (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_readable.js:278:11) + at DestroyableTransform.Readable.push (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_readable.js:245:10) + at DestroyableTransform.Transform.push (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:148:32) + at DestroyableTransform.write [as _transform] (/synbiohub/node_modules/binary-split/index.js:27:14) + at DestroyableTransform.Transform._read (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:184:10) + at DestroyableTransform.Transform._write (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:172:83) + at doWrite (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:428:64) + at writeOrBuffer (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:417:5) + at DestroyableTransform.Writable.write (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:334:11) + at Socket.ondata (_stream_readable.js:666:20) + at Socket.emit (events.js:182:13) + at addChunk (_stream_readable.js:283:12)

© 2018 Newcastle University, University of Utah, and collaborators
About SynBioHub +| +View Source on Github +| +Report an Issue +
| v1.6.1 (6d694887)
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zAO$1FLcoLWMo!q=5k1p~<~mU^r4-V0Q3slwrU`WTsqvX*kygtF$L?QhP#G%LU#ZCUv{8 zeU7ZK+JO>2o7E0#RdVf@dHy_tfY*s2H_y&T0EXz@2YFAh9Xc3E<_s9Ht%$*}ns^Xn zlS@3{6}|{ijkha5V+Snu27u#bAj}XJG0_7qYq_OOT|C)vFq)lQVo?wBh5&3~0ZV@$ zq|$ZnSIo9S+`>Jbdtor}H+Epj-?@9?VXsyucY@D9z6b`E%m&^%Rz~RES3rT>uo1#9 zCnRywot=#aeI^_L3!j&a*ZZeut9DjmibrOO3)OA{R?Kh+*Z{l$fntbC+H|(63KbP~ zz@wg_@~A)8P0j)F765pQ*oy0P-Ov?`3{c$0vJ>n%rkP1xN6nZWe&MVFA4ne;VQ>VI zOkp=;$p^-rYG?i!6nnC81#D6ctU=y!p2lF_Nd<9+@FD0Bv%P~s1blcPF0__^ID8eF zd!1(_SxUgZwdkhh78fl4Hj6KmvC3bkgAU>4_3aZ6H9~0!2~|a>d0>ouau&=~w;kfY zlEY8W2`fe2mby9 zV>`WmJa`6q8cds~Z;runP`E~X0-)m3G zWJYd>7|h2v51o$D-Z6=FbknC3mTF#YmgkACNVC+2*TZ6;)j$>@fQ4gIN3M*(Y(|Db z*T$0^_iJa7c|wvQ0w(C(&%`dWK=XM{hcb*s0SWesB^bbQQTx(4Yg9)~4q)Zb!2s3n zrJIpp(eTq0fNcj{cx)P+0;vcBsWeu>r0D451?4~F&AJls4MBHEdeENu|o?1FbR$t4^K(ckBl>m=pPh3U}3EWIb95<`$X&$+KOVRQjj zSc;#@0qkH`QwY6kDi@}^00j8pGxFu zgNIJ%@Y3lF_(RFugwr-|bJ~9Rk0p3-29l#PBcIWj?cdbj;k2_8yx6%_YwWoupJvvs z`*0XAjLsq_%hcU=MXA0aaAYyqKox{(_GSX(T2%(kn412;i{$*_Gl{+PsS09XM)7o!&^wmB>i1~=`3 z@W;^s@!Nd+;ZbhI3}F=~#4-m!uc2#ZR)q`04)KDkxtE|WZM+VPZwm@J>vL=IOlb2k zbUIzJrz#%X{Iq>y#hGNTEdWPQQ2$uA$41`np3lER}`G7QY{ z2*g8ewQM^XBOsDdw7mao841T(oMN2dZS>^}pdxXA+b-P>j*4 - - - BBa_R0040 + + + BBa_C0012 1 - + - - - BBa_J61101 + + + ECK120029600 1 - + - - - BBa_C0012 + + + BBa_R0040 1 - + - - - ECK120029600 + + + BBa_J61101 1 - + @@ -231,68 +231,68 @@ - - - ECK120033736 + + + BBa_J61120 1 - + - - - BBa_R0010 + + + BBa_E0040 1 - + - - - BBa_J61130 + + + BBa_C0040 1 - + - - - BBa_J61120 + + + ECK120033736 1 - + - - - BBa_E0040 + + + BBa_R0010 1 - + - - - BBa_C0040 + + + BBa_J61130 1 - + diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml index b161bf9b7..0fe72f519 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-sbol_.xml @@ -88,46 +88,46 @@ - - - BBa_R0040 + + + BBa_C0012 1 - + - - - BBa_J61101 + + + ECK120029600 1 - + - - - BBa_C0012 + + + BBa_R0040 1 - + - - - ECK120029600 + + + BBa_J61101 1 - + @@ -231,68 +231,68 @@ - - - ECK120033736 + + + BBa_J61120 1 - + - - - BBa_R0010 + + + BBa_E0040 1 - + - - - BBa_J61130 + + + BBa_C0040 1 - + - - - BBa_J61120 + + + ECK120033736 1 - + - - - BBa_E0040 + + + BBa_R0010 1 - + - - - BBa_C0040 + + + BBa_J61130 1 - + diff --git a/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml b/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml index b161bf9b7..0fe72f519 100644 --- a/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml +++ b/tests/previousresults/get_file_public-:collectionId-:displayId-sbolnr_.xml @@ -88,46 +88,46 @@ - - - BBa_R0040 + + + BBa_C0012 1 - + - - - BBa_J61101 + + + ECK120029600 1 - + - - - BBa_C0012 + + + BBa_R0040 1 - + - - - ECK120029600 + + + BBa_J61101 1 - + @@ -231,68 +231,68 @@ - - - ECK120033736 + + + BBa_J61120 1 - + - - - BBa_R0010 + + + BBa_E0040 1 - + - - - BBa_J61130 + + + BBa_C0040 1 - + - - - BBa_J61120 + + + ECK120033736 1 - + - - - BBa_E0040 + + + BBa_R0010 1 - + - - - BBa_C0040 + + + BBa_J61130 1 - + diff --git a/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml b/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml index 810a24870..dc44833ee 100644 --- a/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml +++ b/tests/previousresults/get_file_user-:userId-:collectionId-:displayId-:version-gff_.xml @@ -1,642 +1,47 @@ - - - - - BBa_R0040 - 1 - pTetR - pTet promoter - - - - - - - - - ECK120029600 - 1 - ECK120029600 - Terminator1 - - - - - - - - - part_pIKELeftCassette_1 - 1 - TetR Inverter - TetR Inverter - - - - - - - - BBa_R0040 - 1 - - - - - - - - - - BBa_J61101 - 1 - - - - - - - - - - ECK120029600 - 1 - - - - - - - - - - BBa_C0012 - 1 - - - - - - - - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 55 - - - - - - - - - - anno3 - 1 - - - - - - location3 - 1 - - - 69 - 1197 - - - - - - - - - - anno4 - 1 - - - - - - location4 - 1 - - - 1198 - 1288 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 56 - 68 - - - - - - - - - - BBa_R0010 - 1 - pLacI - pLacI promoter - - - - - - - - - BBa_J61101 - 1 - BBa_J61101 RBS - RBS1 - - - - - - - - - BBa_C0012 - 1 - lacI - lacI coding sequence - - - - - - - - - ECK120033736 - 1 - ECK120033736 - Terminator2 - - - - - - - - - BBa_E0040 - 1 - gfp - gfp coding sequence - - - - - - - - - BBa_C0040 - 1 - tetR - tetR coding sequence - - - - - - - - - BBa_J61130 - 1 - BBa_J61101 RBS - RBS2 - - - - - - - - - part_pIKERightCassette_1 - 1 - LacI Inverter - LacI Inverter - - - - - - - - ECK120033736 - 1 - - - - - - - - - - BBa_J61130 - 1 - - - - - - - - - - BBa_E0040 - 1 - - - - - - - - - - BBa_R0010 - 1 - - - - - - - - - - BBa_J61120 - 1 - - - - - - - - - - BBa_C0040 - 1 - - - - - - - - - - anno6 - 1 - - - - - - location6 - 1 - - - 1464 - 1554 - - - - - - - - - - anno4 - 1 - - - - - - location4 - 1 - - - 730 - 742 - - - - - - - - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 55 - - - - - - - - - - anno5 - 1 - - - - - - location5 - 1 - - - 743 - 1463 - - - - - - - - - - anno3 - 1 - - - - - - location3 - 1 - - - 69 - 729 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 56 - 68 - - - - - - - - - - part_pIKE_Toggle_1 - 1 - LacI/TetR Toggle Switch - LacI/TetR Toggle Switch - - - - - - - - pIKELeftCassette_1 - 1 - - - - - - - - - - pIKERightCassette_1 - 1 - - - - - - - - - - anno2 - 1 - - - - - - location2 - 1 - - - 1286 - 2834 - - - - - - - - - - anno1 - 1 - - - - - - location1 - 1 - - - 1 - 1285 - - - - - - - - - - BBa_J61120 - 1 - BBa_J61101 RBS - RBS2 - - - - - - - - - part_BBa_E0040 - 1 - - - atgcgtaaaggagaagaacttttcactggagttgtcccaattcttgttgaattagatggtgatgttaatgggcacaaattttctgtcagtggagagggtgaaggtgatgcaacatacggaaaacttacccttaaatttatttgcactactggaaaactacctgttccatggccaacacttgtcactactttcggttatggtgttcaatgctttgcgagatacccagatcatatgaaacagcatgactttttcaagagtgccatgcccgaaggttatgtacaggaaagaactatatttttcaaagatgacgggaactacaagacacgtgctgaagtcaagtttgaaggtgatacccttgttaatagaatcgagttaaaaggtattgattttaaagaagatggaaacattcttggacacaaattggaatacaactataactcacacaatgtatacatcatggcagacaaacaaaagaatggaatcaaagttaacttcaaaattagacacaacattgaagatggaagcgttcaactagcagaccattatcaacaaaatactccaattggcgatggccctgtccttttaccagacaaccattacctgtccacacaatctgccctttcgaaagatcccaacgaaaagagagaccacatggtccttcttgagtttgtaacagctgctgggattacacatggcatggatgaactatacaaataataa - - - - - part_BBa_J61130 - 1 - - - aaagaaacgaca - - - - - part_BBa_J61101 - 1 - - - aaagacaggacc - - - - - part_BBa_J61120 - 1 - - - aaagacaggacc - - - - - part_BBa_C0040 - 1 - - - atgtccagattagataaaagtaaagtgattaacagcgcattagagctgcttaatgaggtcggaatcgaaggtttaacaacccgtaaactcgcccagaagctaggtgtagagcagcctacattgtattggcatgtaaaaaataagcgggctttgctcgacgccttagccattgagatgttagataggcaccatactcacttttgccctttagaaggggaaagctggcaagattttttacgtaataacgctaaaagttttagatgtgctttactaagtcatcgcgatggagcaaaagtacatttaggtacacggcctacagaaaaacagtatgaaactctcgaaaatcaattagcctttttatgccaacaaggtttttcactagagaatgcattatatgcactcagcgctgtggggcattttactttaggttgcgtattggaagatcaagagcatcaagtcgctaaagaagaaagggaaacacctactactgatagtatgccgccattattacgacaagctatcgaattatttgatcaccaaggtgcagagccagccttcttattcggccttgaattgatcatatgcggattagaaaaacaacttaaatgtgaaagtgggtccgctgcaaacgacgaaaactacgctttagtagcttaataa - - - - - part_BBa_R0040 - 1 - - - tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac - - - - - part_BBa_C0012 - 1 - - - atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcgcaaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgatggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcgtcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcctgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattattttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagcaaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctggcataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgccatgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgctggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgcgttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatcccgccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgctgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaaagaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcattaatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaactacgctttagtagcttaataa - - - - - part_ECK120033736 - 1 - - - ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa - - - - - part_ECK120029600 - 1 - - - ttcagccaaaaaacttaagaccgccggtcttgtccactaccttgcagtaatgcggtggacaggatcggcggttttcttttctcttctcaa - - - - - part_BBa_R0010 - 1 - - - tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac - - - +Test Synbiohub

Error

Error: java.lang.NullPointerException + at org.sbolstandard.core2.GFF3.write(GFF3.java:66) + at org.sbolstandard.core2.SBOLWriter.write(SBOLWriter.java:229) + at org.sbolstandard.core2.SBOLValidate.validate(SBOLValidate.java:2848) + at org.synbiohub.ConvertToGenBankJob.execute(ConvertToGenBankJob.java:25) + at org.synbiohub.Main$1.run(Main.java:30) + at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) + at java.util.concurrent.FutureTask.run(FutureTask.java:266) + at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) + at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) + at java.lang.Thread.run(Thread.java:748) + + at responseCallbacks.(anonymous function) (/synbiohub/lib/java.js:69:16) + at DestroyableTransform.javaProcess.stdout.pipe.on (/synbiohub/lib/java.js:40:3) + at DestroyableTransform.emit (events.js:182:13) + at addChunk (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_readable.js:291:12) + at readableAddChunk (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_readable.js:278:11) + at DestroyableTransform.Readable.push (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_readable.js:245:10) + at DestroyableTransform.Transform.push (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:148:32) + at DestroyableTransform.write [as _transform] (/synbiohub/node_modules/binary-split/index.js:27:14) + at DestroyableTransform.Transform._read (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:184:10) + at DestroyableTransform.Transform._write (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:172:83) + at doWrite (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:428:64) + at writeOrBuffer (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:417:5) + at DestroyableTransform.Writable.write (/synbiohub/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:334:11) + at Socket.ondata (_stream_readable.js:666:20) + at Socket.emit (events.js:182:13) + at addChunk (_stream_readable.js:283:12)

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| v1.6.1 (6d694887)
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