bring in all gene and transcript data, but disallow history (or use different uniquenames) if OGS #2401

nathandunn · 2020-03-11T19:19:53Z

fixes #2372

make work for GFF3 track: in https://github.com/GMOD/Apollo/blob/develop/grails-app/services/org/bbop/apollo/FeatureService.groovy#L1293 make sure that we pull in the additional properties if there (gene_product, provenance, comments, dbxref, go, etc. etct.)

Note: have to reload once official track is set.

TEST:

fill out all the way export

test for non-coding
test for single-level
test for variant
verify that this doesn't break NCList data
test against GFF3 loaded NCList data (--type mRNA)
verify use_name
write test for use_cds by modifying CDS in a GFF3 and using it as another example
for feature_event, set organism to current organism (single script?)

history should add properly when doing actions (one at a time)
undo works and redo work, but require a reload
[~~undo and redo without reload~~ inhibit undo / redo if not a full gene
~~ delete should remove feature_events or mark as deleted / change uniquename~~
~~load attribute for everything left (need an exclude list) or is this handled automatically in properties: note that they will have to be cast to lower-case on input~~

nathandunn · 2020-03-12T19:12:28Z

test input:

{"track":"Group1.10","features":[{"location":{"fmin":450633,"fmax":450881,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"mRNA"},"name":"transcriptname1","orig_id":"GB40762-RA","seq_id":"Group1.10","source":null,"score":null,"phase":null,"owner":"ndunn@me.com","parent":{"location":{"fmin":450633,"fmax":450881,"strand":-1},"seq_id":"Group1.10","source":null,"type":{"cv":{"name":"sequence"},"name":"gene"},"score":null,"phase":null,"owner":"ndunn@me.com","symbol":"genesymbol1","go_annotations":"rank=1;aspect=BP;term=GO:0008015;db_xref=generef1:12312312;evidence=ECO:0000353;gene_product_relationship=RO:0004035;negate=true;note=[\\"gene note 1\\"];based_on=[\\"geneprefixwith1:123123\\"];last_updated=2020-03-12 11:52:04.339;date_created=2020-03-12 11:52:04.339,rank=2;aspect=MF;term=GO:0018742;db_xref=gogeneref2:22222;evidence=ECO:0000316;gene_product_relationship=RO:0002326;negate=false;note=[\\"gene note 2 a\\",\\"gene note 2\\"];based_on=[\\"gogeneprefix2:2222\\",\\"gogeneprefix2:33333\\"];last_updated=2020-03-12 11:53:54.202;date_created=2020-03-12 11:53:54.202","description":["gene comment 1","gene comment 2"],"name":"genename1","date_creation":"2020-03-12","provenance":"rank=1;field=SYNONYM;db_xref=geneprovref:1111;evidence=ECO:0000315;note=null;based_on=[\\"geneprove1:2222\\",\\"geneprove1:1111\\"];last_updated=2020-03-12 11:57:07.316;date_created=2020-03-12 11:57:07.316,rank=2;field=ATTRIBUTE;db_xref=geneprovref2:2222;evidence=ECO:0000269;note=null;based_on=[\\"geneprovwith2:333\\"];last_updated=2020-03-12 11:57:33.296;date_created=2020-03-12 11:57:33.296","alias":["genesyn1","genesyn2"],"geneattr1":"1111","gene_product":"rank=1;term=geneproduct2;db_xref=genereference2:11111;evidence=ECO:0000318;alternate=true;note=[];based_on=[\\"genewith2:11111\\"];last_updated=2020-03-12 11:55:20.712;date_created=2020-03-12 11:55:20.712,rank=2;term=geneproduc1;db_xref=genereference:1111;evidence=ECO:0000250;alternate=true;note=[];based_on=[\\"genewith1:2222\\",\\"genewith1:1111\\"];last_updated=2020-03-12 11:54:43.307;date_created=2020-03-12 11:54:43.307","uniquename":"958d7047-7342-4275-b91d-ddf68ecd3b80","date_last_modified":"2020-03-12","dbxref":["genename1dbxref:1212","genename2dbxref:2222"],"status":"under review","geneattr2":"2222"},"description":["trans comment 2 v1","trans comment 2 v 2"],"date_creation":"2020-03-12","transattr1":"1111","provenance":"rank=1;field=ATTRIBUTE;db_xref=transref1:11111;evidence=ECO:0000316;note=null;based_on=[\\"transattr1v2:2222\\",\\"transattr1:1111\\"];last_updated=2020-03-12 12:03:05.811;date_created=2020-03-12 12:03:05.811,rank=2;field=SYNONYM;db_xref=transprovref:1111;evidence=ECO:0000353;note=null;based_on=[\\"transprov1v2:2222\\",\\"transprov1:1111\\"];last_updated=2020-03-12 12:02:06.013;date_created=2020-03-12 12:02:06.013","transattr2":"2222","alias":["transyn2","transyn1"],"gene_product":"rank=1;term=trans prod 1;db_xref=transprodref1:1111;evidence=ECO:0000318;alternate=true;note=[];based_on=[\\"transprod1wtih2:2222\\",\\"transprod1with1:1111\\"];last_updated=2020-03-12 12:01:01.382;date_created=2020-03-12 12:01:01.38,rank=2;term=trans prod 2;db_xref=transref2:2222;evidence=ECO:0000315;alternate=false;note=[];based_on=[\\"trandprod2:33333\\"];last_updated=2020-03-12 12:01:28.469;date_created=2020-03-12 12:01:28.469","uniquename":"GB40762-RA","date_last_modified":"2020-03-12","dbxref":["transdbxref:22222","transdbxref2:11111"],"status":"under review","parent_id":"958d7047-7342-4275-b91d-ddf68ecd3b80","children":[{"location":{"fmin":450633,"fmax":450681,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"},"name":"c41dab40-ff33-42a5-898d-c97244f4eb4e","orig_id":"c41dab40-ff33-42a5-898d-c97244f4eb4e"},{"location":{"fmin":450788,"fmax":450881,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"},"name":"f862fe8b-ec8a-4188-a697-4269a5afd476","orig_id":"f862fe8b-ec8a-4188-a697-4269a5afd476"},{"location":{"fmin":450633,"fmax":450881,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"CDS"}}]}],"operation":"add_transcript","clientToken":"14918555161196787143"}

…a location (eg. genes) and not removing things from transcripts properly

nathandunn · 2020-03-12T21:23:57Z

notes:

                 name                 |        class         
--------------------------------------+----------------------
 genename1-00001                      | org.bbop.apollo.MRNA
 c41dab40-ff33-42a5-898d-c97244f4eb4e | org.bbop.apollo.Exon
 f862fe8b-ec8a-4188-a697-4269a5afd476 | org.bbop.apollo.Exon
 0395c20f-7f6b-49ef-854e-d34d746522cd | org.bbop.apollo.CDS
(4 rows)

apollo-none=# select this_.name,this_.class from feature this_ inner join feature_location featureloc1_ on this_.id=featureloc1_.feature_id inner join sequence sequence_a2_ on featureloc1_.sequence_id=sequence_a2_.id where ((sequence_a2_.organism_id=39969));

If I extended this to MRNA and other transcript types, it returns mRNA as the top-level feature (not what we want).

nathandunn · 2020-03-12T21:40:09Z

This was the original one:

select s.name, f.id,f.name,f.class from feature f join feature_location fl on fl.feature_id = f.id join Sequence s on s.id = fl.sequence_id where class like '%Gene' ;
   name    |  id   |   name    |        class         
-----------+-------+-----------+----------------------
 Group1.10 | 22137 | genename1 | org.bbop.apollo.Gene

vs

=# select f.id,f.name,f.class from feature f where class like '%Gene' ;
  id   |             name             |        class         
-------+------------------------------+----------------------
  7259 | Apple3                       | org.bbop.apollo.Gene
  7799 | mRNA8198a                    | org.bbop.apollo.Gene
  7786 | mRNA8198                     | org.bbop.apollo.Gene
  8124 | Group11.18-00001aasdfasdasdf | org.bbop.apollo.Gene
 20477 | GB55593-RA                   | org.bbop.apollo.Gene
 22137 | genename1                    | org.bbop.apollo.Gene
  8433 | GB55426-RAa                  | org.bbop.apollo.Gene
  8369 | GB42840-RAasdasdfa           | org.bbop.apollo.Gene
 14211 | GB45005-RA                   | org.bbop.apollo.Gene
  8011 | Group11.18-00001asdf         | org.bbop.apollo.Gene
  7769 | mRNA8197a                    | org.bbop.apollo.Gene
  7756 | mRNA8197                     | org.bbop.apollo.Gene
  8398 | GB50198-RAasdfasdf           | org.bbop.apollo.Gene
  8542 | GB55428-RA                   | org.bbop.apollo.Gene
 20522 | GB55595-RA                   | org.bbop.apollo.Gene
 20442 | GB42659-RA                   | org.bbop.apollo.Gene
 20571 | GB55427-RA                   | org.bbop.apollo.Gene
 20782 | Apple3                       | org.bbop.apollo.Gene

Which is weird as this doesn't show up:

even though the GFF3 is legal:

##gff-version 3
##sequence-region Group1.10 1 1405242
Group1.10	.	gene	450634	450881	.	-	.	owner=ndunn@me.com;symbol=genesymbol1;Alias=genesyn1,genesyn2;Note=gene comment 1,gene comment 2;geneattr1=1111;description=gene description 1;ID=958d7047-7342-4275-b91d-ddf68ecd3b80;date_last_modified=2020-03-12;Name=genename1;status=under review;geneattr2=2222;date_creation=2020-03-12
Group1.10	.	mRNA	450634	450881	.	-	.	owner=ndunn@me.com;Parent=958d7047-7342-4275-b91d-ddf68ecd3b80;description=["trans comment 2 v1"%2C"trans comment 2 v 2"];ID=GB40762-RA;orig_id=GB40762-RA;date_last_modified=2020-03-12;Name=genename1-00001;status=under review;date_creation=2020-03-12
Group1.10	.	exon	450634	450681	.	-	.	Parent=GB40762-RA;ID=2cec439d-d950-45fc-91db-1ea259fffc68;Name=c41dab40-ff33-42a5-898d-c97244f4eb4e
Group1.10	.	CDS	450789	450881	.	-	0	Parent=GB40762-RA;ID=e6576f93-9091-4dd6-9590-cc6a3e55e325;Name=e6576f93-9091-4dd6-9590-cc6a3e55e325
Group1.10	.	CDS	450634	450681	.	-	0	Parent=GB40762-RA;ID=e6576f93-9091-4dd6-9590-cc6a3e55e325;Name=e6576f93-9091-4dd6-9590-cc6a3e55e325
Group1.10	.	exon	450789	450881	.	-	.	Parent=GB40762-RA;ID=2aa426c7-a391-4589-a574-4826cae4392e;Name=f862fe8b-ec8a-4188-a697-4269a5afd476
###

nathandunn · 2020-03-12T21:44:57Z

Need to confirm that the gene location is not sent or otherwise created on upload (which I think is the case).

nathandunn · 2020-03-12T21:55:01Z

Sent this info:

{"track":"Group1.10","features":[{"location":{"fmin":450633,"fmax":450881,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"mRNA"},"name":"transcriptname1","orig_id":"GB40762-RA","seq_id":"Group1.10","source":null,"score":null,"phase":null,"owner":"ndunn@me.com","parent":{"location":{"fmin":450633,"fmax":450881,"strand":-1},"seq_id":"Group1.10","source":null,"type":{"cv":{"name":"sequence"},"name":"gene"},"score":null,"phase":null,"owner":"ndunn@me.com","symbol":"genesymbol1","go_annotations":"rank=1;aspect=BP;term=GO:0008015;db_xref=generef1:12312312;evidence=ECO:0000353;gene_product_relationship=RO:0004035;negate=true;note=['gene note 1'];based_on=['geneprefixwith1:123123'];last_updated=2020-03-12 11:52:04.339;date_created=2020-03-12 11:52:04.339,rank=2;aspect=MF;term=GO:0018742;db_xref=gogeneref2:22222;evidence=ECO:0000316;gene_product_relationship=RO:0002326;negate=false;note=['gene note 2 a','gene note 2'];based_on=['gogeneprefix2:2222','gogeneprefix2:33333'];last_updated=2020-03-12 11:53:54.202;date_created=2020-03-12 11:53:54.202","description":["gene comment 1","gene comment 2"],"name":"genename1","date_creation":"2020-03-12","provenance":"rank=1;field=SYNONYM;db_xref=geneprovref:1111;evidence=ECO:0000315;note=null;based_on=['geneprove1:2222','geneprove1:1111'];last_updated=2020-03-12 11:57:07.316;date_created=2020-03-12 11:57:07.316,rank=2;field=ATTRIBUTE;db_xref=geneprovref2:2222;evidence=ECO:0000269;note=null;based_on=['geneprovwith2:333'];last_updated=2020-03-12 11:57:33.296;date_created=2020-03-12 11:57:33.296","alias":["genesyn1","genesyn2"],"geneattr1":"1111","gene_product":"rank=1;term=geneproduct2;db_xref=genereference2:11111;evidence=ECO:0000318;alternate=true;note=[];based_on=['genewith2:11111'];last_updated=2020-03-12 11:55:20.712;date_created=2020-03-12 11:55:20.712,rank=2;term=geneproduc1;db_xref=genereference:1111;evidence=ECO:0000250;alternate=true;note=[];based_on=['genewith1:2222','genewith1:1111'];last_updated=2020-03-12 11:54:43.307;date_created=2020-03-12 11:54:43.307","uniquename":"958d7047-7342-4275-b91d-ddf68ecd3b80","date_last_modified":"2020-03-12","dbxref":["genename1dbxref:1212","genename2dbxref:2222"],"status":"under review","geneattr2":"2222"},"description":["trans comment 2 v1","trans comment 2 v 2"],"date_creation":"2020-03-12","transattr1":"1111","provenance":"rank=1;field=ATTRIBUTE;db_xref=transref1:11111;evidence=ECO:0000316;note=null;based_on=['transattr1v2:2222','transattr1:1111'];last_updated=2020-03-12 12:03:05.811;date_created=2020-03-12 12:03:05.811,rank=2;field=SYNONYM;db_xref=transprovref:1111;evidence=ECO:0000353;note=null;based_on=['transprov1v2:2222','transprov1:1111'];last_updated=2020-03-12 12:02:06.013;date_created=2020-03-12 12:02:06.013","transattr2":"2222","alias":["transyn2","transyn1"],"gene_product":"rank=1;term=trans prod 1;db_xref=transprodref1:1111;evidence=ECO:0000318;alternate=true;note=[];based_on=['transprod1wtih2:2222','transprod1with1:1111'];last_updated=2020-03-12 12:01:01.382;date_created=2020-03-12 12:01:01.38,rank=2;term=trans prod 2;db_xref=transref2:2222;evidence=ECO:0000315;alternate=false;note=[];based_on=['trandprod2:33333'];last_updated=2020-03-12 12:01:28.469;date_created=2020-03-12 12:01:28.469","uniquename":"GB40762-RA","date_last_modified":"2020-03-12","dbxref":["transdbxref:22222","transdbxref2:11111"],"status":"under review","parent_id":"958d7047-7342-4275-b91d-ddf68ecd3b80","children":[{"location":{"fmin":450788,"fmax":450881,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"},"name":"f862fe8b-ec8a-4188-a697-4269a5afd476","orig_id":"f862fe8b-ec8a-4188-a697-4269a5afd476"},{"location":{"fmin":450633,"fmax":450681,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"exon"},"name":"c41dab40-ff33-42a5-898d-c97244f4eb4e","orig_id":"c41dab40-ff33-42a5-898d-c97244f4eb4e"},{"location":{"fmin":450633,"fmax":450881,"strand":-1},"type":{"cv":{"name":"sequence"},"name":"CDS"}}]}],"operation":"add_transcript","clientToken":"14918555161196787143"}

Received:

{"features":[{"owner":"ndunn@me.com","parent_name":"genename1","uniquename":"GB40762-RA","description":"[\"trans comment 2 v1\",\"trans comment 2 v 2\"]","type":{"cv":{"name":"sequence"},"name":"mRNA"},"parent_type":{"cv":{"name":"sequence"},"name":"gene"},"date_creation":1584049789873,"sequence":"Group1.10","children":[{"owner":"None","parent_name":"genename1-00001","uniquename":"9e3fe24b-75c0-4936-bc17-581e2362a720","type":{"cv":{"name":"sequence"},"name":"CDS"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1584049789862,"sequence":"Group1.10","parent_id":"GB40762-RA","name":"9e3fe24b-75c0-4936-bc17-581e2362a720","location":{"strand":-1,"id":51296,"fmin":450633,"fmax":450881},"id":51295,"properties":[],"date_last_modified":1584049790375},{"owner":"None","parent_name":"genename1-00001","uniquename":"0d82ff59-e67c-4bf2-b3aa-f010fea2a43d","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1584049789817,"sequence":"Group1.10","parent_id":"GB40762-RA","name":"c41dab40-ff33-42a5-898d-c97244f4eb4e","location":{"strand":-1,"id":51292,"fmin":450633,"fmax":450681},"id":51291,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"c41dab40-ff33-42a5-898d-c97244f4eb4e"}],"date_last_modified":1584049789856},{"owner":"None","parent_name":"genename1-00001","uniquename":"ab8363e6-bb84-4ae3-9b15-e152f9607539","type":{"cv":{"name":"sequence"},"name":"exon"},"parent_type":{"cv":{"name":"sequence"},"name":"mRNA"},"date_creation":1584049789752,"sequence":"Group1.10","parent_id":"GB40762-RA","name":"f862fe8b-ec8a-4188-a697-4269a5afd476","location":{"strand":-1,"id":51288,"fmin":450788,"fmax":450881},"id":51287,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"f862fe8b-ec8a-4188-a697-4269a5afd476"}],"date_last_modified":1584049789812}],"parent_id":"958d7047-7342-4275-b91d-ddf68ecd3b80","name":"genename1-00001","location":{"strand":-1,"id":51286,"fmin":450633,"fmax":450881},"id":51285,"properties":[{"name":"orig_id","type":{"cv":{"name":"feature_property"}},"value":"GB40762-RA"}],"date_last_modified":1584049790488,"status":"under review"}],"sequenceAlterationEvent":false,"operation":"ADD"}

GFF3:

##gff-version 3
##sequence-region Group1.10 1 1405242
Group1.10	.	gene	450634	450881	.	-	.	owner=ndunn@me.com;symbol=genesymbol1;Alias=genesyn1,genesyn2;Note=gene comment 1,gene comment 2;geneattr1=1111;description=gene description 1;ID=958d7047-7342-4275-b91d-ddf68ecd3b80;date_last_modified=2020-03-12;Name=genename1;status=under review;geneattr2=2222;date_creation=2020-03-12
Group1.10	.	mRNA	450634	450881	.	-	.	owner=ndunn@me.com;Parent=958d7047-7342-4275-b91d-ddf68ecd3b80;description=["trans comment 2 v1"%2C"trans comment 2 v 2"];ID=GB40762-RA;orig_id=GB40762-RA;date_last_modified=2020-03-12;Name=genename1-00001;status=under review;date_creation=2020-03-12
Group1.10	.	exon	450634	450681	.	-	.	Parent=GB40762-RA;ID=2cec439d-d950-45fc-91db-1ea259fffc68;Name=c41dab40-ff33-42a5-898d-c97244f4eb4e
Group1.10	.	CDS	450789	450881	.	-	0	Parent=GB40762-RA;ID=e6576f93-9091-4dd6-9590-cc6a3e55e325;Name=e6576f93-9091-4dd6-9590-cc6a3e55e325
Group1.10	.	CDS	450634	450681	.	-	0	Parent=GB40762-RA;ID=e6576f93-9091-4dd6-9590-cc6a3e55e325;Name=e6576f93-9091-4dd6-9590-cc6a3e55e325
Group1.10	.	exon	450789	450881	.	-	.	Parent=GB40762-RA;ID=2aa426c7-a391-4589-a574-4826cae4392e;Name=f862fe8b-ec8a-4188-a697-4269a5afd476
###

nathandunn · 2020-03-12T22:32:50Z

When deleting the same GFF3 non-official from here it works:

##gff-version 3
##sequence-region Group1.10 1 1405242
Group1.10	.	gene	450634	450881	.	-	.	owner=ndunn@me.com;ID=d47490d8-3bae-4bc8-9993-3bbea99b0887;date_last_modified=2020-03-12;Name=transcriptname1;date_creation=2020-03-12
Group1.10	.	mRNA	450634	450881	.	-	.	owner=ndunn@me.com;Parent=d47490d8-3bae-4bc8-9993-3bbea99b0887;ID=5e8e5a1d-cbd9-4b82-ad37-7cb90b7fbc13;orig_id=GB40762-RA;date_last_modified=2020-03-12;Name=transcriptname1-00001;date_creation=2020-03-12
Group1.10	.	exon	450634	450681	.	-	.	Parent=5e8e5a1d-cbd9-4b82-ad37-7cb90b7fbc13;ID=ee3d76d8-ddbd-4fab-8a52-4e5e92ac55f5;Name=ee3d76d8-ddbd-4fab-8a52-4e5e92ac55f5
Group1.10	.	exon	450789	450881	.	-	.	Parent=5e8e5a1d-cbd9-4b82-ad37-7cb90b7fbc13;ID=661971f6-4e22-4c17-9629-8ebf28ca7786;Name=661971f6-4e22-4c17-9629-8ebf28ca7786
Group1.10	.	CDS	450789	450881	.	-	0	Parent=5e8e5a1d-cbd9-4b82-ad37-7cb90b7fbc13;ID=537de717-7f55-44cb-80d5-f0f2177499c7;Name=537de717-7f55-44cb-80d5-f0f2177499c7
Group1.10	.	CDS	450634	450681	.	-	0	Parent=5e8e5a1d-cbd9-4b82-ad37-7cb90b7fbc13;ID=537de717-7f55-44cb-80d5-f0f2177499c7;Name=537de717-7f55-44cb-80d5-f0f2177499c7
###

when we add it as an official track:

##gff-version 3
##sequence-region Group1.10 1 1405242
Group1.10	.	gene	450634	450881	.	-	.	owner=ndunn@me.com;symbol=genesymbol1;Alias=genesyn1,genesyn2;Note=gene comment 1,gene comment 2;geneattr1=1111;description=gene description 1;ID=958d7047-7342-4275-b91d-ddf68ecd3b80;date_last_modified=2020-03-12;Name=genename1;status=under review;geneattr2=2222;date_creation=2020-03-12
Group1.10	.	mRNA	450634	450881	.	-	.	owner=ndunn@me.com;Parent=958d7047-7342-4275-b91d-ddf68ecd3b80;description=["trans comment 2 v1"%2C"trans comment 2 v 2"];ID=GB40762-RA;orig_id=GB40762-RA;date_last_modified=2020-03-12;Name=genename1-00001;status=under review;date_creation=2020-03-12
Group1.10	.	exon	450634	450681	.	-	.	Parent=GB40762-RA;ID=2cec439d-d950-45fc-91db-1ea259fffc68;Name=c41dab40-ff33-42a5-898d-c97244f4eb4e
Group1.10	.	CDS	450789	450881	.	-	0	Parent=GB40762-RA;ID=e6576f93-9091-4dd6-9590-cc6a3e55e325;Name=e6576f93-9091-4dd6-9590-cc6a3e55e325
Group1.10	.	CDS	450634	450681	.	-	0	Parent=GB40762-RA;ID=e6576f93-9091-4dd6-9590-cc6a3e55e325;Name=e6576f93-9091-4dd6-9590-cc6a3e55e325
Group1.10	.	exon	450789	450881	.	-	.	Parent=GB40762-RA;ID=2aa426c7-a391-4589-a574-4826cae4392e;Name=f862fe8b-ec8a-4188-a697-4269a5afd476
###

I get the error:

Hibernate operation: could not execute statement; SQL [n/a]; ERROR: update or delete on table "feature" violates foreign key constraint "fk_72kmd92rdc6gne0nrh026o1j0" on table "feature_relationship" Detail: Key (id)=(22137) is still referenced from table "feature_relationship".; nested exception is org.postgresql.util.PSQLException: ERROR: update or delete on table "feature" violates foreign key constraint "fk_72kmd92rdc6gne0nrh026o1j0" on table "feature_relationship" Detail: Key (id)=(22137) is still referenced from table "feature_relationship".

which makes no sense as the database structure looks identical:

select f.name, f.class, ch.name,ch.class,  fr.* from feature f join feature_relationship fr on fr.parent_feature_id = f.id join feature_location fl on fl.feature_id=f.id join sequence s on s.id=fl.sequence_id join organism o on o.id=s.organism_id join feature ch on fr.child_feature_id=ch.id  where o.common_name='bee9' ;
apollo-none=# select f.name, f.class, ch.name,ch.class,  fr.* from feature f join feature_relationship fr on fr.parent_feature_id = f.id join feature_location fl on fl.feature_id=f.id join sequence s on s.id=fl.sequence_id join organism o on o.id=s.organism_id join feature ch on fr.child_feature_id=ch.id  where o.common_name='bee9' ;

      name       |        class         |                 name                 |        class         |  id   | version | child_feature_id | parent_feature_id | rank | value 
-----------------+----------------------+--------------------------------------+----------------------+-------+---------+------------------+-------------------+------+-------
 genename1-00001 | org.bbop.apollo.MRNA | c41dab40-ff33-42a5-898d-c97244f4eb4e | org.bbop.apollo.Exon | 68326 |       0 |            68323 |             68321 |    0 | 
 genename1-00001 | org.bbop.apollo.MRNA | f862fe8b-ec8a-4188-a697-4269a5afd476 | org.bbop.apollo.Exon | 68330 |       0 |            68327 |             68321 |    0 | 
 genename1-00001 | org.bbop.apollo.MRNA | 0dc1741d-3660-42cb-ae72-f5f53cf2d6d2 | org.bbop.apollo.CDS  | 68333 |       0 |            68331 |             68321 |    0 | 
 genename1       | org.bbop.apollo.Gene | genename1-00001                      | org.bbop.apollo.MRNA | 68336 |       0 |            68321 |             68319 |    0 | 
(4 rows)

However, if we are replicating unique names.

When loaded fresh however, its not a problem, so something else is going on during the deletion process.

nathandunn · 2020-03-13T00:20:13Z

De novo features as official tracks are actually okay.

Removing gene_products, provenance, etc. doesn't seem to have an effect.

Deleting status gives another result. Possibly as its not deleting an orphan (as we share the same, I think).

Something is wrong with the uniqueNames . . not sure.

nathandunn · 2020-04-15T18:32:58Z

Original Test GFF3:

##gff-version 3
##sequence-region Group11.18 1 4736299
Group11.18	.	gene	2583914	2593823	.	+	.	owner=admin@local.host;symbol=genesymbol;go_annotations=rank%3D1%3Baspect%3DMF%3Bterm%3DGO:0051018%3Bdb_xref%3Dgenegoreference:asdfasf1%3Bevidence%3DECO:0000315%3Bgene_product_relationship%3DRO:0002327%3Bnegate%3Dtrue%3Bnote%3D["genegonote"]%3Bbased_on%3D["genegowith:123213"]%3Blast_updated%3D2020-04-15 11:31:12.753%3Bdate_created%3D2020-04-15 11:31:12.753;description=genedescriptioin;geneattrributekey=asdfasdf;Name=genename;date_creation=2020-04-15;provenance=rank%3D1%3Bfield%3DDESCRIPTION%3Bdb_xref%3Dgeneprovenanceref:asdfasdf%3Bevidence%3DECO:0000353%3Bnote%3D["geneprovenancenote"]%3Bbased_on%3D["geneprovenanceiwth:12313"]%3Blast_updated%3D2020-04-15 11:32:18.564%3Bdate_created%3D2020-04-15 11:32:18.564;Alias=genealias;Note=genecomment;gene_product=rank%3D1%3Bterm%3Dgenegeneproduct%3Bdb_xref%3Dgenegeneproductreference:123132%3Bevidence%3DECO:0000316%3Balternate%3Dfalse%3Bnote%3D["asdfasdfafs"]%3Bbased_on%3D["genegeneproductwith:asdf"]%3Blast_updated%3D2020-04-15 11:31:46.603%3Bdate_created%3D2020-04-15 11:31:46.603;ID=1424751f-1276-41da-9d34-350499e940c6;date_last_modified=2020-04-15;Dbxref=genedbxref:asdfasdf
Group11.18	.	mRNA	2583914	2593823	.	+	.	owner=admin@local.host;Parent=1424751f-1276-41da-9d34-350499e940c6;go_annotations=rank%3D1%3Baspect%3DMF%3Bterm%3DGO:0140399%3Bdb_xref%3Dtranscriptgoref:123123%3Bevidence%3DECO:0000315%3Bgene_product_relationship%3DRO:0002326%3Bnegate%3Dfalse%3Bnote%3D["transcriptgonote"]%3Bbased_on%3D["transcriptgo:1231313"]%3Blast_updated%3D2020-04-15 11:27:43.295%3Bdate_created%3D2020-04-15 11:27:43.295;description=transcriptdescription;orig_id=GB45157-RA;Name=transcriptname;date_creation=2020-04-15;provenance=rank%3D1%3Bfield%3DNAME%3Bdb_xref%3Dtranscriptprovenanceref:1231321%3Bevidence%3DECO:0000316%3Bnote%3D["transcriptprovenancenote"]%3Bbased_on%3D["transcriptnamewithprov:123132"]%3Blast_updated%3D2020-04-15 11:29:54.618%3Bdate_created%3D2020-04-15 11:29:54.618;transcriptattribtute=asdfasdf;Alias=transcriptalias;Note=transcriptcomment;gene_product=rank%3D1%3Bterm%3Dtranscriptgeneproductnote%3Bdb_xref%3Dtranscriptgeneproductreference:123131%3Bevidence%3DECO:0000319%3Balternate%3Dtrue%3Bnote%3D["transcriptgeneproductnote"]%3Bbased_on%3D["transcriptwithgeneproductprefix:123123"]%3Blast_updated%3D2020-04-15 11:28:30.814%3Bdate_created%3D2020-04-15 11:28:30.814;ID=GB45157-RA;date_last_modified=2020-04-15;Dbxref=transcriptdbxref:12312312
Group11.18	.	exon	2583914	2584376	.	+	.	Parent=GB45157-RA;ID=b48e9c2e-76b9-4462-b786-347e3d931f64;Name=b48e9c2e-76b9-4462-b786-347e3d931f64
Group11.18	.	exon	2591333	2593823	.	+	.	Parent=GB45157-RA;ID=7d791cf8-1fb2-4da9-8423-f3b4f0183b28;Name=7d791cf8-1fb2-4da9-8423-f3b4f0183b28
Group11.18	.	exon	2584843	2585034	.	+	.	Parent=GB45157-RA;ID=33d284d0-5f50-4c4c-be55-49ab6c92c29a;Name=33d284d0-5f50-4c4c-be55-49ab6c92c29a
Group11.18	.	CDS	2584185	2584376	.	+	0	Parent=GB45157-RA;ID=01831f8e-c457-4733-80dc-7f4f07fc2277;Name=01831f8e-c457-4733-80dc-7f4f07fc2277
Group11.18	.	CDS	2584843	2585034	.	+	0	Parent=GB45157-RA;ID=01831f8e-c457-4733-80dc-7f4f07fc2277;Name=01831f8e-c457-4733-80dc-7f4f07fc2277
Group11.18	.	CDS	2591333	2591707	.	+	0	Parent=GB45157-RA;ID=01831f8e-c457-4733-80dc-7f4f07fc2277;Name=01831f8e-c457-4733-80dc-7f4f07fc2277
###

nathandunn · 2020-04-15T18:59:47Z

Note that the mRNA is the same, but the gene is missing from the imported evidence:

Group11.18	.	mRNA	2583914	2593823	.	+	.	owner=admin@local.host;go_annotations=rank%3D1%3Baspect%3DMF%3Bterm%3DGO:0140399%3Bdb_xref%3Dtranscriptgoref:123123%3Bevidence%3DECO:0000315%3Bgene_product_relationship%3DRO:0002326%3Bnegate%3Dfalse%3Bnote%3D["transcriptgonote"]%3Bbased_on%3D["transcriptgo:1231313"]%3Blast_updated%3D2020-04-15 11:27:43.295%3Bdate_created%3D2020-04-15 11:27:43.295;description=transcriptdescription;orig_id=GB45157-RA;Name=transcriptname;date_creation=2020-04-15;provenance=rank%3D1%3Bfield%3DNAME%3Bdb_xref%3Dtranscriptprovenanceref:1231321%3Bevidence%3DECO:0000316%3Bnote%3D["transcriptprovenancenote"]%3Bbased_on%3D["transcriptnamewithprov:123132"]%3Blast_updated%3D2020-04-15 11:29:54.618%3Bdate_created%3D2020-04-15 11:29:54.618;transcriptattribtute=asdfasdf;Alias=transcriptalias;Note=transcriptcomment;gene_product=rank%3D1%3Bterm%3Dtranscriptgeneproductnote%3Bdb_xref%3Dtranscriptgeneproductreference:123131%3Bevidence%3DECO:0000319%3Balternate%3Dtrue%3Bnote%3D["transcriptgeneproductnote"]%3Bbased_on%3D["transcriptwithgeneproductprefix:123123"]%3Blast_updated%3D2020-04-15 11:28:30.814%3Bdate_created%3D2020-04-15 11:28:30.814;ID=GB45157-RA;date_last_modified=2020-04-15;Dbxref=transcriptdbxref:12312312
Group11.18	.	exon	2583914	2584376	.	+	.	Parent=GB45157-RA;ID=b48e9c2e-76b9-4462-b786-347e3d931f64;Name=b48e9c2e-76b9-4462-b786-347e3d931f64
Group11.18	.	exon	2591333	2593823	.	+	.	Parent=GB45157-RA;ID=7d791cf8-1fb2-4da9-8423-f3b4f0183b28;Name=7d791cf8-1fb2-4da9-8423-f3b4f0183b28
Group11.18	.	exon	2584843	2585034	.	+	.	Parent=GB45157-RA;ID=33d284d0-5f50-4c4c-be55-49ab6c92c29a;Name=33d284d0-5f50-4c4c-be55-49ab6c92c29a
Group11.18	.	CDS	2584185	2584376	.	+	0	Parent=GB45157-RA;ID=01831f8e-c457-4733-80dc-7f4f07fc2277;Name=01831f8e-c457-4733-80dc-7f4f07fc2277
Group11.18	.	CDS	2584843	2585034	.	+	0	Parent=GB45157-RA;ID=01831f8e-c457-4733-80dc-7f4f07fc2277;Name=01831f8e-c457-4733-80dc-7f4f07fc2277
Group11.18	.	CDS	2591333	2591707	.	+	0	Parent=GB45157-RA;ID=01831f8e-c457-4733-80dc-7f4f07fc2277;Name=01831f8e-c457-4733-80dc-7f4f07fc2277

nathandunn · 2020-04-15T20:12:23Z

round-trip GFF3 is:

##gff-version 3
##sequence-region Group11.18 1 4736299
Group11.18	.	gene	2583914	2593823	.	+	.	owner=admin@local.host;symbol=genesymbol;go_annotations=rank%3D1%3Baspect%3DMF%3Bterm%3DGO:0051018%3Bdb_xref%3Dgenegoreference:asdfasf1%3Bevidence%3DECO:0000315%3Bgene_product_relationship%3DRO:0002327%3Bnegate%3Dtrue%3Bnote%3D['genegonote']%3Bbased_on%3D['genegowith:123213']%3Blast_updated%3D2020-04-15 13:11:23.753%3Bdate_created%3D2020-04-15 13:11:23.753;description=genedescriptioin;Name=genename;date_creation=2020-04-15;provenance=rank%3D1%3Bfield%3DDESCRIPTION%3Bdb_xref%3Dgeneprovenanceref:asdfasdf%3Bevidence%3DECO:0000353%3Bnote%3D['geneprovenancenote']%3Bbased_on%3D['geneprovenanceiwth:12313']%3Blast_updated%3D2020-04-15 13:11:23.747%3Bdate_created%3D2020-04-15 13:11:23.747;Alias=genealias;Note=genecomment;gene_product=rank%3D1%3Bterm%3Dgenegeneproduct%3Bdb_xref%3Dgenegeneproductreference:123132%3Bevidence%3DECO:0000316%3Balternate%3Dtrue%3Bnote%3D['asdfasdfafs']%3Bbased_on%3D['genegeneproductwith:asdf']%3Blast_updated%3D2020-04-15 13:11:23.742%3Bdate_created%3D2020-04-15 13:11:23.742;ID=1424751f-1276-41da-9d34-350499e940c6;date_last_modified=2020-04-15;Dbxref=genedbxref:asdfasdf
Group11.18	.	mRNA	2583914	2593823	.	+	.	owner=admin@local.host;Parent=1424751f-1276-41da-9d34-350499e940c6;go_annotations=rank%3D1%3Baspect%3DMF%3Bterm%3DGO:0140399%3Bdb_xref%3Dtranscriptgoref:123123%3Bevidence%3DECO:0000315%3Bgene_product_relationship%3DRO:0002326%3Bnegate%3Dtrue%3Bnote%3D['transcriptgonote']%3Bbased_on%3D['transcriptgo:1231313']%3Blast_updated%3D2020-04-15 13:11:23.7%3Bdate_created%3D2020-04-15 13:11:23.7;description=transcriptdescription;orig_id=GB45157-RA;Name=transcriptname;date_creation=2020-04-15;provenance=rank%3D1%3Bfield%3DNAME%3Bdb_xref%3Dtranscriptprovenanceref:1231321%3Bevidence%3DECO:0000316%3Bnote%3D['transcriptprovenancenote']%3Bbased_on%3D['transcriptnamewithprov:123132']%3Blast_updated%3D2020-04-15 13:11:23.534%3Bdate_created%3D2020-04-15 13:11:23.534;Alias=transcriptalias;Note=transcriptcomment;gene_product=rank%3D1%3Bterm%3Dtranscriptgeneproductnote%3Bdb_xref%3Dtranscriptgeneproductreference:123131%3Bevidence%3DECO:0000319%3Balternate%3Dtrue%3Bnote%3D['transcriptgeneproductnote']%3Bbased_on%3D['transcriptwithgeneproductprefix:123123']%3Blast_updated%3D2020-04-15 13:11:23.42%3Bdate_created%3D2020-04-15 13:11:23.42;ID=GB45157-RA;date_last_modified=2020-04-15;Dbxref=transcriptdbxref:12312312
Group11.18	.	exon	2583914	2584376	.	+	.	Parent=GB45157-RA;ID=09e598c5-1a2c-480f-93da-2ee4a363a371;Name=b48e9c2e-76b9-4462-b786-347e3d931f64
Group11.18	.	CDS	2584185	2584376	.	+	0	Parent=GB45157-RA;ID=46c8c230-abc2-4757-886b-392f5b29a46f;Name=46c8c230-abc2-4757-886b-392f5b29a46f
Group11.18	.	CDS	2584843	2585034	.	+	0	Parent=GB45157-RA;ID=46c8c230-abc2-4757-886b-392f5b29a46f;Name=46c8c230-abc2-4757-886b-392f5b29a46f
Group11.18	.	CDS	2591333	2591707	.	+	0	Parent=GB45157-RA;ID=46c8c230-abc2-4757-886b-392f5b29a46f;Name=46c8c230-abc2-4757-886b-392f5b29a46f
Group11.18	.	exon	2591333	2593823	.	+	.	Parent=GB45157-RA;ID=8143a0c0-3162-4082-9cd4-d3ce59797c1c;Name=7d791cf8-1fb2-4da9-8423-f3b4f0183b28
Group11.18	.	exon	2584843	2585034	.	+	.	Parent=GB45157-RA;ID=419ff462-7c94-4a8f-84c6-0a07655ee2b9;Name=33d284d0-5f50-4c4c-be55-49ab6c92c29a
###

nathandunn · 2020-04-15T20:20:57Z

Seems to pull in everything but attributes, which is fine and potentially this is a good feature as important arbitrary attributes may be problematic.

nathandunn · 2020-04-15T20:27:31Z

I think that this is going to be problematic to introduce this without a refactor

all of the data kind of comes through

2d741e9

nathandunn changed the title ~~all of the data kind of comes through~~ bring in all gene and transcript data Mar 11, 2020

nathandunn added 4 commits March 11, 2020 12:47

merging in develop

28f6391

updated

4cd0af6

fixed gene prodcut inclusion

39dfeac

stays on gene when editing gene

41842b7

nathandunn added 2 commits March 12, 2020 13:22

fixed bug when adding bizarre strings and features that may not have …

6973108

…a location (eg. genes) and not removing things from transcripts properly

added use_cds and use_name

64a7d32

updated usecase

ff22bd6

not quite working sadly

6646aa6

nathandunn added 12 commits March 12, 2020 17:40

updated call to handle null

65d9605

synonym added

1ff93de

got dbxref working

ddc68c2

all json converted to lower-case for some reason, so keeping as-is

42aa8b9

fixed description coming in properly

c194875

comments fixed now

8595d44

converted back to use the original

09ac850

gene product is doing round-trip I think

45843bc

fixed most of the updateFeature code

9d75bf5

updated for provenance

7ee4df0

gene product and GO shows up

d22957a

reverted transcript visibility

f11746e

nathandunn added 4 commits April 8, 2020 14:06

merged in development

7093d9d

redid json doc id

87d6ab7

working on fixing a few more tests

0238897

fixed a couple of very small bugs

a487e06

nathandunn added 3 commits April 10, 2020 17:36

Merge branch 'develop' into fix-2372

4fee2d1

merged in

81f54b5

Merge branch 'develop' into fix-2372

983f7d8

nathandunn marked this pull request as draft April 13, 2020 20:10

nathandunn added 7 commits April 13, 2020 16:14

dbxref fixed

915d1ad

remove extra stuff

8128f6a

fixed canned comment

da93b74

fixed a lot of the product operations

a9927a4

Merge branch 'develop' into fix-2372

2803f4a

Merge branch 'develop' of https://github.com/GMOD/Apollo into fix-2372

5c6cf62

Merge branch 'develop' into fix-2372

f22e053

fixed deletion error

1356101

nathandunn added 2 commits April 15, 2020 13:23

handle other cases of GFF3 import for single or multiple values

9b53ba7

cleaned up

d21fc26

nathandunn closed this Apr 15, 2020

This was referenced May 7, 2020

Implement the OGS code for a “new model” in a branch nathandunn/apollo-performance#7

Open

fix python gff3 loader in python nathandunn/apollo-performance#10

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nathandunn mentioned this pull request May 4, 2021

Add topLevel option to getFeatures endpoint #2616

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bring in all gene and transcript data, but disallow history (or use different uniquenames) if OGS #2401

bring in all gene and transcript data, but disallow history (or use different uniquenames) if OGS #2401

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bring in all gene and transcript data, but disallow history (or use different uniquenames) if OGS #2401

bring in all gene and transcript data, but disallow history (or use different uniquenames) if OGS #2401

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nathandunn commented Mar 11, 2020 • edited Loading

make work for GFF3 track: in https://github.com/GMOD/Apollo/blob/develop/grails-app/services/org/bbop/apollo/FeatureService.groovy#L1293 make sure that we pull in the additional properties if there (gene_product, provenance, comments, dbxref, go, etc. etct.)

fill out all the way export

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