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amalic / bern-docker

Docker image for a neural named entity recognition and multi-type normalization tool for biomedical text mining
MIT License
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Gene normalizer don't work #1

Closed shipse92 closed 4 years ago

shipse92 commented 4 years ago

I built this docker image and run this image with your command. Then openned web browser, called like this. http://localhost:8008/?pmid=30429604&format=pubtator

Result : 30429604 15 19 CD95 gene CUI-less 30429604 20 29 PLCgamma1 gene CUI-less 30429604 51 55 Th17 gene CUI-less 30429604 77 82 CD95L gene CUI-less 30429604 110 117 m-CD95L gene CUI-less 30429604 138 154 metalloproteases gene CUI-less 30429604 184 191 s-CD95L gene CUI-less 30429604 201 208 m-CD95L gene CUI-less 30429604 230 237 s-CD95L gene CUI-less 30429604 242 246 CD95 gene CUI-less

All Gene ID is CUI-less. So, I saw the nohup_gene.out, file was logging like this.

nohup_gene.out : java.io.IOException: Cannot run program "./Ab3P": error=13, Permission denied at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at java.lang.Runtime.exec(Runtime.java:620) at java.lang.Runtime.exec(Runtime.java:450) at java.lang.Runtime.exec(Runtime.java:347) at GNormPluslib.GNR.LoadInputFile(GNR.java:72) at GNormPluslib.GNormPlus.run(GNormPlus.java:315) at GNormPluslib.GNormPlusServer.main(GNormPlusServer.java:35) Caused by: java.io.IOException: error=13, Permission denied at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more

How can i do that?

amalic commented 4 years ago

?

shipse92 commented 4 years ago

I mean GNormPlusServer don't work. permission error occurs.

Can you help me?

amalic commented 4 years ago

I would help you if I could. But this repo is only dockerizing Bern, which was originally developed in this repository.

I recommend to create a ticket in the Bern repo.

Please close this ticket and open a new on in case I need to update something here.

shipse92 commented 4 years ago

I know original repo. And I used original bern but original didn't occur error like this.

This error occurs only docker environment I think. How is your result?

amalic commented 4 years ago

I just tried your call with my Docker image but with port 80 instead of 8008. And this is the output

URI used: http://localhost/?pmid=30429604&format=pubtator

30429604|t|Disrupting the CD95-PLCgamma1 interaction prevents Th17-driven inflammation.
30429604|a|CD95L is a transmembrane ligand (m-CD95L) that is cleaved by metalloproteases to release a soluble ligand (s-CD95L). Unlike m-CD95L, interaction between s-CD95L and CD95 fails to recruit caspase-8 and FADD to trigger apoptosis and instead induces a Ca2+ response via docking of PLCgamma1 to the calcium-inducing domain (CID) within CD95. This signaling pathway induces accumulation of inflammatory Th17 cells in damaged organs of lupus patients, thereby aggravating disease pathology. A large-scale screen revealed that the HIV protease inhibitor ritonavir is a potent disruptor of the CD95-PLCgamma1 interaction. A structure-activity relationship approach highlighted that ritonavir is a peptidomimetic that shares structural characteristics with CID with respect to docking to PLCgamma1. Thus, we synthesized CID peptidomimetics abrogating both the CD95-driven Ca2+ response and transmigration of Th17 cells. Injection of ritonavir and the CID peptidomimetic into lupus mice alleviated clinical symptoms, opening a new avenue for the generation of drugs for lupus patients.
30429604    15  19  CD95    gene    CUI-less
30429604    20  29  PLCgamma1   gene    CUI-less
30429604    51  55  Th17    gene    CUI-less
30429604    77  82  CD95L   gene    CUI-less
30429604    110 117 m-CD95L gene    CUI-less
30429604    138 154 metalloproteases    gene    CUI-less
30429604    184 191 s-CD95L gene    CUI-less
30429604    201 208 m-CD95L gene    CUI-less
30429604    230 237 s-CD95L gene    CUI-less
30429604    242 246 CD95    gene    CUI-less
30429604    264 273 caspase-8   gene    CUI-less
30429604    278 282 FADD    gene    CUI-less
30429604    326 330 Ca2+    drug    CHEBI:29108|BERN:287734103
30429604    355 364 PLCgamma1   gene    CUI-less
30429604    372 379 calcium drug    CHEBI:22984|BERN:4175403
30429604    409 413 CD95    gene    CUI-less
30429604    507 512 lupus   disease BERN:256340901
30429604    601 613 HIV protease    gene    CUI-less
30429604    601 604 HIV species NCBI:txid12721
30429604    624 633 ritonavir   drug    MESH:D019438|BERN:4225903
30429604    663 667 CD95    gene    CUI-less
30429604    668 677 PLCgamma1   gene    CUI-less
30429604    751 760 ritonavir   drug    MESH:D019438|BERN:4225903
30429604    856 865 PLCgamma1   gene    CUI-less
30429604    928 932 CD95    gene    CUI-less
30429604    940 944 Ca2+    drug    CHEBI:29108|BERN:287734103
30429604    1001    1010    ritonavir   drug    MESH:D019438|BERN:4225903
30429604    1043    1048    lupus   disease BERN:256340901
30429604    1049    1053    mice    species NCBI:txid10095
30429604    1137    1142    lupus   disease BERN:256340901
amalic commented 4 years ago

Same result when running on port 8008. Maybe your docker installation or network config is not allowing access to external services.

shipse92 commented 4 years ago

My result same with you.

Focus on gene ID. Drug, disease, species has IDs. But, Gene is all CUI-less. You can find error message like this if you see your nohup_gene.out.

java.io.IOException: Cannot run program "./Ab3P": error=13, Permission denied at java.lang.ProcessBuilder.start(ProcessBuilder.java:1048) at java.lang.Runtime.exec(Runtime.java:620) at java.lang.Runtime.exec(Runtime.java:450) at java.lang.Runtime.exec(Runtime.java:347) at GNormPluslib.GNR.LoadInputFile(GNR.java:72) at GNormPluslib.GNormPlus.run(GNormPlus.java:315) at GNormPluslib.GNormPlusServer.main(GNormPlusServer.java:35) Caused by: java.io.IOException: error=13, Permission denied at java.lang.UNIXProcess.forkAndExec(Native Method) at java.lang.UNIXProcess.(UNIXProcess.java:247) at java.lang.ProcessImpl.start(ProcessImpl.java:134) at java.lang.ProcessBuilder.start(ProcessBuilder.java:1029) ... 6 more

shipse92 commented 4 years ago

Oh, I did it. call this http://localhost:8008/?pmid=30429604&format=pubtator

result is 

30429604|t|Disrupting the CD95-PLCgamma1 interaction prevents Th17-driven inflammation.
30429604|a|CD95L is a transmembrane ligand (m-CD95L) that is cleaved by metalloproteases to release a soluble ligand (s-CD95L). Unlike m-CD95L, interaction between s-CD95L and CD95 fails to recruit caspase-8 and FADD to trigger apoptosis and instead induces a Ca2+ response via docking of PLCgamma1 to the calcium-inducing domain (CID) within CD95. This signaling pathway induces accumulation of inflammatory Th17 cells in damaged organs of lupus patients, thereby aggravating disease pathology. A large-scale screen revealed that the HIV protease inhibitor ritonavir is a potent disruptor of the CD95-PLCgamma1 interaction. A structure-activity relationship approach highlighted that ritonavir is a peptidomimetic that shares structural characteristics with CID with respect to docking to PLCgamma1. Thus, we synthesized CID peptidomimetics abrogating both the CD95-driven Ca2+ response and transmigration of Th17 cells. Injection of ritonavir and the CID peptidomimetic into lupus mice alleviated clinical symptoms, opening a new avenue for the generation of drugs for lupus patients.
30429604    15  19  CD95    gene    MIM:134637|HGNC:11920|Ensembl:ENSG00000026103|BERN:323737202
30429604    20  29  PLCgamma1   gene    MIM:172420|HGNC:9065|Ensembl:ENSG00000124181|BERN:324301002
30429604    51  55  Th17    gene    BERN:326428902
30429604    77  82  CD95L   gene    MIM:134638|HGNC:11936|Ensembl:ENSG00000117560|BERN:323738202
30429604    110 117 m-CD95L gene    CUI-less
30429604    138 154 metalloproteases    gene    CUI-less
30429604    184 191 s-CD95L gene    CUI-less
30429604    201 208 m-CD95L gene    CUI-less
30429604    230 237 s-CD95L gene    CUI-less
30429604    242 246 CD95    gene    MIM:134637|HGNC:11920|Ensembl:ENSG00000026103|BERN:323737202
30429604    264 273 caspase-8   gene    MIM:601763|HGNC:1509|Ensembl:ENSG00000064012|BERN:325295202
30429604    278 282 FADD    gene    MIM:602457|HGNC:3573|Ensembl:ENSG00000168040|BERN:325389602
30429604    326 330 Ca2+    drug    CHEBI:29108|BERN:287734103
30429604    355 364 PLCgamma1   gene    MIM:172420|HGNC:9065|Ensembl:ENSG00000124181|BERN:324301002
30429604    372 379 calcium drug    CHEBI:22984|BERN:4175403
30429604    409 413 CD95    gene    MIM:134637|HGNC:11920|Ensembl:ENSG00000026103|BERN:323737202
30429604    507 512 lupus   disease BERN:256340901
30429604    601 604 HIV species NCBI:txid12721
30429604    601 613 HIV protease    gene    CUI-less
30429604    624 633 ritonavir   drug    MESH:D019438|BERN:4225903
30429604    663 667 CD95    gene    MIM:134637|HGNC:11920|Ensembl:ENSG00000026103|BERN:323737202
30429604    668 677 PLCgamma1   gene    MIM:172420|HGNC:9065|Ensembl:ENSG00000124181|BERN:324301002
30429604    751 760 ritonavir   drug    MESH:D019438|BERN:4225903
30429604    856 865 PLCgamma1   gene    MIM:172420|HGNC:9065|Ensembl:ENSG00000124181|BERN:324301002
30429604    928 932 CD95    gene    MIM:134637|HGNC:11920|Ensembl:ENSG00000026103|BERN:323737202
30429604    940 944 Ca2+    drug    CHEBI:29108|BERN:287734103
30429604    1001    1010    ritonavir   drug    MESH:D019438|BERN:4225903
30429604    1043    1048    lupus   disease BERN:256340901
30429604    1049    1053    mice    species NCBI:txid10095
30429604    1137    1142    lupus   disease BERN:256340901

Gene ID is come back now.

Permission was wrong.

resources/normalizers/gene/CRF/crf_test resources/normalizers/gene/Ab3P

Two files must have executable permission.

Fine. It works! Thank you.

shipse92 commented 4 years ago

Now this issue closing myself. Thankyou