julesjacobsen
commented
2 years ago Hi @MauricioMoldes! Sorry, this validator project has been merged with the phenopacket-tools. If you checkout the develop branch - https://github.com/phenopackets/phenopacket-tools/tree/develop and build it then this is how you'd go about trying the validator:
wget https://zenodo.org/record/3905420/files/phenopackets.zip?download=1
unzip phenopackets.zip
# validate all files in a directory
java -jar phenotools-cli-0.0.2-SNAPSHOT.jar validate ./phenopackets/*
# alternatively for a single file
java -jar phenotools-cli-0.0.2-SNAPSHOT.jar validate ./phenopackets/Abdul_Wahab-2016-GCDH-Patient_5.jsonThis is all still a bit of a work-in-progress.
MauricioMoldes
Hi !
I am currently exploring this phenopacket validator tool re-using the 384 phenopacket dataset from https://zenodo.org/record/3905420#.YajQ3r_MJH5
######## Command
########
$ java -jar validator-cli-0.1.1-SNAPSHOT.jar validate -p=/home/mmoldes/Documents/EGA/bioteam/pheno_test/phenopackets/phenopackets/Yang-2016-MFN2-patient.json####### Issue #######
It seems that the positionals are correct, and so is the file path.
mycommand was called with --rare=false and positionals: [validate]However, the tool is outputting file not found, in a different directory than filepath.
org.phenopackets.schema.validator.core.except.PhenopacketValidatorRuntimeException: Could not find input json file "/home/mmoldes/Documents/EGA/bioteam/pheno_test/phenopacket-validator/validator-cli/target/validate"Am I doing something wrong?
######## output log ########
14:54:06.732 [main] INFO org.phenopackets.schema.validator.cli.ValidatorApplication - STARTING THE APPLICATION __. __ \ | __ _____ __ | | _/ | | / | _/ \ / \ / \___ \ \ _/ | |/ // \ \ | | | Y \ /| | ( <_> ) |> > \ \| <\ /| | |____| || /_ >| /__/| (__ /\ >| \ >| \/ \/ \/ || \/ \/ \/ \/ . . ._ \ \ / /__ | | || | _/__ / | ____ \ Y /_ \ | | | |/ |\ \ _\/ _ \ \ / / | || / // | / | | ( <_> ) | \/ _/ (__ /__/__ |(__ /| __/|__| \/ \/ \/
2021-12-02 14:54:07.222 INFO 33200 --- [ main] o.p.s.v.cli.ValidatorApplication : Starting ValidatorApplication v0.1.1-SNAPSHOT using Java 11.0.11 on mmoldes-GE66-Raider-10UE with PID 33200 (/home/mmoldes/Documents/EGA/bioteam/pheno_test/phenopacket-validator/validator-cli/target/validator-cli-0.1.1-SNAPSHOT.jar started by mmoldes in /home/mmoldes/Documents/EGA/bioteam/pheno_test/phenopacket-validator/validator-cli/target) 2021-12-02 14:54:07.223 INFO 33200 --- [ main] o.p.s.v.cli.ValidatorApplication : No active profile set, falling back to default profiles: default 2021-12-02 14:54:07.665 INFO 33200 --- [ main] o.p.s.v.cli.ValidatorApplication : Started ValidatorApplication in 0.834 seconds (JVM running for 1.119) 2021-12-02 14:54:07.714 WARN 33200 --- [ main] picocli.spring.PicocliSpringFactory : Unable to get bean of class interface java.util.List, using default Picocli factory mycommand was called with --rare=false and positionals: [validate] 2021-12-02 14:54:07.716 INFO 33200 --- [ main] o.p.s.validator.cli.ValidateCommand : EXECUTING : command line runner org.phenopackets.schema.validator.core.except.PhenopacketValidatorRuntimeException: Did not recognize error type: "enum" at org.phenopackets.schema.validator.core.validation.ErrorType.stringToErrorType(ErrorType.java:34) at org.phenopackets.schema.validator.core.jsonschema.JsonValidationError.(JsonValidationError.java:18)
at org.phenopackets.schema.validator.core.jsonschema.JsonSchemaValidator.lambda$validate$0(JsonSchemaValidator.java:76)
at java.base/java.lang.Iterable.forEach(Iterable.java:75)
at org.phenopackets.schema.validator.core.jsonschema.JsonSchemaValidator.validate(JsonSchemaValidator.java:76)
at org.phenopackets.schema.validator.core.PhenopacketValidator.genericValidation(PhenopacketValidator.java:90)
at org.phenopackets.schema.validator.core.PhenopacketValidator.(PhenopacketValidator.java:56)
at org.phenopackets.schema.validator.cli.ValidateCommand.call(ValidateCommand.java:45)
at org.phenopackets.schema.validator.cli.ValidateCommand.call(ValidateCommand.java:17)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine.execute(CommandLine.java:2078)
at org.phenopackets.schema.validator.cli.ValidatorApplicationRunner.run(ValidatorApplicationRunner.java:32)
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791)
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:345)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332)
at org.phenopackets.schema.validator.cli.ValidatorApplication.main(ValidatorApplication.java:22)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)
org.phenopackets.schema.validator.core.except.PhenopacketValidatorRuntimeException: Could not find input json file "/home/mmoldes/Documents/EGA/bioteam/pheno_test/phenopacket-validator/validator-cli/target/validate"
at org.phenopackets.schema.validator.core.PhenopacketValidator.additionalValidation(PhenopacketValidator.java:66)
at org.phenopackets.schema.validator.core.PhenopacketValidator.(PhenopacketValidator.java:58)
at org.phenopackets.schema.validator.cli.ValidateCommand.call(ValidateCommand.java:45)
at org.phenopackets.schema.validator.cli.ValidateCommand.call(ValidateCommand.java:17)
at picocli.CommandLine.executeUserObject(CommandLine.java:1953)
at picocli.CommandLine.access$1300(CommandLine.java:145)
at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2346)
at picocli.CommandLine$RunLast.handle(CommandLine.java:2311)
at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179)
at picocli.CommandLine.execute(CommandLine.java:2078)
at org.phenopackets.schema.validator.cli.ValidatorApplicationRunner.run(ValidatorApplicationRunner.java:32)
at org.springframework.boot.SpringApplication.callRunner(SpringApplication.java:791)
at org.springframework.boot.SpringApplication.callRunners(SpringApplication.java:775)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:345)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343)
at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332)
at org.phenopackets.schema.validator.cli.ValidatorApplication.main(ValidatorApplication.java:22)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:108)
at org.springframework.boot.loader.Launcher.launch(Launcher.java:58)
at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:88)
2021-12-02 14:54:07.850 INFO 33200 --- [ main] o.p.s.v.cli.ValidatorApplication : APPLICATION FINISHED