feat(genome): add GFF3 annotation support for genome submissions (TTENA-207) #162
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Contributor
There was a problem hiding this comment. Same for this validator just like Gff3Validator above: Following existing practice, this should be placed in gff3tools unless there is a good reason or everybody agrees that there is no harm in keeping them here in webin-cli.
Contributor
There was a problem hiding this comment. Agreed that we could move Gff3Validator to gff3tools, but I think SequenceSubmissionValidator should be in webin-cli because it is a generic logic to perform both submissionValidator.validate() and gff3Validation.validate()
Author
There was a problem hiding this comment. The engine-orchestration core (build ValidationEngine + CompositeSequenceProvider, read GFF3, collect errors/warnings) has no ENA-specific data or credentials in it, so it's a fair candidate to eventually live in gff3tools as a public convenience API, mirroring what sequencetools/readtools/txmbtools already do with SubmissionValidator/ReadsValidator/TxmbValidator. That said, I'd treat it as a follow-up rather than part of this PR, it means a gff3tools release plus a dependency bump here, and the report-writing/SubmissionFile adaptation needs to stay in webin-cli regardless (gff3tools shouldn't depend on webin-cli-validator types). I'm opening gff3tools PR to extract that piece. For SequenceSubmissionValidator, it should stay in webin-cli. Its whole job is composing SubmissionValidator (sequencetools) + Gff3Validator for a webin-cli submission context; there's no ENA-internal logic in it that would justify moving it, and gff3tools shouldn't need to know about webin-cli's Manifest/Validator interfaces. |
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| /* | ||
| * Copyright 2018-2023 EMBL - European Bioinformatics Institute | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); you may not use this | ||
| * file except in compliance with the License. You may obtain a copy of the License at | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * Unless required by applicable law or agreed to in writing, software distributed under the | ||
| * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR | ||
| * CONDITIONS OF ANY KIND, either express or implied. See the License for the | ||
| * specific language governing permissions and limitations under the License. | ||
| */ | ||
| package uk.ac.ebi.ena.webin.cli.context; | ||
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| import java.util.List; | ||
| import uk.ac.ebi.embl.api.validation.submission.SubmissionValidator; | ||
| import uk.ac.ebi.ena.webin.cli.context.genome.Gff3Validator; | ||
| import uk.ac.ebi.ena.webin.cli.validator.api.ValidationResponse; | ||
| import uk.ac.ebi.ena.webin.cli.validator.api.Validator; | ||
| import uk.ac.ebi.ena.webin.cli.validator.file.SubmissionFile; | ||
| import uk.ac.ebi.ena.webin.cli.validator.manifest.Manifest; | ||
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| /** | ||
| * Composite validator for genome, transcriptome, and sequence submissions. Runs the sequencetools | ||
| * {@link SubmissionValidator} first, then performs client-side GFF3 validation when the manifest | ||
| * declares a GFF3 file. | ||
| * | ||
| * <p>Instantiated reflectively by {@link uk.ac.ebi.ena.webin.cli.WebinCliContext}, so a public | ||
| * no-arg constructor is required. | ||
| */ | ||
| public class SequenceSubmissionValidator implements Validator<Manifest<?>, ValidationResponse> { | ||
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| private static final String GFF3_TYPE = "GFF3"; | ||
| private static final String FASTA_TYPE = "FASTA"; | ||
| private static final String FLATFILE_TYPE = "FLATFILE"; | ||
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| private final SubmissionValidator submissionValidator; | ||
| private final Gff3Validator gff3Validator; | ||
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| public SequenceSubmissionValidator() { | ||
| this(new SubmissionValidator(), new Gff3Validator()); | ||
| } | ||
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| SequenceSubmissionValidator( | ||
| SubmissionValidator submissionValidator, Gff3Validator gff3Validator) { | ||
| this.submissionValidator = submissionValidator; | ||
| this.gff3Validator = gff3Validator; | ||
| } | ||
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| @Override | ||
| public ValidationResponse validate(Manifest<?> manifest) { | ||
| List<? extends SubmissionFile<?>> gff3Files = manifest.filesWithTypeName(GFF3_TYPE); | ||
| List<? extends SubmissionFile<?>> fastaFiles = manifest.filesWithTypeName(FASTA_TYPE); | ||
| boolean gff3Only = | ||
| !gff3Files.isEmpty() | ||
| && fastaFiles.isEmpty() | ||
| && manifest.filesWithTypeName(FLATFILE_TYPE).isEmpty(); | ||
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| ValidationResponse response; | ||
| if (gff3Only) { | ||
| // sequencetools' SubmissionValidator requires at least one FASTA/FLATFILE sequence | ||
| // to compute contig/scaffold/chromosome counts, which a GFF3-only submission never | ||
| // has. Skip it entirely and rely on Gff3Validator below instead. | ||
| response = new ValidationResponse(ValidationResponse.status.VALIDATION_SUCCESS); | ||
| } else { | ||
| response = submissionValidator.validate(manifest); | ||
| if (response == null) { | ||
| response = new ValidationResponse(); | ||
| } | ||
| } | ||
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| if (!gff3Files.isEmpty() && !gff3Validator.validate(gff3Files, fastaFiles)) { | ||
| response.setStatus(ValidationResponse.status.VALIDATION_ERROR); | ||
| } | ||
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| return response; | ||
| } | ||
| } |
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Do we not need a version number update for this change?