diff --git a/pom.xml b/pom.xml index fe8e746e..243e5a6b 100644 --- a/pom.xml +++ b/pom.xml @@ -128,7 +128,7 @@ data-model-lib life.qbic - 2.25.0 + 2.27.0 org.mockito diff --git a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy index c1318a1d..8362a035 100644 --- a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy +++ b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy @@ -3,6 +3,7 @@ package life.qbic.utils import com.fasterxml.jackson.databind.ObjectMapper import groovy.json.JsonSlurper import groovy.util.logging.Log4j2 +import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputDoradoMinimal import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputMinimal import net.jimblackler.jsonschemafriend.Schema import net.jimblackler.jsonschemafriend.SchemaStore @@ -14,7 +15,6 @@ import java.nio.file.Path import java.nio.file.Paths import java.text.ParseException import life.qbic.datamodel.datasets.OxfordNanoporeExperiment - import java.util.stream.Collectors @Log4j2 @@ -95,8 +95,8 @@ class NanoporeParser { jsonStarted = true } if (jsonStarted) { - def split = line.replaceAll("\\s+","").split(":") - if(split.size() == 2 && split[1].replaceAll('"',"").size() <= 1){ + def split = line.replaceAll("\\s+", "").split(":") + if (split.size() == 2 && split[1].replaceAll('"', "").size() <= 1) { log.info("Metadata value ${split[0]} missing in ${reportFile["path"]}") } buffer.append(line) @@ -110,12 +110,11 @@ class NanoporeParser { new File(Paths.get(root.toString(), summaryFile["path"].toString()) as String) .readLines().each { line -> def split = line.split("=") - if(split.size() > 1){ + if (split.size() > 1) { finalMetaData[split[0]] = split[1] - } - else { + } else { log.info("Metadata value ${split[0]} missing in ${summaryFile["path"]}, defaulting to empty value") - finalMetaData[split[0]] = "" + finalMetaData[split[0]] = "" } } return finalMetaData @@ -178,18 +177,27 @@ class NanoporeParser { * @throws net.jimblackler.jsonschemafriend.ValidationException */ private static void validateJson(String json) throws ValidationException { - // Step 1: load schema + // Step 1: load json ObjectMapper objectMapper = new ObjectMapper() Object jsonObject = objectMapper.readValue(json, Object) + SchemaStore schemaStore = new SchemaStore() - Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputMinimal.getSchemaAsStream()) Validator validator = new Validator() - validator.validate(schema, jsonObject) + try { + //Validate against Fast5 Based Oxford Measurement + Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputMinimal.getSchemaAsStream()) + validator.validate(schema, jsonObject) + } catch (ValidationException ignored) { + //Validate against Pod5 Based Oxford Measurement + Schema schema = schemaStore.loadSchema(OxfordNanoporeInstrumentOutputDoradoMinimal.getSchemaAsStream()) + validator.validate(schema, jsonObject) + } } /* * Converts a file tree into a json object. */ + private static class DirectoryConverter { private static final PREDEFINED_EXTENSIONS = ["fastq.gz"] private static final IGNORED_FOLDERNAMES = ["qc"] @@ -239,11 +247,11 @@ class NanoporeParser { List children = currentDirectory.listFiles() List visibleChildren = children.stream() - .filter(file -> !file.isHidden()).collect(Collectors.toList()); + .filter(file -> !file.isHidden()).collect(Collectors.toList()) for (File file : children) { if (!visibleChildren.contains(file)) { - hiddenFiles.add(file); + hiddenFiles.add(file) } } @@ -252,11 +260,11 @@ class NanoporeParser { return !IGNORED_FOLDERNAMES.contains(currentFolderName) }.collect { file -> - if (file.isFile()) { - convertFile(file.toPath()) - } else if (file.isDirectory()) { - convertDirectory(file.toPath()) - } + if (file.isFile()) { + convertFile(file.toPath()) + } else if (file.isDirectory()) { + convertDirectory(file.toPath()) + } } def convertedDirectory = [ diff --git a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy index e76af9a1..5f161a12 100644 --- a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy +++ b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy @@ -125,6 +125,41 @@ class NanoporeParserSpec extends Specification { thrown(ValidationException) } + def "parsing a valid minimal file structure for dorado based basecalling containing additional unknown files and folder still returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_minimal") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + assert experiment instanceof OxfordNanoporeExperiment + // Check that the metadata from the report file has been retrieved + assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094" + // Check that the metadata from the summary file has been retrieved + assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" + } + + def "parsing a valid file structure for dorado based basecalling containing additional unknown files and folder still returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + assert experiment instanceof OxfordNanoporeExperiment + // Check that the metadata from the report file has been retrieved + assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094" + // Check that the metadata from the summary file has been retrieved + assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" + } + + def "parsing an invalid minimal file structure for dorado based basecalling leads to a ValidationException"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + thrown(ValidationException) + } + def "parsing the alternative valid file structure with metadata missing returns an OxfordNanoporeExperiment Object"() { given: def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal") diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz similarity index 100% rename from src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz rename to src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git 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a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt new file mode 100644 index 00000000..900f4d7e --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/fails/QABCD001AB_E12A345a01_PAE12345_missing_skip_folder/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt @@ -0,0 +1,17 @@ +instrument=PCT0094 +position=1-A3-D3 +flow_cell_id=PAE24142 +sample_id=QNANO027AE_E19D023a01_200211 +protocol_group_id=20200211_QNANO +protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL +protocol_run_id=5a7cfc2a-81b0-412d-baa0-51b939cd8e76 +acquisition_run_id=c6028297dff19d01e7c5fba6487de807d1e99c05 +started=2020-02-11T15:52:10.465982+01:00 +acquisition_stopped=2020-02-14T08:39:54.688916+01:00 +processing_stopped=2020-02-14T08:39:58.804639+01:00 +basecalling_enabled=1 +sequencing_summary_file=sequencing_summary_PAE24142_c6028297.txt 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b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ 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b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz @@ -1 +0,0 @@ -This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz @@ -1 +0,0 @@ -This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz @@ -1 +0,0 @@ -This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz index a46c98ae..e69de29b 100644 --- a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_valid_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz @@ -1 +0,0 @@ -This is some text