diff --git a/pom.xml b/pom.xml index e7324889..b8b62904 100644 --- a/pom.xml +++ b/pom.xml @@ -128,7 +128,7 @@ data-model-lib life.qbic - 2.20.0 + 2.21.0 org.mockito diff --git a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy index 71751c29..7a06610f 100644 --- a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy +++ b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy @@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.ObjectMapper import groovy.json.JsonSlurper import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutput import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputV2 +import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputV3 import org.everit.json.schema.Schema import org.everit.json.schema.ValidationException import org.everit.json.schema.loader.SchemaLoader @@ -16,10 +17,14 @@ import java.nio.file.Paths import java.text.ParseException import life.qbic.datamodel.datasets.OxfordNanoporeExperiment +import java.util.stream.Collectors + class NanoporeParser { + private static Set hiddenFiles = new HashSet<>() /** - * Generates a map representing the folder structure + * Generates a map representing the folder structure, if it is a correct structure + * Deletes any hidden files, if the structure fits one of the Nanopore models * @param directory path of directory whose fileTree should be converted into map */ static OxfordNanoporeExperiment parseFileStructure(Path directory) { @@ -35,6 +40,10 @@ class NanoporeParser { def finalMap = parseMetaData(convertedDirectory, directory) // Step5: Create the final OxfordNanoporeExperiment from the map OxfordNanoporeExperiment convertedExperiment = OxfordNanoporeExperiment.create(finalMap) + // Step6: This is a valid experiment, we can now delete the hidden files + for (File hiddenFile : hiddenFiles) { + deleteFile(hiddenFile) + } return convertedExperiment } catch (ValidationException validationException) { // we have to fetch all validation exceptions @@ -43,6 +52,15 @@ class NanoporeParser { } } + private static void deleteFile(File file) { + if(file.isDirectory()) { + for(File child : file.listFiles()) { + deleteFile(child) + } + } + file.delete() + } + /** * The main metadata we need to provide for the OxfordNanoporeExperiment is in * the report markdown file and final summary file. @@ -163,7 +181,11 @@ class NanoporeParser { // Step 2: validate against schema return if valid, throw exception if invalid validateUsingSchema(OxfordNanoporeInstrumentOutput.getSchemaAsStream(), jsonObject) } catch (ValidationException validationException) { - validateUsingSchema(OxfordNanoporeInstrumentOutputV2.getSchemaAsStream(), jsonObject) + try { + validateUsingSchema(OxfordNanoporeInstrumentOutputV2.getSchemaAsStream(), jsonObject) + } catch (ValidationException validationExceptionV2) { + validateUsingSchema(OxfordNanoporeInstrumentOutputV3.getSchemaAsStream(), jsonObject) + } } } @@ -214,6 +236,8 @@ class NanoporeParser { /** * Convert a directory structure to a map, following the Nanopore schema. + * Ignores hidden files in the structure and adds them to a global set to be + * dealt with later. * @param a path to the current location in recursion * @return a map representing a directory with name, path and children as keys */ @@ -224,22 +248,33 @@ class NanoporeParser { if (IGNORED_FOLDERNAMES.contains(name)) { return null } - List children = currentDirectory.listFiles().findAll { file -> + List children = currentDirectory.listFiles() + + List visibleChildren = children.stream() + .filter(file -> !file.isHidden()).collect(Collectors.toList()); + + for (File file : children) { + if (!visibleChildren.contains(file)) { + hiddenFiles.add(file); + } + } + + visibleChildren = visibleChildren.findAll { file -> String currentFolderName = file.getName() 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 = [ "name" : name, "path" : path, - "children": children + "children": visibleChildren ] return convertedDirectory diff --git a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy index 8476e0d2..4c9f3327 100644 --- a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy +++ b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy @@ -25,6 +25,19 @@ class NanoporeParserSpec extends Specification { assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109" } + def "parsing a valid file structure with an html report returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report") + 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" + } + def "parsing the alternative valid file structure returns an OxfordNanoporeExperiment Object"() { given: def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new") @@ -38,6 +51,19 @@ class NanoporeParserSpec extends Specification { assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" } + def "parsing the newest valid file structure returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3") + 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 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/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/drift_correction_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/drift_correction_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/duty_time_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/duty_time_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/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_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/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_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/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_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/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_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/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_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt new file mode 100644 index 00000000..3b388d5e --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/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:True +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 +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 \ No newline at end of file diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/mux_scan_data_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/mux_scan_data_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.html b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.html new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "19.12.5", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2020-01-28T15:17:38Z", + "flow_cell_id": "PAE26989", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "3.2.8+bd67289", + "heatsink_temp": "36.179111", + "hostname": "PCT0094", + "hublett_board_id": "0132136faade2e15", + "hublett_firmware_version": "2.0.12", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 16.04", + "protocol_group_id": "20200128_QNANO", + "protocol_run_id": "", + "protocols_version": "4.3.16", + "run_id": "db9e9383d44d80bbe1e2600c7a7419056610d46d", + "sample_id": "QNANO036AD_E19D023b04", + "satellite_board_id": "0000000000000000", + "satellite_firmware_version": "2.0.12", + "usb_config": "firm_1.2.3_ware#rbt_4.5.6_rbt#ctrl#USB3", + "version": "3.6.1" +} + +Duty Time +========= + +ID: db9e9383d44d80bbe1e2600c7a7419056610d46d + +Channel State,Experiment Time (minutes),State Time (samples), +strand,0,144832342 +strand,1,158421270 +strand,2,378095352 +strand,3,472685319 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/throughput_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_html_report/20200122_1217_1-A1-B1-PAE12345_1234567a/throughput_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_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_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/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_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_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/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_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 +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/other_reports/pore_scan_data_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/other_reports/pore_scan_data_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/pore_activity_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/pore_activity_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.html b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.html new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.json b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.json new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "19.12.5", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2020-01-28T15:17:38Z", + "flow_cell_id": "PAE26989", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "3.2.8+bd67289", + "heatsink_temp": "36.179111", + "hostname": "PCT0094", + "hublett_board_id": "0132136faade2e15", + "hublett_firmware_version": "2.0.12", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 16.04", + "protocol_group_id": "20200128_QNANO", + "protocol_run_id": "", + "protocols_version": "4.3.16", + "run_id": "db9e9383d44d80bbe1e2600c7a7419056610d46d", + "sample_id": "QNANO036AD_E19D023b04", + "satellite_board_id": "0000000000000000", + "satellite_firmware_version": "2.0.12", + "usb_config": "firm_1.2.3_ware#rbt_4.5.6_rbt#ctrl#USB3", + "version": "3.6.1" +} + +Duty Time +========= + +ID: db9e9383d44d80bbe1e2600c7a7419056610d46d + +Channel State,Experiment Time (minutes),State Time (samples), +strand,0,144832342 +strand,1,158421270 +strand,2,378095352 +strand,3,472685319 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/sample_sheet_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/sample_sheet_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/throughput_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v3/20200122_1217_1-A1-B1-PAE12345_1234567a/throughput_.csv new file mode 100644 index 00000000..e69de29b