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remove unnecessary newline to trigger PR checks again
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@Steffengreiner
Steffengreiner committed Nov 3, 2023
1 parent ec6b2b3 commit bf75090
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Showing 3 changed files with 300 additions and 2 deletions.
4 changes: 3 additions & 1 deletion src/main/groovy/life/qbic/datamodel/datasets/OxfordNanoporeExperiment.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -301,11 +301,13 @@ final class OxfordNanoporeExperiment implements ExperimentFolder {
FAST5_PASS_FOLDER(FQDN_FOLDERS + ".Fast5PassFolder"),
FAST5_FAIL_FOLDER(FQDN_FOLDERS + ".Fast5FailFolder"),
FAST5_SKIP_FOLDER(FQDN_FOLDERS + ".Fast5SkipFolder"),
POD5_SKIP_FOLDER(FQDN_FOLDERS + ".Pod5SkipFolder"),
FASTQ_PASS_FOLDER(FQDN_FOLDERS + ".FastQPassFolder"),
FASTQ_FAIL_FOLDER(FQDN_FOLDERS + ".FastQFailFolder"),
UNCLASSIFIED_FAST5_FOLDER(FQDN_FOLDERS + ".UnclassifiedFast5Folder"),
UNCLASSIFIED_FASTQ_FOLDER(FQDN_FOLDERS + ".UnclassifiedFastQFolder"),
POD5_PASS_FOLDER(FQDN_FOLDERS + ".Pod5PassFolder"),
POD5_FAIL_FOLDER(FQDN_FOLDERS + ".Pod5FailFolder"),
POD5_SKIP_FOLDER(FQDN_FOLDERS + ".Pod5SkipFolder"),
OTHER_REPORTS_FOLDER(FQDN_FOLDERS + ".OtherReportsFolder"),
BASECALLING_FOLDER(FQDN_FOLDERS + ".BasecallingFolder"),

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29 changes: 28 additions & 1 deletion ...est/groovy/life/qbic/datamodel/datasets/datastructure/OxfordNanoporeExperimentSpec.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,9 @@ class OxfordNanoporeExperimentSpec extends Specification {
@Shared
Map minimalDoradoDataStructure

@Shared
Map fullDoradoDataStructure

def setupSpec() {
def folder = "nanopore/"
InputStream stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example.json")
Expand Down Expand Up @@ -96,6 +99,10 @@ class OxfordNanoporeExperimentSpec extends Specification {
stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-minimal-structure-dorado-basecaller.json")
minimalDoradoDataStructure = (Map) new JsonSlurper().parse(stream)
stream.close()
// read in minimal required example with dorado based basecalling
stream = Thread.currentThread().getContextClassLoader().getResourceAsStream(folder+"valid-example-dorado-basecaller.json")
fullDoradoDataStructure = (Map) new JsonSlurper().parse(stream)
stream.close()
}

def "Create simple sample Oxford Nanopore experiment successfully"() {
Expand Down Expand Up @@ -203,7 +210,7 @@ class OxfordNanoporeExperimentSpec extends Specification {
assert measurements[0].asicTemp == "32.631687"
}

def "Create sample Oxford Nanopore experiment successfully for dorado basecaller generated structure"() {
def "Create sample Oxford Nanopore experiment successfully for dorado basecaller generated minimal structure"() {
given:
final def example = minimalDoradoDataStructure

Expand All @@ -219,6 +226,26 @@ class OxfordNanoporeExperimentSpec extends Specification {
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("fast5skip")
}

def "Create sample Oxford Nanopore experiment successfully for dorado basecaller generated full structure"() {
given:
final def example = fullDoradoDataStructure

when:
final def experiment = OxfordNanoporeExperiment.create(example)
final def measurements = experiment.getMeasurements()

then:
assert experiment.sampleCode == "QABCD001AB"
assert measurements.size() == 1
assert measurements[0].asicTemp == "32.631687"
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("pod5skip")
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("fast5skip")
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("fast5pass")
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("fast5fail")
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("pod5pass")
assert measurements[0].getRawDataPerSample(experiment).get("QABCD001AB").containsKey("pod5fail")
}

def "Create a simple pooled Oxford Nanopore experiment successfully"() {
given:
final def example = pooledDataStructure
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269 changes: 269 additions & 0 deletions src/test/resources/nanopore/valid-example-dorado-basecaller.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,269 @@
{
"name": "QABCD001AB_E12A345a01_PAE12345",
"path": "./",
"children": [
{
"name": "20200122_1217_1-A1-B1-PAE12345_1234567a",
"metadata": {
"adapter": "flongle",
"asic_temp": "32.631687",
"base_caller": "",
"base_caller_version": "3.2.8+bd67289",
"device_type": "promethion",
"flow_cell_id": "PAE26306",
"flow_cell_product_code": "FLO-PRO002",
"flow_cell_position": "2-A3-D3",
"hostname": "PCT0094",
"protocol": "sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109:True",
"started": "2020-02-11T15:52:10.465982+01:00"
},
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a",
"children": [
{
"name": "report_.md",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md",
"file_type": "md"
},
{
"name": "final_summary_.txt",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt",
"file_type": "txt"
},
{
"name": "sequencing_summary_.txt",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt",
"file_type": "txt"
},
{
"name": "additional_file_.new",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/additional_file_.new",
"file_type": "new"
},
{
"name": "not_relevant_file_.wow",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/not_relevant_file_.wow",
"file_type": "wow"
},
{
"name": "unknown_folder",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder",
"children": [
{
"name": "unknown_child_folder",
"path": "20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/unknown_child_folder",
"children": [
{
"name": "unknown_file_.new",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/unknown_child_folder/unknown_file_.new",
"file_type": "new"
}
]
},
{
"name": "unknown_file_.new",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/unknown_file_.new",
"file_type": "new"
}
]
},
{
"name": "fast5_skip",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/",
"children": [
{
"name": "myfile2.fast5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5",
"file_type": "fast5"
},
{
"name": "myfile4.fast5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5",
"file_type": "fast5"
},
{
"name": "myfile3.fast5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5",
"file_type": "fast5"
},
{
"name": "myfile5.fast5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5",
"file_type": "fast5"
},
{
"name": "myfile.fast5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5",
"file_type": "fast5"
}
]
},
{
"name": "pod5_skip",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/",
"children": [
{
"name": "myfile2.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5",
"file_type": "pod5"
},
{
"name": "myfile4.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5",
"file_type": "pod5"
},
{
"name": "myfile3.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5",
"file_type": "pod5"
},
{
"name": "myfile5.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5",
"file_type": "pod5"
},
{
"name": "myfile.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5",
"file_type": "pod5"
}
]
},
{
"name": "pod5_pass",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass",
"children": [
{
"name": "myfile2.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5",
"file_type": "pod5"
},
{
"name": "myfile4.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5",
"file_type": "pod5"
},
{
"name": "myfile3.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5",
"file_type": "pod5"
},
{
"name": "myfile5.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5",
"file_type": "pod5"
},
{
"name": "myfile.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5",
"file_type": "pod5"
}
]
},
{
"name": "pod5_fail",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/",
"children": [
{
"name": "myfile2.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5",
"file_type": "pod5"
},
{
"name": "myfile4.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5",
"file_type": "pod5"
},
{
"name": "myfile3.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5",
"file_type": "pod5"
},
{
"name": "myfile5.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5",
"file_type": "pod5"
},
{
"name": "myfile.pod5",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5",
"file_type": "pod5"
}
]
},
{
"name": "basecalling",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling",
"children": [
{
"name": "fastq_pass",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass",
"children": [
{
"name": "myfile3.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile2.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile4.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile5.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile1.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz",
"file_type": "fastq.gz"
}
]
},
{
"name": "fastq_fail",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/",
"children": [
{
"name": "myfile3.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile2.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile4.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile5.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz",
"file_type": "fastq.gz"
},
{
"name": "myfile.fastq.gz",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz",
"file_type": "fastq.gz"
}
]
},
{
"name": "guppy_basecall_client_log*.log",
"path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log*.log",
"file_type": "log"
}
]
}
]
}
]
}

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