Add Full data structure example

qbicsoftware · Nov 3, 2023 · 24d9a37 · 24d9a37
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diff --git a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy
@@ -138,6 +138,19 @@ class NanoporeParserSpec extends Specification {
     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")

diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/barcode_alignment_.tsv
diff --git a/...do_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz b/...do_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile.fastq.gz
@@ -0,0 +1 @@
+This is some text
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile2.fastq.gz
@@ -0,0 +1 @@
+This is some text
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile3.fastq.gz
@@ -0,0 +1 @@
+This is some text
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile4.fastq.gz
@@ -0,0 +1 @@
+This is some text
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_fail/myfile5.fastq.gz
@@ -0,0 +1 @@
+This is some text
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile1.fastq.gz
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile2.fastq.gz
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile3.fastq.gz
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile4.fastq.gz
diff --git a/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz b/...o_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/fastq_pass/myfile5.fastq.gz
diff --git a/...xample/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log b/...xample/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/guppy_basecall_client_log-.log
diff --git a/...orado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt b/...orado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_summary_.txt
diff --git a/...rado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js b/...rado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/basecalling/sequencing_telemetry_.js
diff --git a/...pore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5 b/...pore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile.fast5
@@ -0,0 +1 @@
+This is some text
diff --git a/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5 b/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile2.fast5
@@ -0,0 +1 @@
+This is some text
diff --git a/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5 b/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile3.fast5
@@ -0,0 +1 @@
+This is some text
diff --git a/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5 b/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile4.fast5
@@ -0,0 +1 @@
+This is some text
diff --git a/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5 b/...ore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_skip/myfile5.fast5
@@ -0,0 +1 @@
+This is some text
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile1.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz
diff --git a/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz b/..._valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz
diff --git a/..._nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/..._nanopore_valid_dorado_example/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/...nopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5 b/...nopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile2.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile3.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile4.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_fail/myfile5.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...nopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5 b/...nopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile2.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile3.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile4.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_pass/myfile5.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...nopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5 b/...nopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile2.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile3.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile4.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5 b/...opore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/pod5_skip/myfile5.pod5
@@ -0,0 +1 @@
+This is some text
diff --git a/...anopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/...anopore_valid_dorado_example/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/...pore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt b/...pore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/sequencing_summary_.txt
diff --git a/...45_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new b/...45_nanopore_valid_dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_file.new
diff --git a/...dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here b/...dorado_example/20200122_1217_1-A1-B1-PAE12345_1234567a/unknown_folder/subfolder_file.here