Prepare version 1.11.0 (#98)

* Sync with hotfix 1.9.2 (#69)

* Hotfix 1.9.1 (#66)

* Fix RST syntax error

* Remove orphaned print statement

* Update CL

* Bump version 1.9.1 -> 1.9.2

Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>

* Update maxquant file parser (#74)

The summary file is now searched within the summary folder

* Remove qube files and Bump version to 1.11.0-SNAPSHOT

* Bump conf.py to current version

* Bump version to 1.11.0-SNAPSHOT

* Include groovydoc plugin in report generation (#59)

* Feature/update nanopore (#91)

* increase some versions, fix testing env

* add tests for alternative nanopore structure

* Add worflow triggers (#93)

* Add triggers

* Reorder git commands

* Use master as base, not main

* parser

* update workflows (#94)

* Set version to 1.10.6

* update pom

* Fix project setup (#96)

* add possibility of some metadata values being empty

* comments

* extract method to validate a single schema

Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de>
Co-authored-by: JohnnyQ5 <support@qbic.zendesk.com>
Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>
Co-authored-by: Sven F <9976560+sven1103@users.noreply.github.com>

* Feature/update nanopore (#97)

* increase some versions, fix testing env

* add tests for alternative nanopore structure

* Add worflow triggers (#93)

* Add triggers

* Reorder git commands

* Use master as base, not main

* parser

* update workflows (#94)

* Set version to 1.10.6

* update pom

* Fix project setup (#96)

* add possibility of some metadata values being empty

* comments

* extract method to validate a single schema

* use data-model-lib release

Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de>
Co-authored-by: JohnnyQ5 <support@qbic.zendesk.com>
Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>
Co-authored-by: Sven F <9976560+sven1103@users.noreply.github.com>

* Update CHANGELOG.rst

Co-authored-by: Tobias Koch <KochTobi@users.noreply.github.com>

Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de>
Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de>
Co-authored-by: jnnfr <jennifer.boedker@qbic.uni-tuebingen.de>
Co-authored-by: JohnnyQ5 <support@qbic.zendesk.com>
Co-authored-by: Sven F <9976560+sven1103@users.noreply.github.com>
Co-authored-by: Tobias Koch <KochTobi@users.noreply.github.com>

CHANGELOG.rst

@@ -4,6 +4,8 @@ Changelog
 
 This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
+For information about newer versions please refer to `our GitHub releases <https://github.com/qbicsoftware/core-utils-lib/releases>`_
+
 1.10.4 (2022-01-04)
 ------------------
 
@@ -105,6 +107,7 @@ This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
 **Deprecated**
 
+
 1.9.2 (2021-07-20)
 ------------------
 
@@ -114,6 +117,8 @@ This project adheres to `Semantic Versioning <https://semver.org/>`_.
 
 * Removes orphaned log statement
 
+* Update 'life.qbic.utils.MaxQuantParser', parsing the summary file from a new summary folder (`#74 <https://github.com/qbicsoftware/core-utils-lib/pull/74>`_)
+
 **Dependencies**
 
 **Deprecated**

docs/conf.py

@@ -55,9 +55,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = '1.10.2'
+version = '1.11.0-SNAPSHOT'
 # The full version, including alpha/beta/rc tags.
-release = '1.10.2'
+release = '1.11.0-SNAPSHOT'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pom.xml

@@ -1,12 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <project
-  xmlns="http://maven.apache.org/POM/4.0.0">
+  xmlns="http://maven.apache.org/POM/4.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
   <groupId>life.qbic</groupId>
   <artifactId>core-utils-lib</artifactId>
   <description>Collection of non-Vaadin, non-Liferay utilities.</description>
   <modelVersion>4.0.0</modelVersion>
   <name>Core Utilities Library</name>
-  <version>1.10.6</version>
+  <version>1.11.0-SNAPSHOT</version>
   <url>https://github.com/qbicsoftware/core-utils-lib</url>
   <packaging>jar</packaging>
   <properties>
@@ -125,7 +127,7 @@
     <dependency>
       <artifactId>data-model-lib</artifactId>
       <groupId>life.qbic</groupId>
-      <version>2.16.1</version>
+      <version>2.18.0</version>
     </dependency>
     <dependency>
       <groupId>org.mockito</groupId>
@@ -213,12 +215,12 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-site-plugin</artifactId>
-        <version>3.7.1</version>
+        <version>3.9.1</version>
       </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-project-info-reports-plugin</artifactId>
-        <version>3.0.0</version>
+        <version>3.1.1</version>
       </plugin>
       <plugin>
         <groupId>life.qbic</groupId>
@@ -249,4 +251,12 @@
       </plugin>
     </plugins>
   </build>
+  <reporting>
+    <plugins>
+      <plugin>
+        <groupId>life.qbic</groupId>
+        <artifactId>groovydoc-maven-plugin</artifactId>
+      </plugin>
+    </plugins>
+  </reporting>
 </project>

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 life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutput
+import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputV2
 import org.everit.json.schema.Schema
 import org.everit.json.schema.ValidationException
 import org.everit.json.schema.loader.SchemaLoader
@@ -38,7 +39,7 @@ class NanoporeParser {
         } catch (ValidationException validationException) {
             // we have to fetch all validation exceptions
             def causes = validationException.getAllMessages().collect{ it }.join("\n")
-            throw validationException
+            throw new ValidationException(causes)
         }
     }
 
@@ -87,12 +88,13 @@ class NanoporeParser {
                 jsonEnded = true
             }
         }
-        def finalMetaData = (Map) jsonSlurper.parseText(buffer.toString())
 
+        def finalMetaData = (Map) jsonSlurper.parseText(buffer.toString())
         new File(Paths.get(root.toString(), summaryFile["path"].toString()) as String)
                 .readLines().each { line ->
             def split = line.split("=")
-            finalMetaData[split[0]] = split[1]
+            def value = split.size() > 1 ? split[1] : ""
+            finalMetaData[split[0]] = value
         }
 
         return finalMetaData
@@ -155,15 +157,26 @@ class NanoporeParser {
      * @throws org.everit.json.schema.ValidationException
      */
     private static void validateJson(String json) throws ValidationException {
-        // Step1: load schema
+        // Step 1: load schema
         JSONObject jsonObject = new JSONObject(json)
-        InputStream schemaStream = OxfordNanoporeInstrumentOutput.getSchemaAsStream()
-        JSONObject rawSchema = new JSONObject(new JSONTokener(schemaStream))
-        Schema jsonSchema = SchemaLoader.load(rawSchema)
-        // Step2: validate against schema return if valid, throw exception if invalid
+        try {
+            // Step 2: validate against schema return if valid, throw exception if invalid
+            validateUsingSchema(OxfordNanoporeInstrumentOutput.getSchemaAsStream(), jsonObject)
+        } catch (ValidationException validationException) {
+            validateUsingSchema(OxfordNanoporeInstrumentOutputV2.getSchemaAsStream(), jsonObject)
+        }
+    }
+
+    private static void validateUsingSchema(InputStream schemaAsStream, JSONObject jsonObject) throws ValidationException {
+        Schema jsonSchema = loadSchemaFromStream(schemaAsStream)
         jsonSchema.validate(jsonObject)
     }
 
+    private static Schema loadSchemaFromStream(InputStream stream) {
+        JSONObject rawSchema = new JSONObject(new JSONTokener(stream))
+        return SchemaLoader.load(rawSchema)
+    }
+
     /*
      * Converts a file tree into a json object.
      */

src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy

@@ -25,6 +25,36 @@ class NanoporeParserSpec extends Specification {
     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")
+    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")
+    when:
+    def experiment = NanoporeParser.parseFileStructure(pathToDirectory)
+    then:
+    assert experiment instanceof OxfordNanoporeExperiment
+    // Check that the metadata from the report file is parsed
+    assert experiment.getMeasurements().get(0).getFlowCellType() == "FLO-PRO002"
+    // Check that the metadata from the summary file has been retrieved, but data can also be empty
+    assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL"
+    assert experiment.getMeasurements().get(0).getFlowcellId() == "flow_cell_from_summary"
+    assert experiment.getMeasurements().get(0).getAsicTemp() == ""
+    assert experiment.getMeasurements().get(0).getMachineHost() == ""
+    assert experiment.getMeasurements().get(0).getStartDate() == ""
+  }
+
   def "qc folder is ignored"() {
     given:
     def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/with_qc_folder/QABCD001AB_E12A345a01_PAE12345")

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/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

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new/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

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz

@@ -0,0 +1 @@
+This is some text

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt

@@ -0,0 +1,17 @@
+instrument=
+position=1-A3-D3
+flow_cell_id=flow_cell_from_summary
+sample_id=QNANO027AE_E19D023a01_200211
+protocol_group_id=
+protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL
+protocol_run_id=
+acquisition_run_id=
+started=
+acquisition_stopped=2020-02-14T08:39:54.688916+01:00
+processing_stopped=2020-02-14T08:39:58.804639+01:00
+basecalling_enabled=
+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

src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md

@@ -0,0 +1,52 @@
+Tracking ID
+===========
+
+{
+    "asic_id": "",
+    "asic_id_eeprom": "",
+    "asic_temp": "",
+    "asic_version": "",
+    "auto_update": "",
+    "auto_update_source": "",
+    "bream_is_standard": "",
+    "configuration_version": "",
+    "device_id": "",
+    "device_type": "promethion",
+    "distribution_status": "",
+    "distribution_version": "",
+    "exp_script_name": "",
+    "exp_script_purpose": "",
+    "exp_start_time": "2020-01-28T15:17:38Z",
+    "flow_cell_id": "flow_cell_from_report",
+    "flow_cell_product_code": "FLO-PRO002",
+    "guppy_version": "3.2.8+bd67289",
+    "heatsink_temp": "",
+    "hostname": "",
+    "hublett_board_id": "",
+    "hublett_firmware_version": "",
+    "installation_type": "",
+    "ip_address": "",
+    "local_firmware_file": "",
+    "mac_address": "",
+    "operating_system": "",
+    "protocol_group_id": "",
+    "protocol_run_id": "",
+    "protocols_version": "",
+    "run_id": "",
+    "sample_id": "QNANO036AD_E19D023b04",
+    "satellite_board_id": "",
+    "satellite_firmware_version": "",
+    "usb_config": "",
+    "version": ""
+}
+
+Duty Time
+=========
+
+ID: db9e9383d44d80bbe1e2600c7a7419056610d46d
+
+Channel State,Experiment Time (minutes),State Time (samples),
+strand,0,144832342
+strand,1,158421270
+strand,2,378095352
+strand,3,472685319