diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 55d123d..ecaba48 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -17,16 +17,19 @@ jobs: strategy: matrix: - go: [ "1.16" ] - baton: [ "2.1.0" ] - experimental: [false] include: - - irods: "4.2.7" + # iRODS 4.2.10 clients vs 4.2.7 server + - go: "1.17" + irods: "4.2.10" server_image: "wsinpg/ub-16.04-irods-4.2.7:latest" + baton: "3.1.0" + experimental: false + # iRODS 4.2.10 clients vs 4.2.10 server + - go: "1.17" + irods: "4.2.10" + server_image: "wsinpg/ub-18.04-irods-4.2.10:latest" + baton: "3.1.0" experimental: false - - irods: "4.2.8" - server_image: "wsinpg/ub-18.04-irods-4.2.8:latest" - experimental: true services: irods: @@ -53,14 +56,13 @@ jobs: conda config --set auto_update_conda False conda config --prepend channels "$WSI_CONDA_CHANNEL" - conda config --append channels conda-forge conda info - name: "Install iRODS clients" run: | conda create -y -n "$CONDA_TEST_ENVIRONMENT" - conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands ==${{ matrix.irods }}" - conda install -y -n "$CONDA_TEST_ENVIRONMENT" "baton ==${{ matrix.baton }}" + conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands=${{ matrix.irods }}" + conda install -y -n "$CONDA_TEST_ENVIRONMENT" "baton=${{ matrix.baton }}" - name: "Configure iRODS clients" run: | @@ -74,7 +76,7 @@ jobs: "irods_user_name": "irods", "irods_zone_name": "testZone", "irods_home": "/testZone/home/irods", - "irods_default_resource": "testResc" + "irods_default_resource": "replResc" } EOF diff --git a/.travis.yml b/.travis.yml deleted file mode 100644 index 01f5361..0000000 --- a/.travis.yml +++ /dev/null @@ -1,44 +0,0 @@ -dist: bionic - -services: - - docker - -language: go - -go: - - "1.14" - - "1.15" - -_iRODS_4_2_8: &iRODS_4_2_8 DOCKER_IMAGE="wsinpg/ub-18.04-irods-4.2.8:latest" IRODS_VERSION="==4.2.8" BATON_VERSION=">2.0.1" - -env: - global: - - GO111MODULE=on - - WSI_CONDA_CHANNEL="https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic" - jobs: - - DOCKER_IMAGE="wsinpg/ub-16.04-irods-4.2.7:latest" IRODS_VERSION="==4.2.7" BATON_VERSION=">2.0.1" - - *iRODS_4_2_8 - -jobs: - allow_failures: - - go: "1.14" - env: *iRODS_4_2_8 - - go: "1.15" - env: *iRODS_4_2_8 - -cache: - directories: - - $HOME/.cache/go-build - - $HOME/gopath/pkg/mod - -before_install: - - docker pull "$DOCKER_IMAGE" - - docker run -d -p 1247:1247 "$DOCKER_IMAGE" - - docker ps -a - -install: - - ./scripts/travis_install.sh - -script: - - ./scripts/travis_script.sh - diff --git a/CHANGELOG.md b/CHANGELOG.md index 2cf57d4..f4605e5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -8,17 +8,46 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Added -- Add Github Actions test workflow -- Improve recognition of files to be processed and archived -- Add support for TSV files. -- Add support for compressing CSV files. -- Add new all ONT-specific paths to the exclusion list. +### Changed + +## [1.6.0] - 2022-01-10 + +### Added + +- Support for adding iRODS metadata for PromethION-24 runs. +- Support for BAM files. +- support for BED files (compressed). +- iRODS 4.2.10 support. + +### Changed + +- Build with Go.1.17 + +- Bump github.com/rs/zerolog from 1.21.0 to 1.26.1 +- Bump github.com/onsi/ginkgo from 1.16.2 to 1.16.5 +- Bump github.com/onsi/gomega from 1.11.0 to 1.17.0 +- Bump github.com/spf13/cobra from 0.0.7 to 1.3.0 + +### Removed + +- Travis CI configuration. +- PromethION beta report parsing tests and unused test data. + +## [1.5.0] - 2021-04-15 + +### Added + +- Github Actions test workflow. +- Improve recognition of files to be processed and archived. +- Support for TSV files. +- Support for compressing CSV files. +- Add all ONT-specific paths to the exclusion list. - Add the /data/laboratory WSI-specific path to the exclusion list. -- Add iRODS 4.2.8 support +- iRODS 4.2.8 support. ### Removed -- Remove iRODS 4.1.12 support +- RODS 4.1.12 support. ### Changed @@ -88,13 +117,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Checksum creation improvements using tee'ing to avoid re-reading data. - Make the size of the client pool equal to the number of threads. -- Use pgzip implementation. - Gzip compression of fastq and txt files. - Enhancements to FilePath for handling compressed files. - Find paths immediately, then at intervals. ## Changed +- Use pgzip implementation. + - Bump github.com/wtsi-npg/extendo from 1.0.0 to 1.1.0 - Bump github.com/onsi/gomega from 1.5.0 to 1.7.1 - Bump github.com/onsi/ginkgo from 1.8.0 to 1.10.3 diff --git a/go.mod b/go.mod index c29159e..0fc58fc 100644 --- a/go.mod +++ b/go.mod @@ -1,15 +1,15 @@ module github.com/wtsi-npg/valet -go 1.16 +go 1.17 require ( github.com/klauspost/compress v1.9.1 // indirect github.com/klauspost/pgzip v1.2.5 - github.com/onsi/ginkgo v1.16.1 - github.com/onsi/gomega v1.11.0 + github.com/onsi/ginkgo v1.16.5 + github.com/onsi/gomega v1.17.0 github.com/pkg/errors v0.9.1 - github.com/rs/zerolog v1.21.0 - github.com/spf13/cobra v0.0.7 + github.com/rs/zerolog v1.26.0 + github.com/spf13/cobra v1.2.1 github.com/stretchr/testify v1.7.0 github.com/wtsi-npg/extendo/v2 v2.4.0 github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a @@ -18,4 +18,19 @@ require ( golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 ) +require ( + github.com/davecgh/go-spew v1.1.1 // indirect + github.com/fsnotify/fsnotify v1.4.9 // indirect + github.com/inconshreveable/mousetrap v1.0.0 // indirect + github.com/nxadm/tail v1.4.8 // indirect + github.com/pmezard/go-difflib v1.0.0 // indirect + github.com/spf13/pflag v1.0.5 // indirect + golang.org/x/net v0.0.0-20210805182204-aaa1db679c0d // indirect + golang.org/x/sys v0.0.0-20210809222454-d867a43fc93e // indirect + golang.org/x/text v0.3.6 // indirect + gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 // indirect + gopkg.in/yaml.v2 v2.4.0 // indirect + gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b // indirect +) + // replace github.com/wtsi-npg/extendo/v2 => ../extendo diff --git a/go.sum b/go.sum index 84c4e00..e3858aa 100644 --- a/go.sum +++ b/go.sum @@ -1,235 +1,639 @@ cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= +cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= +cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU= +cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU= +cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY= +cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc= +cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0= +cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To= +cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4= 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+honnef.co/go/tools v0.0.1-2020.1.3/go.mod h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9vFzvIQ3k= +honnef.co/go/tools v0.0.1-2020.1.4/go.mod h1:X/FiERA/W4tHapMX5mGpAtMSVEeEUOyHaw9vFzvIQ3k= +rsc.io/binaryregexp v0.2.0/go.mod h1:qTv7/COck+e2FymRvadv62gMdZztPaShugOCi3I+8D8= +rsc.io/quote/v3 v3.1.0/go.mod h1:yEA65RcK8LyAZtP9Kv3t0HmxON59tX3rD+tICJqUlj0= +rsc.io/sampler v1.3.0/go.mod h1:T1hPZKmBbMNahiBKFy5HrXp6adAjACjK9JXDnKaTXpA= diff --git a/scripts/travis_install.sh b/scripts/travis_install.sh deleted file mode 100755 index fc6aef5..0000000 --- a/scripts/travis_install.sh +++ /dev/null @@ -1,37 +0,0 @@ -#!/bin/bash - -set -e -u -x - -wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh -O ~/miniconda.sh - -/bin/bash ~/miniconda.sh -b -p ~/miniconda -~/miniconda/bin/conda clean -tipsy -echo ". ~/miniconda/etc/profile.d/conda.sh" >> ~/.bashrc -echo "conda activate base" >> ~/.bashrc - -. ~/miniconda/etc/profile.d/conda.sh -conda activate base -conda config --set auto_update_conda False -conda config --prepend channels "$WSI_CONDA_CHANNEL" -conda config --append channels conda-forge - -conda create -y -n travis -conda activate travis -conda install -y irods-icommands"$IRODS_VERSION" -conda install -y baton"$BATON_VERSION" - -mkdir -p ~/.irods - -cat <<'EOF' > ~/.irods/irods_environment.json -{ - "irods_host": "localhost", - "irods_port": 1247, - "irods_user_name": "irods", - "irods_zone_name": "testZone", - "irods_home": "/testZone/home/irods", - "irods_default_resource": "testResc" -} -EOF - -go get github.com/onsi/ginkgo/ginkgo -go get github.com/onsi/gomega/... diff --git a/scripts/travis_script.sh b/scripts/travis_script.sh deleted file mode 100755 index 7723350..0000000 --- a/scripts/travis_script.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash - -set -e -x - -. ~/miniconda/etc/profile.d/conda.sh -conda activate travis - -echo "irods" | script -q -c "iinit" /dev/null -ienv -ils - -which baton-do -baton-do --version - -make test diff --git a/valet/predicates.go b/valet/predicates.go index c680c27..285cf13 100644 --- a/valet/predicates.go +++ b/valet/predicates.go @@ -35,28 +35,32 @@ import ( type FilePredicate func(path FilePath) (bool, error) -const Fast5Suffix string = "fast5" // The recognised suffix for fast5 files -const FastqSuffix string = "fastq" // The recognised suffix for fastq files +const Fast5Suffix string = "fast5" +const FastqSuffix string = "fastq" +const BAMSuffix string ="bam" +const BEDSuffix string ="bed" const CSVSuffix string = "csv" const MarkdownSuffix string = "md" const TxtSuffix string = "txt" -const TsvSuffix string = "tsv" +const TSVSuffix string = "tsv" const PDFSuffix string = "pdf" const MD5Suffix string = "md5" // The recognised suffix for MD5 checksum files const GzipSuffix string = "gz" var fast5Regex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", Fast5Suffix)) var fastqRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", FastqSuffix)) +var bamRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", BAMSuffix)) +var bedRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", BEDSuffix)) var txtRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", TxtSuffix)) -var tsvRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", TsvSuffix)) +var tsvRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", TSVSuffix)) var markdownRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", MarkdownSuffix)) var pdfRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", PDFSuffix)) var csvRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", CSVSuffix)) var gzipRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", GzipSuffix)) var reportRegex = regexp.MustCompile(fmt.Sprintf("(?i)report.*[.]%s$", MarkdownSuffix)) -// Matches the run ID of MinKNOW c. August 2019 for GridION and PromethION -// i.e. of the form: +// MinKNOWRunIDRegex matches the run ID of MinKNOW c. August 2019 for GridION +// and PromethION i.e. of the form: // // 20190701_1522_GA10000_FAK83493_3bba1763 // @@ -64,6 +68,8 @@ var MinKNOWRunIDRegex = regexp.MustCompile(`^\d+_\d+_\S+_[A-Za-z0-9]+_[A-Za-z0-9 var RequiresCopying = Or( IsFast5, + IsBAM, + And(IsBED, IsCompressed), And(IsFastq, IsCompressed), And(IsTxt, IsCompressed), And(IsCSV, IsCompressed), @@ -82,19 +88,19 @@ var RequiresChecksum = And( var HasValidChecksumFile = Not(HasStaleChecksumFile) var RequiresCompression = And( - Or(IsFastq, IsTxt, IsCSV), + Or(IsFastq, IsBED, IsTxt, IsCSV), Not(IsCompressed), Not(HasCompressedVersion)) var RequiresAnnotation = IsMinKNOWReport // IsTrue always returns true. -func IsTrue(path FilePath) (bool, error) { +func IsTrue(_ FilePath) (bool, error) { return true, nil } // IsFalse always returns false -func IsFalse(path FilePath) (bool, error) { +func IsFalse(_ FilePath) (bool, error) { return false, nil } @@ -124,7 +130,7 @@ func And(predicates ...FilePredicate) FilePredicate { } } -// And returns a predicate that returns true if any of its arguments return +// Or returns a predicate that returns true if any of its arguments return // true, or returns false otherwise. func Or(predicates ...FilePredicate) FilePredicate { return func(path FilePath) (bool, error) { @@ -165,14 +171,25 @@ func IsFastq(path FilePath) (bool, error) { return fastqRegex.MatchString(path.UncompressedFilename()), nil } +// IsBED returns true if path matches the recognised BED file pattern. Supports +// compressed versions. +func IsBED(path FilePath) (bool, error) { + return bedRegex.MatchString(path.UncompressedFilename()), nil +} + +// IsBAM returns true if path matches the recognised BAM file pattern. +func IsBAM(path FilePath) (bool, error) { + return bamRegex.MatchString(path.Location), nil +} + // IsTxt returns true if path matches the recognised text file pattern. // Supports compressed versions. func IsTxt(path FilePath) (bool, error) { return txtRegex.MatchString(path.UncompressedFilename()), nil } -// IsMarkdown returns true if path matches the recognised markdown file -// pattern. +// IsMarkdown returns true if path matches the recognised markdown file +// pattern. func IsMarkdown(path FilePath) (bool, error) { return markdownRegex.MatchString(path.UncompressedFilename()), nil } @@ -182,7 +199,8 @@ func IsPDF(path FilePath) (bool, error) { return pdfRegex.MatchString(path.Location), nil } -// IsCSV returns true if path matches the recognised CSV file pattern. +// IsCSV returns true if path matches the recognised CSV file pattern. Supports +// compressed versions. func IsCSV(path FilePath) (bool, error) { return csvRegex.MatchString(path.UncompressedFilename()), nil } @@ -272,7 +290,7 @@ func IsMinKNOWRunDir(path FilePath) (bool, error) { return IsMinKNOWRunID(filepath.Base(path.Location)), nil } -// Is IsMinKNOWReport returns true if path is a MinNKNOW run report file. This +// IsMinKNOWReport returns true if path is a MinNKNOW run report file. This // file is Markdown that contains a section of JSON metadata describing details // of the run. func IsMinKNOWReport(path FilePath) (bool, error) { diff --git a/valet/predicates_test.go b/valet/predicates_test.go index 9f2c8af..53d8d08 100644 --- a/valet/predicates_test.go +++ b/valet/predicates_test.go @@ -88,6 +88,34 @@ func TestIsFastqMatch(t *testing.T) { } } +func TestIsBAMMatch(t *testing.T) { + bam, _ := NewFilePath("./testdata/valet/1/reads/alignments/alignments1.bam") + ok, err := IsBAM(bam) + if assert.NoError(t, err) { + assert.True(t, ok, "expected true for a BAM file") + } + + f5, _ := NewFilePath("./testdata/valet/1/reads/fast5/reads1.fast5") + ok, err = IsBAM(f5) + if assert.NoError(t, err) { + assert.False(t, ok, "expected false for a non-BAM file") + } +} + +func TestIsBEDMatch(t *testing.T) { + bed, _ := NewFilePath("./testdata/valet/1/adaptive_sampling_roi1.bed") + ok, err := IsBED(bed) + if assert.NoError(t, err) { + assert.True(t, ok, "expected true for a BED file") + } + + f5, _ := NewFilePath("./testdata/valet/1/reads/fast5/reads1.fast5") + ok, err = IsBED(f5) + if assert.NoError(t, err) { + assert.False(t, ok, "expected false for a non-BED file") + } +} + func TestIsGzipFastqMatch(t *testing.T) { fq, _ := NewFilePath("./testdata/valet/1/reads/fastq/reads2.fastq.gz") diff --git a/valet/report.go b/valet/report.go index 751b672..9610101 100644 --- a/valet/report.go +++ b/valet/report.go @@ -24,6 +24,7 @@ import ( "encoding/json" "io/ioutil" "regexp" + "strconv" "strings" "github.com/pkg/errors" @@ -48,6 +49,33 @@ type MinKNOWReport struct { var gridionDeviceIDRegex = regexp.MustCompile(`^(?:GA|X)(\d)`) +var promethion24DeviceIDMap = map[string]int{ + "1A": 1, + "1B": 2, + "1C": 3, + "1D": 4, + "1E": 5, + "1F": 6, + "1G": 7, + "1H": 8, + "2A": 9, + "2B": 10, + "2C": 11, + "2D": 12, + "2E": 13, + "2F": 14, + "2G": 15, + "2H": 16, + "3A": 17, + "3B": 18, + "3C": 19, + "3D": 20, + "3E": 21, + "3F": 22, + "3G": 23, + "3H": 24, +} + // ParseMinKNOWReport parses a file at path and extracts MinKNOW run metadata // from it. func ParseMinKNOWReport(path string) (MinKNOWReport, error) { @@ -115,8 +143,11 @@ func (report MinKNOWReport) AsMetadata() []ex.AVU { // The value is added under the attribute 'instrument_slot' // // Slot positions are more complex for the PromethION as they are arranged in a -// grid and therefore have an X and Y position. We have not decided how to -// convert the position into a slot value. +// grid and therefore have an X and Y position. The PromethION beta and +// PromethION-24 have different nomenclature. +// +// For the PromethION-24 we are following the column-major order used by ONT's +// MinKNOW API i.e. 1A - 1H, 2A - 2H, 3A - 3H. // func (report MinKNOWReport) AsEnhancedMetadata() ([]ex.AVU, error) { avus := report.AsMetadata() @@ -133,7 +164,21 @@ func (report MinKNOWReport) AsEnhancedMetadata() ([]ex.AVU, error) { WithNamespace(OxfordNanoporeNamespace) avus = append(avus, slot) } - expt := ex.AVU{Attr:"experiment_name", Value: report.ProtocolGroupID}. + + if report.DeviceType == "promethion" { + deviceID := report.DeviceID + id, ok := promethion24DeviceIDMap[deviceID] + if !ok { + return avus, errors.Errorf("Failed to parse device ID '%s'", + deviceID) + } + + slot := ex.AVU{Attr: "instrument_slot", Value: strconv.Itoa(id)}. + WithNamespace(OxfordNanoporeNamespace) + avus = append(avus, slot) + } + + expt := ex.AVU{Attr: "experiment_name", Value: report.ProtocolGroupID}. WithNamespace(OxfordNanoporeNamespace) avus = append(avus, expt) diff --git a/valet/report_test.go b/valet/report_test.go index b4c77a5..d599bbc 100644 --- a/valet/report_test.go +++ b/valet/report_test.go @@ -21,25 +21,26 @@ package valet import ( + "path/filepath" + "strconv" "testing" "github.com/stretchr/testify/assert" ex "github.com/wtsi-npg/extendo/v2" ) -func TestParsePromethIONReport(t *testing.T) { - path := "./testdata/valet/report_PAE48813_20200130_0940_16917585.md" +func TestParsePromethION24Report(t *testing.T) { + path := "./testdata/valet/report_PAH48449_20211215_1420_227842f4.md" report, err := ParseMinKNOWReport(path) if assert.NoError(t, err) { - assert.Equal(t,"2-E1-H1", report.DeviceID) + assert.Equal(t, "1A", report.DeviceID) assert.Equal(t, "promethion", report.DeviceType) - assert.Equal(t, "19.12.5", report.DistributionVersion) - assert.Equal(t, "PAE48813", report.FlowcellID) - assert.Equal(t, "3.2.8+bd67289", report.GuppyVersion) - assert.Equal(t, "PCT0016", report.Hostname) - assert.Equal(t, "mMelMel3", report.ProtocolGroupID) - assert.Equal(t, "52a0d863bccd1d78530c425e8077150d5391fc34", report.RunID) - assert.Equal(t, "mMelMel3", report.SampleID) + assert.Equal(t, "21.10.8", report.DistributionVersion) + assert.Equal(t, "5.0.17+99baa5b27", report.GuppyVersion) + assert.Equal(t, "PC24B148", report.Hostname) + assert.Equal(t, "lambda_p24_all_positions", report.ProtocolGroupID) + assert.Equal(t, "39ae988ba41499479e0dc1fcae29fa4059701d08", report.RunID) + assert.Equal(t, "lambda_151221_1", report.SampleID) } } @@ -47,7 +48,7 @@ func TestParseGridIONReport(t *testing.T) { path := "./testdata/valet/report_ABQ808_20200204_1257_e2e93dd1.md" report, err := ParseMinKNOWReport(path) if assert.NoError(t, err) { - assert.Equal(t,"X2", report.DeviceID) + assert.Equal(t, "X2", report.DeviceID) assert.Equal(t, "gridion", report.DeviceType) assert.Equal(t, "19.12.2", report.DistributionVersion) assert.Equal(t, "ABQ808", report.FlowcellID) @@ -59,23 +60,23 @@ func TestParseGridIONReport(t *testing.T) { } } -func TestEnhancedPromethIONMetadata(t *testing.T) { - path := "./testdata/valet/report_PAE48813_20200130_0940_16917585.md" - report, _ := ParseMinKNOWReport(path) +func TestEnhancedPromethION24Report(t *testing.T) { + path := "./testdata/valet/report_PAH48449_20211215_1420_227842f4.md" + report, err := ParseMinKNOWReport(path) metadata, err := report.AsEnhancedMetadata() if assert.NoError(t, err) { expected := []ex.AVU{ - {Attr:"ont:device_id", Value:"2-E1-H1"}, - {Attr:"ont:device_type", Value:"promethion"}, - {Attr:"ont:distribution_version", Value:"19.12.5"}, - {Attr:"ont:flowcell_id", Value:"PAE48813"}, - {Attr:"ont:guppy_version", Value:"3.2.8+bd67289"}, - {Attr:"ont:hostname", Value:"PCT0016"}, - {Attr:"ont:protocol_group_id", Value:"mMelMel3"}, - {Attr:"ont:run_id", Value:"52a0d863bccd1d78530c425e8077150d5391fc34"}, - {Attr:"ont:sample_id", Value:"mMelMel3"}, - // {Attr:"ont:instrument_slot", Value:"2"} TODO: slot not yet supported - {Attr:"ont:experiment_name", Value:"mMelMel3"}} + {Attr: "ont:device_id", Value: "1A"}, + {Attr: "ont:device_type", Value: "promethion"}, + {Attr: "ont:distribution_version", Value: "21.10.8"}, + {Attr: "ont:flowcell_id", Value: "PAH48449"}, + {Attr: "ont:guppy_version", Value: "5.0.17+99baa5b27"}, + {Attr: "ont:hostname", Value: "PC24B148"}, + {Attr: "ont:protocol_group_id", Value: "lambda_p24_all_positions"}, + {Attr: "ont:run_id", Value: "39ae988ba41499479e0dc1fcae29fa4059701d08"}, + {Attr: "ont:sample_id", Value: "lambda_151221_1"}, + {Attr: "ont:instrument_slot", Value: "1"}, + {Attr: "ont:experiment_name", Value: "lambda_p24_all_positions"}} assert.ElementsMatch(t, expected, metadata) } @@ -87,18 +88,47 @@ func TestEnhancedGridIONMetadata(t *testing.T) { metadata, err := report.AsEnhancedMetadata() if assert.NoError(t, err) { expected := []ex.AVU{ - {Attr:"ont:device_id", Value:"X2"}, - {Attr:"ont:device_type", Value:"gridion"}, - {Attr:"ont:distribution_version", Value:"19.12.2"}, - {Attr:"ont:flowcell_id", Value:"ABQ808"}, - {Attr:"ont:guppy_version", Value:"3.2.8+bd67289"}, - {Attr:"ont:hostname", Value:"GXB02004"}, - {Attr:"ont:protocol_group_id", Value:"85"}, - {Attr:"ont:run_id", Value:"5531cbcf622d2d98dbff00af0261c6f19f91340f"}, - {Attr:"ont:sample_id", Value:"DN615089W_B1"}, - {Attr:"ont:instrument_slot", Value:"2"}, - {Attr:"ont:experiment_name", Value:"85"}} + {Attr: "ont:device_id", Value: "X2"}, + {Attr: "ont:device_type", Value: "gridion"}, + {Attr: "ont:distribution_version", Value: "19.12.2"}, + {Attr: "ont:flowcell_id", Value: "ABQ808"}, + {Attr: "ont:guppy_version", Value: "3.2.8+bd67289"}, + {Attr: "ont:hostname", Value: "GXB02004"}, + {Attr: "ont:protocol_group_id", Value: "85"}, + {Attr: "ont:run_id", Value: "5531cbcf622d2d98dbff00af0261c6f19f91340f"}, + {Attr: "ont:sample_id", Value: "DN615089W_B1"}, + {Attr: "ont:instrument_slot", Value: "2"}, + {Attr: "ont:experiment_name", Value: "85"}} assert.ElementsMatch(t, expected, metadata) } } + +func TestPromethion24InstrumentSlots(t *testing.T) { + paths, err := filepath.Glob("./testdata/valet/report_PAH48449_20211215*.md") + if assert.NoError(t, err) { + // The globbed paths are one report file for each slot in flowcell bank + // "A", being "1A" to "1F" + assert.Equal(t, 6, len(paths)) + + // These should have slot values of 1 to 6 + for i, path := range paths { + report, _ := ParseMinKNOWReport(path) + metadata, err := report.AsEnhancedMetadata() + if assert.NoError(t, err) { + found := false + for _, avu := range metadata { + if avu.Attr == "ont:instrument_slot" { + // Slots are indexed from 1 + assert.Equal(t, avu.Value, strconv.Itoa(i+1)) + found = true + break + } + } + assert.True(t, found, "Failed to parse a DeviceID", + "ont:instrument_slot attribute missing from "+ + "metadata for %s", path) + } + } + } +} diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/PCT0016_20190820_163905_PAD71219_promethion_sequencing_run_DN467851H_B2_C2_E2_F2_sequencing_summary.txt b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/PCT0016_20190820_163905_PAD71219_promethion_sequencing_run_DN467851H_B2_C2_E2_F2_sequencing_summary.txt deleted file mode 100644 index 57e2d04..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/PCT0016_20190820_163905_PAD71219_promethion_sequencing_run_DN467851H_B2_C2_E2_F2_sequencing_summary.txt +++ /dev/null @@ -1 +0,0 @@ -52c132f5-f307-4a80-9289-c1fde4c8f24c diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/duty_time.csv b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/duty_time.csv deleted file mode 100644 index 214224d..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/duty_time.csv +++ /dev/null @@ -1 +0,0 @@ -7d8d2e65-23c2-4636-9f77-0b549cbd8760 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_0.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_0.fast5 deleted file mode 100644 index 4ac4707..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_0.fast5 +++ /dev/null @@ -1 +0,0 @@ -e41b900d-c0f7-4eaf-af28-5fa67edf6a88 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_1.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_1.fast5 deleted file mode 100644 index 110d0ba..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_1.fast5 +++ /dev/null @@ -1 +0,0 @@ -829d1323-3d22-4060-841d-b8282d271924 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_2.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_2.fast5 deleted file mode 100644 index c8dbd99..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_2.fast5 +++ /dev/null @@ -1 +0,0 @@ -23799293-de85-487d-8c2f-1b681a34f27d diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_3.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_3.fast5 deleted file mode 100644 index 598418f..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_3.fast5 +++ /dev/null @@ -1 +0,0 @@ -9e826823-658e-4d74-99fa-fa871faec2a4 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_4.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_4.fast5 deleted file mode 100644 index 1173770..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_4.fast5 +++ /dev/null @@ -1 +0,0 @@ -991f4131-8497-4b5d-a9f2-26771ef60be3 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_5.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_5.fast5 deleted file mode 100644 index 4e38c9e..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_5.fast5 +++ /dev/null @@ -1 +0,0 @@ -cd80df8c-2a26-4a9f-b408-745250e20474 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_6.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_6.fast5 deleted file mode 100644 index 6a15fc9..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_6.fast5 +++ /dev/null @@ -1 +0,0 @@ -6604570e-4499-4371-9339-809a9d8b6f8b diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_7.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_7.fast5 deleted file mode 100644 index 48c0da9..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_7.fast5 +++ /dev/null @@ -1 +0,0 @@ -77bf8b4e-e8ff-4025-9563-136e237c8cfa diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_8.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_8.fast5 deleted file mode 100644 index 4ce2b02..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_8.fast5 +++ /dev/null @@ -1 +0,0 @@ -47a574de-b6ae-4c08-94c3-7ad52f536a31 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_9.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_9.fast5 deleted file mode 100644 index da9c737..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_fail/PAD71219_5a61cd0f2001c43c7aaf1f084ff61103267c0c33_9.fast5 +++ /dev/null @@ -1 +0,0 @@ -2be31e34-3d40-4399-9aeb-cb319f0d8d13 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_pass/.gitignore b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_pass/.gitignore deleted file mode 100644 index 5e7d273..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/fast5_pass/.gitignore +++ /dev/null @@ -1,4 +0,0 @@ -# Ignore everything in this directory -* -# Except this file -!.gitignore diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/final_summary.txt b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/final_summary.txt deleted file mode 100644 index 103cc6c..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/final_summary.txt +++ /dev/null @@ -1 +0,0 @@ -0614782a-df81-40dd-a74c-e2ac265d24a2 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/report.md b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/report.md deleted file mode 100644 index cf49cd4..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/report.md +++ /dev/null @@ -1,50 +0,0 @@ -Tracking ID -=========== - -{ - "asic_id": "0004A30B00271C26", - "asic_id_eeprom": "0004A30B00271C26", - "asic_temp": "30.315973", - "asic_version": "Unknown", - "auto_update": "0", - "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", - "bream_is_standard": "0", - "device_id": "2-E7-H7", - "device_type": "promethion", - "distribution_status": "stable", - "distribution_version": "19.06.9", - "exp_script_name": "N/A", - "exp_script_purpose": "sequencing_run", - "exp_start_time": "2019-08-20T15:40:18Z", - "flow_cell_id": "PAD71219", - "guppy_version": "3.0.5+45c3543", - "heatsink_temp": "36.303722", - "hostname": "PCT0016", - "hublett_board_id": "0138a8860239bcc1", - "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": "DN467851H_Multiplex_Pool_1", - "protocol_run_id": "", - "protocols_version": "4.1.8", - "run_id": "5a61cd0f2001c43c7aaf1f084ff61103267c0c33", - "sample_id": "DN467851H_B2_C2_E2_F2", - "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": "3.4.6" -} - -Duty Time -========= - -ID: 5a61cd0f2001c43c7aaf1f084ff61103267c0c33 - -Channel State,Experiment Time (minutes),State Time (samples), -strand,0,183372819 -strand,1,174467713 -strand,2,338669372 -strand,3,453221196 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/report.pdf b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/report.pdf deleted file mode 100644 index 298ed65..0000000 Binary files a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/report.pdf and /dev/null differ diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/stats b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/stats deleted file mode 100644 index b98a016..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/stats +++ /dev/null @@ -1 +0,0 @@ -037f9be4-509a-4827-8859-49f14ddbf4d6 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/throughput.csv b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/throughput.csv deleted file mode 100644 index 790da5f..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_1/DN467851H_B2_C2_E2_F2/20190820_1538_2-E7-H7_PAD71219_a4a384ec/throughput.csv +++ /dev/null @@ -1 +0,0 @@ -df6339df-63be-4592-83df-988bd451b531 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/PCT0016_20190821_164534_PAD73195_promethion_sequencing_run_DN467851H_A3_F3_G3_H3_sequencing_summary.txt b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/PCT0016_20190821_164534_PAD73195_promethion_sequencing_run_DN467851H_A3_F3_G3_H3_sequencing_summary.txt deleted file mode 100644 index c0e4481..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/PCT0016_20190821_164534_PAD73195_promethion_sequencing_run_DN467851H_A3_F3_G3_H3_sequencing_summary.txt +++ /dev/null @@ -1 +0,0 @@ -a6095ad1-2f29-407f-a0e0-d551154fa60a diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/duty_time.csv b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/duty_time.csv deleted file mode 100644 index f5d3785..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/duty_time.csv +++ /dev/null @@ -1 +0,0 @@ -f260f85e-1139-459c-85dc-17e061413360 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/fast5_fail/PAD73195_86b15e57ca99113b4bb75b4ad1e8da937dde06d9_0.fast5 b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/fast5_fail/PAD73195_86b15e57ca99113b4bb75b4ad1e8da937dde06d9_0.fast5 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b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/final_summary.txt deleted file mode 100644 index 707ce14..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/final_summary.txt +++ /dev/null @@ -1 +0,0 @@ -bc87c5e0-734f-464a-9472-996fc62b09cb diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/report.md b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/report.md deleted file mode 100644 index 0c2b894..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/report.md +++ /dev/null @@ -1,50 +0,0 @@ -Tracking ID -=========== - -{ - "asic_id": "0004A30B00259368", - "asic_id_eeprom": "0004A30B00259368", - "asic_temp": "31.289753", - "asic_version": "Unknown", - "auto_update": "0", - "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", - "bream_is_standard": "0", - "device_id": "1-A1-D1", - "device_type": "promethion", - "distribution_status": "stable", - "distribution_version": "19.06.9", - "exp_script_name": "N/A", - "exp_script_purpose": "sequencing_run", - "exp_start_time": "2019-08-21T15:46:15Z", - "flow_cell_id": "PAD73195", - "guppy_version": "3.0.5+45c3543", - "heatsink_temp": "35.561672", - "hostname": "PCT0016", - "hublett_board_id": "013bec8739c4bd8a", - "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": "DN467851H_Multiplex_Pool_2", - "protocol_run_id": "", - "protocols_version": "4.1.8", - "run_id": 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differ diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/stats b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/stats deleted file mode 100644 index b538d48..0000000 --- a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/stats +++ /dev/null @@ -1 +0,0 @@ -76e2136e-9c3f-4021-aa82-d15534017003 diff --git a/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/throughput.csv b/valet/testdata/platform/ont/minknow/promethion/DN467851H_Multiplex_Pool_2/DN467851H_A3_F3_G3_H3/20190821_1545_1-A1-D1_PAD73195_440ab859/throughput.csv deleted file mode 100644 index ed997fd..0000000 --- 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b/valet/testdata/valet/report_PAH48449_20211215_1420_227842f4.md new file mode 100644 index 0000000..a12ef1e --- /dev/null +++ b/valet/testdata/valet/report_PAH48449_20211215_1420_227842f4.md @@ -0,0 +1,589 @@ +Tracking ID +=========== + +{ + "asic_id": "", + "asic_id_eeprom": "0004A30B00F1A3CB", + "asic_temp": "5.651082", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "4.4.13", + "device_id": "1A", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "21.10.8", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2021-12-15T14:20:11.355694+00:00", + "flow_cell_id": "PAH48449", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "5.0.17+99baa5b27", + "heatsink_temp": "-34.041740", + "host_product_code": "PRO-PRC024", + "host_product_serial_number": "PC24B148", + "hostname": "PC24B148", + "hublett_board_id": "00012088892c694c", + "hublett_firmware_version": "2.1.10", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 20.04", + "protocol_group_id": "lambda_p24_all_positions", + "protocol_run_id": "", + "protocol_start_time": "", + "protocols_version": "6.3.5", + "run_id": "39ae988ba41499479e0dc1fcae29fa4059701d08", + "sample_id": "lambda_151221_1", + "satellite_board_id": "0138b52903847c4d", + "satellite_firmware_version": "2.1.9", + "usb_config": "fx3_0.0.0#fpga_0.0.0#unknown#unknown", + "version": "4.4.3" +} + +Duty Time +========= + +ID: 39ae988ba41499479e0dc1fcae29fa4059701d08 + +Channel State,Experiment Time (minutes),State Time (samples), +adapter,0,869652 +adapter,1,6128567 +adapter,2,6599075 +adapter,3,9119679 +adapter,4,8854499 +adapter,5,8480611 +adapter,6,8214866 +adapter,7,8089806 +adapter,8,7740656 +adapter,9,7743541 +adapter,10,7496810 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a/valet/testdata/valet/report_PAH48449_20211215_1445_f5d8e5aa.md b/valet/testdata/valet/report_PAH48449_20211215_1445_f5d8e5aa.md new file mode 100644 index 0000000..fa0e153 --- /dev/null +++ b/valet/testdata/valet/report_PAH48449_20211215_1445_f5d8e5aa.md @@ -0,0 +1,716 @@ +Tracking ID +=========== + +{ + "asic_id": "", + "asic_id_eeprom": "0004A30B00F1A3CB", + "asic_temp": "8.365864", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "4.4.13", + "device_id": "1B", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "21.10.8", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2021-12-15T14:45:59.424394+00:00", + "flow_cell_id": "PAH48449", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "5.0.17+99baa5b27", + "heatsink_temp": "-33.917698", + "host_product_code": "PRO-PRC024", + "host_product_serial_number": "PC24B148", + "hostname": "PC24B148", + "hublett_board_id": "00012088892c694c", + "hublett_firmware_version": "2.1.10", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 20.04", + "protocol_group_id": "lambda_p24_all_positions", + "protocol_run_id": "", + "protocol_start_time": "", + "protocols_version": "6.3.5", + "run_id": "0e83ec5a65c57bb7b027e9380d8024baecc6a878", + "sample_id": "lambda_151221_1", + "satellite_board_id": "0138b52903847c4d", + "satellite_firmware_version": "2.1.9", + "usb_config": "fx3_0.0.0#fpga_0.0.0#unknown#unknown", + "version": "4.4.3" +} + +Duty Time +========= + +ID: 0e83ec5a65c57bb7b027e9380d8024baecc6a878 + +Channel State,Experiment Time (minutes),State Time (samples), +adapter,0,436900 +adapter,1,4400794 +adapter,2,4754872 +adapter,3,6356664 +adapter,4,6209147 +adapter,5,6157770 +adapter,6,5828634 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"2021-12-15T15:09:34.951498+00:00", + "flow_cell_id": "PAH48449", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "5.0.17+99baa5b27", + "heatsink_temp": "-34.041740", + "host_product_code": "PRO-PRC024", + "host_product_serial_number": "PC24B148", + "hostname": "PC24B148", + "hublett_board_id": "0001c08f5dc61932", + "hublett_firmware_version": "2.1.10", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 20.04", + "protocol_group_id": "lambda_p24_all_positions", + "protocol_run_id": "", + "protocol_start_time": "", + "protocols_version": "6.3.5", + "run_id": "e70b94f64082d4c5cd6518e0eacc2025b897f5f3", + "sample_id": "lambda_151221_1", + "satellite_board_id": "01343f6230323b2f", + "satellite_firmware_version": "2.1.9", + "usb_config": "fx3_0.0.0#fpga_0.0.0#unknown#unknown", + "version": "4.4.3" +} + +Duty Time +========= + +ID: e70b94f64082d4c5cd6518e0eacc2025b897f5f3 + +Channel State,Experiment Time (minutes),State Time (samples), +adapter,0,353473 +adapter,1,3330863 +adapter,2,3623416 +adapter,3,5249172 +adapter,4,5060800 +adapter,5,5087265 +adapter,6,4883697 +adapter,7,4903221 +adapter,8,4769932 +adapter,9,4599602 +adapter,10,4584761 +adapter,11,4469995 +adapter,12,4550746 +adapter,13,4722735 +adapter,14,4398959 +adapter,15,4245574 +adapter,16,4338938 +adapter,17,3627538 +disabled,0,0 +disabled,1,0 +disabled,2,46903 +disabled,3,389467 +disabled,4,1084547 +disabled,5,1200000 +disabled,6,1445261 +disabled,7,1680000 +disabled,8,1755033 +disabled,9,1920000 +disabled,10,1920000 +disabled,11,1920000 +disabled,12,1920000 +disabled,13,1920000 +disabled,14,1975728 +disabled,15,2331143 +disabled,16,2400000 +disabled,17,2029290 +locked,0,0 +locked,1,0 +locked,2,64101 +locked,3,48913 +locked,4,17839 +locked,5,7764 +locked,6,14543 +locked,7,4043 +locked,8,11536 +locked,9,6963 +locked,10,924 +locked,11,4921 +locked,12,4015 +locked,13,4744 +locked,14,1256 +locked,15,2776 +locked,16,6282 +locked,17,6703 +multiple,0,142856 +multiple,1,3522631 +multiple,2,2024498 +multiple,3,46687 +multiple,4,7403 +multiple,5,1927 +multiple,6,9745 +multiple,7,1551 +multiple,8,3093 +multiple,9,2540 +multiple,10,3229 +multiple,11,1410 +multiple,12,0 +multiple,13,0 +multiple,14,974 +multiple,15,0 +multiple,16,0 +multiple,17,653 +no_pore,0,0 +no_pore,1,0 +no_pore,2,25374351 +no_pore,3,73920000 +no_pore,4,73920000 +no_pore,5,73920000 +no_pore,6,73920000 +no_pore,7,73920000 +no_pore,8,73920000 +no_pore,9,73920000 +no_pore,10,73920000 +no_pore,11,73920000 +no_pore,12,73920000 +no_pore,13,73920000 +no_pore,14,73920000 +no_pore,15,73920000 +no_pore,16,73920000 +no_pore,17,62433547 +pending_manual_reset,0,0 +pending_manual_reset,1,0 +pending_manual_reset,2,9155446 +pending_manual_reset,3,0 +pending_manual_reset,4,0 +pending_manual_reset,5,0 +pending_manual_reset,6,0 +pending_manual_reset,7,0 +pending_manual_reset,8,0 +pending_manual_reset,9,0 +pending_manual_reset,10,0 +pending_manual_reset,11,0 +pending_manual_reset,12,0 +pending_manual_reset,13,0 +pending_manual_reset,14,0 +pending_manual_reset,15,0 +pending_manual_reset,16,0 +pending_manual_reset,17,0 +pending_mux_change,0,21789202 +pending_mux_change,1,10372261 +pending_mux_change,2,11034698 +pending_mux_change,3,840831 +pending_mux_change,4,839960 +pending_mux_change,5,821319 +pending_mux_change,6,766045 +pending_mux_change,7,848956 +pending_mux_change,8,811334 +pending_mux_change,9,835810 +pending_mux_change,10,826555 +pending_mux_change,11,760629 +pending_mux_change,12,841788 +pending_mux_change,13,803699 +pending_mux_change,14,752415 +pending_mux_change,15,862696 +pending_mux_change,16,756533 +pending_mux_change,17,6756419 +pore,0,7079885 +pore,1,54153515 +pore,2,48639995 +pore,3,81568908 +pore,4,76736244 +pore,5,76054992 +pore,6,68856274 +pore,7,68910491 +pore,8,68758220 +pore,9,63428058 +pore,10,62210172 +pore,11,62530521 +pore,12,63246686 +pore,13,61795207 +pore,14,61155220 +pore,15,60028394 +pore,16,58738012 +pore,17,50319753 +saturated,0,113019524 +saturated,1,119972314 +saturated,2,66197845 +saturated,3,0 +saturated,4,0 +saturated,5,6561 +saturated,6,0 +saturated,7,0 +saturated,8,0 +saturated,9,0 +saturated,10,0 +saturated,11,0 +saturated,12,0 +saturated,13,9630 +saturated,14,0 +saturated,15,52 +saturated,16,0 +saturated,17,14953516 +strand,0,5822698 +strand,1,243693470 +strand,2,251360038 +strand,3,539592819 +strand,4,544254514 +strand,5,544580631 +strand,6,552593543 +strand,7,550451737 +strand,8,553075268 +strand,9,557935591 +strand,10,559759481 +strand,11,559878543 +strand,12,558464541 +strand,13,559912339 +strand,14,561705661 +strand,15,560825741 +strand,16,562937843 +strand,17,453064548 +unavailable,0,29205870 +unavailable,1,17544894 +unavailable,2,11132029 +unavailable,3,7014296 +unavailable,4,7069978 +unavailable,5,6833490 +unavailable,6,6498225 +unavailable,7,7376622 +unavailable,8,6542269 +unavailable,9,6397845 +unavailable,10,6172868 +unavailable,11,6174960 +unavailable,12,6004303 +unavailable,13,6216804 +unavailable,14,5991297 +unavailable,15,6598578 +unavailable,16,6240903 +unavailable,17,5066706 +unblocking,0,1161330 +unblocking,1,12268924 +unblocking,2,7117197 +unblocking,3,6987771 +unblocking,4,6767462 +unblocking,5,6871475 +unblocking,6,6317796 +unblocking,7,7156840 +unblocking,8,6046931 +unblocking,9,6200320 +unblocking,10,5789904 +unblocking,11,5663609 +unblocking,12,6147369 +unblocking,13,6348613 +unblocking,14,6149390 +unblocking,15,6388288 +unblocking,16,6129489 +unblocking,17,5171162 +unclassified,0,133530600 +unclassified,1,65192247 +unclassified,2,64579466 +unclassified,3,2532377 +unclassified,4,2859912 +unclassified,5,3072067 +unclassified,6,3329860 +unclassified,7,3601543 +unclassified,8,3472746 +unclassified,9,3844134 +unclassified,10,3904626 +unclassified,11,3767660 +unclassified,12,3871899 +unclassified,13,3488992 +unclassified,14,2989249 +unclassified,15,3761573 +unclassified,16,3601633 +unclassified,17,4156963 +unclassified_following_reset,0,0 +unclassified_following_reset,1,0 +unclassified_following_reset,2,9327781 +unclassified_following_reset,3,0 +unclassified_following_reset,4,0 +unclassified_following_reset,5,0 +unclassified_following_reset,6,0 +unclassified_following_reset,7,0 +unclassified_following_reset,8,0 +unclassified_following_reset,9,0 +unclassified_following_reset,10,0 +unclassified_following_reset,11,0 +unclassified_following_reset,12,0 +unclassified_following_reset,13,0 +unclassified_following_reset,14,0 +unclassified_following_reset,15,0 +unclassified_following_reset,16,0 +unclassified_following_reset,17,0 +unknown_negative,0,25638151 +unknown_negative,1,104999233 +unknown_negative,2,80795983 +unknown_negative,3,0 +unknown_negative,4,0 +unknown_negative,5,0 +unknown_negative,6,0 +unknown_negative,7,0 +unknown_negative,8,0 +unknown_negative,9,0 +unknown_negative,10,0 +unknown_negative,11,0 +unknown_negative,12,0 +unknown_negative,13,0 +unknown_negative,14,0 +unknown_negative,15,0 +unknown_negative,16,0 +unknown_negative,17,0 +unknown_positive,0,232608107 +unknown_positive,1,14278904 +unknown_positive,2,7251895 +unknown_positive,3,1692785 +unknown_positive,4,1158012 +unknown_positive,5,1208855 +unknown_positive,6,1137790 +unknown_positive,7,992197 +unknown_positive,8,756054 +unknown_positive,9,771340 +unknown_positive,10,799806 +unknown_positive,11,786750 +unknown_positive,12,812463 +unknown_positive,13,679844 +unknown_positive,14,682674 +unknown_positive,15,777394 +unknown_positive,16,793859 +unknown_positive,17,656286 +zero,0,149648304 +zero,1,70670744 +zero,2,122274358 +zero,3,115974 +zero,4,223329 +zero,5,333654 +zero,6,227221 +zero,7,152799 +zero,8,77584 +zero,9,137797 +zero,10,107674 +zero,11,121002 +zero,12,216190 +zero,13,177393 +zero,14,277177 +zero,15,257791 +zero,16,136508 +zero,17,157528 +--- + + +Throughput +========== + +ID: e70b94f64082d4c5cd6518e0eacc2025b897f5f3 + +Experiment Time (minutes),Reads,Basecalled Reads Passed,Basecalled Reads Failed,Basecalled Reads Skipped,Selected Raw Samples,Selected Events,Estimated Bases,Basecalled Bases,Basecalled Samples, +0,0,0,0,0,0,0,0,0,0, +1,4350,157,125,0,228482538,9510933,17117976,740523,11417290, +2,8956,828,442,0,472041201,19852849,35731563,4184657,52600837, +3,17722,1292,669,0,994713739,48523544,87335321,6487160,80463748, +4,26275,1986,861,0,1528283920,77746519,139933251,10072148,120704401, +5,34849,2533,945,0,2064616046,107090439,192748934,13342883,155084596, +6,43683,3019,1083,0,2614775917,137279094,247084949,16468138,189877805, +7,52341,3486,1367,0,3156043958,166964031,300514343,19967172,234956428, +8,61075,3754,1575,0,3697919407,196689851,354017381,22317235,266409349, +9,69937,4213,1771,0,4248090331,226912375,408414351,25285421,302662680, +10,78875,4730,1852,0,4804050292,257438988,463358677,28983523,340881594, +11,87760,5178,1928,0,5354208028,287655191,517744276,32080963,372799653, 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+ "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "4.4.13", + "device_id": "1D", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "21.10.8", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2021-12-15T15:32:41.577686+00:00", + "flow_cell_id": "PAH48449", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "5.0.17+99baa5b27", + "heatsink_temp": "-33.979721", + "host_product_code": "PRO-PRC024", + "host_product_serial_number": "PC24B148", + "hostname": "PC24B148", + "hublett_board_id": "0001c08f5dc61932", + "hublett_firmware_version": "2.1.10", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 20.04", + "protocol_group_id": "lambda_p24_all_positions", + "protocol_run_id": "", + "protocol_start_time": "", + "protocols_version": "6.3.5", + "run_id": "4fb758ce0727d99cd71c977276419f925805fe24", + "sample_id": "lambda_151221_1", + "satellite_board_id": "01343f6230323b2f", + "satellite_firmware_version": "2.1.9", + "usb_config": "fx3_0.0.0#fpga_0.0.0#unknown#unknown", + "version": "4.4.3" +} + +Duty Time +========= + +ID: 4fb758ce0727d99cd71c977276419f925805fe24 + +Channel State,Experiment Time (minutes),State Time (samples), +adapter,0,343372 +adapter,1,2931007 +adapter,2,3040038 +adapter,3,4428897 +adapter,4,4419742 +adapter,5,4360971 +adapter,6,4109803 +adapter,7,4197505 +adapter,8,4144163 +adapter,9,3901913 +adapter,10,4028623 +adapter,11,4043150 +adapter,12,4012287 +adapter,13,3920461 +adapter,14,4044048 +adapter,15,4029456 +adapter,16,4068483 +adapter,17,3797879 +disabled,0,0 +disabled,1,0 +disabled,2,128754 +disabled,3,1269318 +disabled,4,2111325 +disabled,5,2791454 +disabled,6,3046576 +disabled,7,3192333 +disabled,8,3401477 +disabled,9,3600000 +disabled,10,3600000 +disabled,11,3600000 +disabled,12,3743364 +disabled,13,3840000 +disabled,14,3840000 +disabled,15,3840000 +disabled,16,3840000 +disabled,17,3930048 +locked,0,0 +locked,1,0 +locked,2,65141 +locked,3,75297 +locked,4,28054 +locked,5,18458 +locked,6,7854 +locked,7,11387 +locked,8,12935 +locked,9,5759 +locked,10,8854 +locked,11,9154 +locked,12,3692 +locked,13,0 +locked,14,8088 +locked,15,0 +locked,16,5846 +locked,17,7340 +multiple,0,87066 +multiple,1,3638909 +multiple,2,1758073 +multiple,3,49393 +multiple,4,11592 +multiple,5,6531 +multiple,6,3850 +multiple,7,0 +multiple,8,6490 +multiple,9,3491 +multiple,10,1415 +multiple,11,1993 +multiple,12,0 +multiple,13,0 +multiple,14,5020 +multiple,15,0 +multiple,16,0 +multiple,17,6419 +no_pore,0,0 +no_pore,1,0 +no_pore,2,26071915 +no_pore,3,74400000 +no_pore,4,74400000 +no_pore,5,74400000 +no_pore,6,74400000 +no_pore,7,74400000 +no_pore,8,74400000 +no_pore,9,74400000 +no_pore,10,74400000 +no_pore,11,74400000 +no_pore,12,74400000 +no_pore,13,74400000 +no_pore,14,74400000 +no_pore,15,74400000 +no_pore,16,74400000 +no_pore,17,71607991 +pending_manual_reset,0,0 +pending_manual_reset,1,0 +pending_manual_reset,2,7840411 +pending_manual_reset,3,0 +pending_manual_reset,4,0 +pending_manual_reset,5,0 +pending_manual_reset,6,0 +pending_manual_reset,7,0 +pending_manual_reset,8,0 +pending_manual_reset,9,0 +pending_manual_reset,10,0 +pending_manual_reset,11,0 +pending_manual_reset,12,0 +pending_manual_reset,13,0 +pending_manual_reset,14,0 +pending_manual_reset,15,0 +pending_manual_reset,16,0 +pending_manual_reset,17,0 +pending_mux_change,0,22091269 +pending_mux_change,1,10050311 +pending_mux_change,2,15549960 +pending_mux_change,3,904296 +pending_mux_change,4,891216 +pending_mux_change,5,893723 +pending_mux_change,6,868194 +pending_mux_change,7,828015 +pending_mux_change,8,830211 +pending_mux_change,9,754421 +pending_mux_change,10,793335 +pending_mux_change,11,807084 +pending_mux_change,12,810672 +pending_mux_change,13,795720 +pending_mux_change,14,752586 +pending_mux_change,15,756487 +pending_mux_change,16,799458 +pending_mux_change,17,6753247 +pore,0,6292817 +pore,1,43730193 +pore,2,39624412 +pore,3,62880231 +pore,4,62890731 +pore,5,60061399 +pore,6,55228397 +pore,7,56255159 +pore,8,55051739 +pore,9,52014322 +pore,10,52574677 +pore,11,52956124 +pore,12,53157103 +pore,13,51704440 +pore,14,52264929 +pore,15,52947867 +pore,16,51669851 +pore,17,48400654 +saturated,0,112784021 +saturated,1,119843536 +saturated,2,64764182 +saturated,3,11060 +saturated,4,17 +saturated,5,0 +saturated,6,558 +saturated,7,5184 +saturated,8,0 +saturated,9,3141 +saturated,10,0 +saturated,11,0 +saturated,12,20 +saturated,13,0 +saturated,14,0 +saturated,15,0 +saturated,16,0 +saturated,17,3902729 +strand,0,7128891 +strand,1,262481048 +strand,2,257108672 +strand,3,557891855 +strand,4,557586307 +strand,5,559790553 +strand,6,565695795 +strand,7,564666041 +strand,8,565157573 +strand,9,569783155 +strand,10,568049078 +strand,11,568082188 +strand,12,568213606 +strand,13,569172514 +strand,14,568956102 +strand,15,567328139 +strand,16,569619769 +strand,17,539002242 +unavailable,0,41257594 +unavailable,1,16865026 +unavailable,2,10357274 +unavailable,3,7042397 +unavailable,4,6739088 +unavailable,5,6733642 +unavailable,6,6499050 +unavailable,7,6245894 +unavailable,8,6510177 +unavailable,9,5868461 +unavailable,10,6111321 +unavailable,11,6121572 +unavailable,12,6308696 +unavailable,13,6045416 +unavailable,14,5955082 +unavailable,15,6148371 +unavailable,16,5758852 +unavailable,17,6524099 +unblocking,0,1479205 +unblocking,1,11343498 +unblocking,2,6680390 +unblocking,3,6409931 +unblocking,4,6321100 +unblocking,5,6153881 +unblocking,6,5931648 +unblocking,7,6124632 +unblocking,8,5986217 +unblocking,9,5808669 +unblocking,10,6095767 +unblocking,11,6171987 +unblocking,12,5922721 +unblocking,13,6063152 +unblocking,14,5714469 +unblocking,15,6120274 +unblocking,16,5817572 +unblocking,17,5487250 +unclassified,0,126197843 +unclassified,1,65579765 +unclassified,2,62252843 +unclassified,3,2637801 +unclassified,4,3127539 +unclassified,5,3387030 +unclassified,6,3162919 +unclassified,7,2842514 +unclassified,8,3287965 +unclassified,9,2863672 +unclassified,10,3211605 +unclassified,11,2822768 +unclassified,12,2499357 +unclassified,13,3167235 +unclassified,14,3052288 +unclassified,15,3473690 +unclassified,16,3164452 +unclassified,17,3000504 +unclassified_following_reset,0,0 +unclassified_following_reset,1,0 +unclassified_following_reset,2,8133755 +unclassified_following_reset,3,0 +unclassified_following_reset,4,0 +unclassified_following_reset,5,0 +unclassified_following_reset,6,0 +unclassified_following_reset,7,0 +unclassified_following_reset,8,0 +unclassified_following_reset,9,0 +unclassified_following_reset,10,0 +unclassified_following_reset,11,0 +unclassified_following_reset,12,0 +unclassified_following_reset,13,0 +unclassified_following_reset,14,0 +unclassified_following_reset,15,0 +unclassified_following_reset,16,0 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+374,147091,125343,21638,0,8986402214,487012411,876563481,858538057,8980340414, +375,147091,125438,21653,0,8986402214,487012411,876563481,859132108,8986402214, +--- + + diff --git a/valet/testdata/valet/report_PAH48449_20211215_1553_3720e75e.md b/valet/testdata/valet/report_PAH48449_20211215_1553_3720e75e.md new file mode 100644 index 0000000..14b4b72 --- /dev/null +++ b/valet/testdata/valet/report_PAH48449_20211215_1553_3720e75e.md @@ -0,0 +1,732 @@ +Tracking ID +=========== + +{ + "asic_id": "", + "asic_id_eeprom": "0004A30B00F1A3CB", + "asic_temp": "6.426734", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "4.4.13", + "device_id": "1E", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "21.10.8", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2021-12-15T15:53:55.294680+00:00", + "flow_cell_id": "PAH48449", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "5.0.17+99baa5b27", + "heatsink_temp": "-34.103760", + "host_product_code": "PRO-PRC024", + "host_product_serial_number": "PC24B148", + "hostname": "PC24B148", + "hublett_board_id": "0001258a57bc2948", + "hublett_firmware_version": "2.1.10", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 20.04", + "protocol_group_id": "lambda_p24_all_positions", + "protocol_run_id": "", + "protocol_start_time": "", + "protocols_version": "6.3.5", + "run_id": "f75f290c56995e3f48c0cbb6c31d375054b53f38", + "sample_id": "lambda_151221_1", + "satellite_board_id": "013e5d89d6d8cbfd", + "satellite_firmware_version": "2.1.9", + "usb_config": "fx3_0.0.0#fpga_0.0.0#unknown#unknown", + "version": "4.4.3" +} + +Duty Time +========= + +ID: f75f290c56995e3f48c0cbb6c31d375054b53f38 + +Channel State,Experiment Time (minutes),State Time (samples), +adapter,0,253659 +adapter,1,2770564 +adapter,2,3014457 +adapter,3,4482469 +adapter,4,4554056 +adapter,5,4300897 +adapter,6,4223195 +adapter,7,4434176 +adapter,8,4128982 +adapter,9,3923401 +adapter,10,4079388 +adapter,11,4064908 +adapter,12,3768309 +adapter,13,3769885 +adapter,14,3780674 +adapter,15,3650127 +adapter,16,3737015 +adapter,17,2994148 +disabled,0,0 +disabled,1,0 +disabled,2,122617 +disabled,3,1449368 +disabled,4,1995602 +disabled,5,2220981 +disabled,6,2612665 +disabled,7,2640000 +disabled,8,2640000 +disabled,9,2640000 +disabled,10,2729317 +disabled,11,3052853 +disabled,12,3120000 +disabled,13,3120000 +disabled,14,3277398 +disabled,15,3360000 +disabled,16,3360000 +disabled,17,2835098 +locked,0,0 +locked,1,0 +locked,2,32854 +locked,3,41285 +locked,4,30740 +locked,5,30441 +locked,6,14442 +locked,7,7503 +locked,8,7015 +locked,9,13660 +locked,10,18409 +locked,11,3308 +locked,12,8605 +locked,13,5362 +locked,14,1989 +locked,15,5918 +locked,16,4563 +locked,17,3001 +multiple,0,84233 +multiple,1,3651855 +multiple,2,1962799 +multiple,3,36851 +multiple,4,18023 +multiple,5,12038 +multiple,6,3944 +multiple,7,5903 +multiple,8,6100 +multiple,9,3668 +multiple,10,0 +multiple,11,2964 +multiple,12,2104 +multiple,13,1613 +multiple,14,3717 +multiple,15,2473 +multiple,16,1917 +multiple,17,0 +no_pore,0,0 +no_pore,1,0 +no_pore,2,23337255 +no_pore,3,73680000 +no_pore,4,73680000 +no_pore,5,73680000 +no_pore,6,73680000 +no_pore,7,73680000 +no_pore,8,73680000 +no_pore,9,73680000 +no_pore,10,73680000 +no_pore,11,73680000 +no_pore,12,73680000 +no_pore,13,73680000 +no_pore,14,73680000 +no_pore,15,73680000 +no_pore,16,73680000 +no_pore,17,62169649 +pending_manual_reset,0,0 +pending_manual_reset,1,0 +pending_manual_reset,2,18069995 +pending_manual_reset,3,0 +pending_manual_reset,4,0 +pending_manual_reset,5,0 +pending_manual_reset,6,0 +pending_manual_reset,7,0 +pending_manual_reset,8,0 +pending_manual_reset,9,0 +pending_manual_reset,10,0 +pending_manual_reset,11,0 +pending_manual_reset,12,0 +pending_manual_reset,13,0 +pending_manual_reset,14,0 +pending_manual_reset,15,0 +pending_manual_reset,16,0 +pending_manual_reset,17,0 +pending_mux_change,0,27294358 +pending_mux_change,1,11056783 +pending_mux_change,2,13746174 +pending_mux_change,3,709094 +pending_mux_change,4,705679 +pending_mux_change,5,624364 +pending_mux_change,6,686162 +pending_mux_change,7,740934 +pending_mux_change,8,723687 +pending_mux_change,9,698913 +pending_mux_change,10,731408 +pending_mux_change,11,730159 +pending_mux_change,12,738088 +pending_mux_change,13,877029 +pending_mux_change,14,751614 +pending_mux_change,15,680016 +pending_mux_change,16,764603 +pending_mux_change,17,6891542 +pore,0,4812279 +pore,1,42836213 +pore,2,42348348 +pore,3,65791561 +pore,4,65564740 +pore,5,62701028 +pore,6,60344149 +pore,7,59578980 +pore,8,59016992 +pore,9,53302962 +pore,10,53616796 +pore,11,52313216 +pore,12,49006917 +pore,13,48318524 +pore,14,47291722 +pore,15,44885794 +pore,16,46549190 +pore,17,38600307 +saturated,0,112058006 +saturated,1,121047661 +saturated,2,67913971 +saturated,3,0 +saturated,4,0 +saturated,5,5387 +saturated,6,231 +saturated,7,0 +saturated,8,0 +saturated,9,0 +saturated,10,6816 +saturated,11,898 +saturated,12,0 +saturated,13,0 +saturated,14,0 +saturated,15,738 +saturated,16,0 +saturated,17,29 +strand,0,5498069 +strand,1,249660477 +strand,2,249230409 +strand,3,559850060 +strand,4,559731081 +strand,5,562918686 +strand,6,564246910 +strand,7,564087601 +strand,8,564133183 +strand,9,570724677 +strand,10,570148147 +strand,11,571325184 +strand,12,573866261 +strand,13,572033474 +strand,14,574452930 +strand,15,576815274 +strand,16,574640133 +strand,17,479717214 +unavailable,0,17837998 +unavailable,1,17219870 +unavailable,2,10723972 +unavailable,3,5403957 +unavailable,4,5317021 +unavailable,5,4740569 +unavailable,6,5092832 +unavailable,7,5074571 +unavailable,8,5462188 +unavailable,9,5602452 +unavailable,10,5929864 +unavailable,11,5437788 +unavailable,12,5581213 +unavailable,13,6653543 +unavailable,14,5915953 +unavailable,15,5585474 +unavailable,16,5801482 +unavailable,17,4779492 +unblocking,0,1392652 +unblocking,1,12597780 +unblocking,2,7449623 +unblocking,3,5068352 +unblocking,4,4824368 +unblocking,5,4837309 +unblocking,6,4878525 +unblocking,7,5352538 +unblocking,8,5671091 +unblocking,9,5352699 +unblocking,10,5652908 +unblocking,11,5347697 +unblocking,12,5693238 +unblocking,13,6614801 +unblocking,14,6136098 +unblocking,15,6013085 +unblocking,16,6261981 +unblocking,17,4684614 +unclassified,0,132090506 +unclassified,1,66987813 +unclassified,2,67602372 +unclassified,3,2281823 +unclassified,4,2459709 +unclassified,5,2996917 +unclassified,6,3155471 +unclassified,7,3001442 +unclassified,8,3365823 +unclassified,9,3157495 +unclassified,10,2585692 +unclassified,11,3170772 +unclassified,12,3376062 +unclassified,13,3973461 +unclassified,14,3775106 +unclassified,15,4470929 +unclassified,16,4201146 +unclassified,17,3807926 +unclassified_following_reset,0,0 +unclassified_following_reset,1,0 +unclassified_following_reset,2,838177 +unclassified_following_reset,3,0 +unclassified_following_reset,4,0 +unclassified_following_reset,5,0 +unclassified_following_reset,6,0 +unclassified_following_reset,7,0 +unclassified_following_reset,8,0 +unclassified_following_reset,9,0 +unclassified_following_reset,10,0 +unclassified_following_reset,11,0 +unclassified_following_reset,12,0 +unclassified_following_reset,13,0 +unclassified_following_reset,14,0 +unclassified_following_reset,15,0 +unclassified_following_reset,16,0 +unclassified_following_reset,17,0 +unknown_negative,0,33782577 +unknown_negative,1,120251814 +unknown_negative,2,80047637 +unknown_negative,3,0 +unknown_negative,4,0 +unknown_negative,5,0 +unknown_negative,6,0 +unknown_negative,7,0 +unknown_negative,8,0 +unknown_negative,9,0 +unknown_negative,10,0 +unknown_negative,11,0 +unknown_negative,12,0 +unknown_negative,13,0 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-0,0 +1,712 @@ +Tracking ID +=========== + +{ + "asic_id": "", + "asic_id_eeprom": "0004A30B00F1A3CB", + "asic_temp": "12.035035", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "4.4.13", + "device_id": "1F", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "21.10.8", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": "2021-12-15T16:17:47.465328+00:00", + "flow_cell_id": "PAH48449", + "flow_cell_product_code": "FLO-PRO002", + "guppy_version": "5.0.17+99baa5b27", + "heatsink_temp": "-34.165779", + "host_product_code": "PRO-PRC024", + "host_product_serial_number": "PC24B148", + "hostname": "PC24B148", + "hublett_board_id": "0001258a57bc2948", + "hublett_firmware_version": "2.1.10", + "installation_type": "nc", + "ip_address": "", + "local_firmware_file": "1", + "mac_address": "", + "operating_system": "ubuntu 20.04", + "protocol_group_id": "lambda_p24_all_positions", + "protocol_run_id": "", + "protocol_start_time": "", + "protocols_version": "6.3.5", + "run_id": "5846cbe2c5217dc592f6c13121f3e93b00ab4ae5", + "sample_id": "lambda_151221_1", + "satellite_board_id": "013e5d89d6d8cbfd", + "satellite_firmware_version": "2.1.9", + "usb_config": "fx3_0.0.0#fpga_0.0.0#unknown#unknown", + "version": "4.4.3" +} + +Duty Time +========= + +ID: 5846cbe2c5217dc592f6c13121f3e93b00ab4ae5 + +Channel State,Experiment Time (minutes),State Time (samples), +adapter,0,339157 +adapter,1,2374167 +adapter,2,2569213 +adapter,3,3712384 +adapter,4,3723223 +adapter,5,3793484 +adapter,6,3522719 +adapter,7,3649146 +adapter,8,3558372 +adapter,9,3595869 +adapter,10,3567445 +adapter,11,3684000 +adapter,12,3532829 +adapter,13,3666141 +adapter,14,3602637 +adapter,15,3561206 +adapter,16,3559244 +adapter,17,2552077 +disabled,0,0 +disabled,1,0 +disabled,2,24683 +disabled,3,586934 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+336,149156,117267,19621,0,9095665518,492837201,887047417,794657798,8337866074, +337,149156,118539,19811,0,9095665518,492837201,887047417,803477714,8429712698, +338,149156,120081,20012,0,9095665518,492837201,887047417,814015279,8539200021, +339,149156,121626,20214,0,9095665518,492837201,887047417,824100667,8643938524, +340,149156,123360,20452,0,9095665518,492837201,887047417,835613213,8762961913, +341,149156,126190,20806,0,9095665518,492837201,887047417,854832302,8961160598, +342,149156,128085,21071,0,9095665518,492837201,887047417,867820989,9095665518, +--- + + diff --git a/valet/valet_suite_test.go b/valet/valet_suite_test.go index 375913f..2daf233 100644 --- a/valet/valet_suite_test.go +++ b/valet/valet_suite_test.go @@ -69,6 +69,7 @@ var _ = Describe("Find directories)", func() { ".", "1", "1/reads", + "1/reads/alignments", "1/reads/fast5", "1/reads/fastq", "testdir", @@ -111,7 +112,9 @@ var _ = Describe("Find regular files)", func() { When("using a file predicate", func() { It("should find files", func() { expectedPaths := []string{ + "1/adaptive_sampling_roi1.bed", "1/ancillary.csv.gz", + "1/reads/alignments/alignments1.bam", "1/reads/fast5/reads1.fast5", "1/reads/fast5/reads1.fast5.md5", "1/reads/fast5/reads2.fast5", @@ -123,6 +126,12 @@ var _ = Describe("Find regular files)", func() { "1/reads/fastq/reads3.fastq", "report_ABQ808_20200204_1257_e2e93dd1.md", "report_PAE48813_20200130_0940_16917585.md", + "report_PAH48449_20211215_1420_227842f4.md", + "report_PAH48449_20211215_1445_f5d8e5aa.md", + "report_PAH48449_20211215_1509_e045091f.md", + "report_PAH48449_20211215_1532_2a0a5bc7.md", + "report_PAH48449_20211215_1553_3720e75e.md", + "report_PAH48449_20211215_1617_fa1a14d5.md", "testdir/.gitignore", } Expect(foundFiles).To(WithTransform(pathTransform, @@ -281,7 +290,9 @@ var _ = Describe("Find files at intervals", func() { dataDir = "testdata/valet" expectedPaths = []string{ + "1/adaptive_sampling_roi1.bed", "1/ancillary.csv.gz", + "1/reads/alignments/alignments1.bam", "1/reads/fast5/reads1.fast5", "1/reads/fast5/reads1.fast5.md5", "1/reads/fast5/reads2.fast5", @@ -1052,9 +1063,24 @@ var _ = Describe("Archive MINKnow files", func() { }) var _ = Describe("Count files without a checksum", func() { + // We expect checksums for files that either don't need to be compressed, or + // do need to be compressed and have been e.g. bam, csv.gz, fast5, fastq.gz + // and md (reports). + // + // We don't expect checksums for files that need to be compressed and + // haven't been e.g. fastq. Ideally we would also checksum the uncompressed + // data. + // + // iRODS doesn't support this (it will calculate a checksum of the + // compressed file once uploaded, but has no specific place for an original + // checksum. We could add an original checksum to the file metadata. + // However, we're already adding the compressed file checksum there (because + // iRODS has a history of checksum-related bugs) and it would be potentially + // confusing for customers. + var ( numFilesFound uint64 - numFilesExpected uint64 = 6 // csv, fast5, fastq.gz and md (reports) + numFilesExpected uint64 = 13 ) BeforeEach(func() {