quantification

package
v4.9.3 Latest Latest
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 Go to latest Published: Apr 26, 2024 License: Apache-2.0 Imports: 37 Imported by: 0

Documentation

Overview

Example (CalculateTotals_AB_NeedsCombined) 
q, err := readQuantificationFile("./testdata/AB.bin")
fmt.Printf("%v\n", err)

if err == nil {
	result, err := calculateTotals(q, []int{90, 91, 95})

	fmt.Printf("%v|%v\n", result, err)
}

Output:

<nil>
map[]|Quantification must be for Combined detectors
Example (CalculateTotals_NoPMC) 
q, err := readQuantificationFile("./testdata/combined.bin")
fmt.Printf("%v\n", err)

if err == nil {
	result, err := calculateTotals(q, []int{68590, 68591, 68595})

	fmt.Printf("%v|%v\n", result, err)
}

Output:

<nil>
map[]|Quantification had no valid data for ROI PMCs
Example (CalculateTotals_Success) 
q, err := readQuantificationFile("./testdata/combined.bin")
fmt.Printf("%v\n", err)

if err == nil {
	result, err := calculateTotals(q, []int{90, 91, 95})

	fmt.Printf("%v|%v\n", result, err)
}

Output:

<nil>
map[CaO_%:7.5057006 FeO-T_%:10.621034 SiO2_%:41.48377 TiO2_%:0.7424]|<nil>
Example (CleanLogName) 
// Don't fix it...
fmt.Println(cleanLogName("node00001_data.log"))
// Do fix it...
fmt.Println(cleanLogName("node00001.pmcs_stdout.log"))
// Do fix it...
fmt.Println(cleanLogName("NODE00001.PMCS_stdout.log"))

Output:

node00001_data.log
node00001_stdout.log
NODE00001_stdout.log
Example (CombineQuantOutputs_BadPMC) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
NaN, 7.1, 415, 7840
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

Failed to combine map segment: JobData/abc123/output/node002.pmcs_result.csv, invalid PMC NaN at line 3
Example (CombineQuantOutputs_DownloadError) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	nil,
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

Failed to combine map segment: JobData/abc123/output/node002.pmcs_result.csv
Example (CombineQuantOutputs_DuplicatePMC) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node003.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
18, 7.1, 415, 7840
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row3
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
30, 1.3, 451, 7833
40, 8.1, 455, 7870
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

<nil>
The custom header
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
12, 6.1, 405, 7800
18, 7.1, 415, 7840
30, 5.1, 400, 7890
30, 1.3, 451, 7833
40, 8.1, 455, 7870
Example (CombineQuantOutputs_LastLineCutOff) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
31
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

Failed to combine map segment: JobData/abc123/output/node002.pmcs_result.csv, no PMC at line 3
Example (CombineQuantOutputs_OK) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node002.pmcs_result.csv"),
	},
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node003.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
30, 5.1, 400, 7890
12, 6.1, 405, 7800
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row2
PMC, CaO_%, CaO_int, RTT
18, 7.1, 415, 7840
`))),
	},
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row3
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
40, 8.1, 455, 7870
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
combinedCSV, err := combineQuantOutputs(fs, jobsBucket, "JobData/abc123", "The custom header", []string{"node001.pmcs", "node002.pmcs", "node003.pmcs"})

fmt.Printf("%v\n", err)
fmt.Println(combinedCSV)

Output:

<nil>
The custom header
PMC, CaO_%, CaO_int, RTT
3, 1.1, 450, 7830
12, 6.1, 405, 7800
18, 7.1, 415, 7840
30, 5.1, 400, 7890
40, 8.1, 455, 7870
Example (ConvertQuantificationData) 
data := csvData{
	[]string{"PMC", "Ca_%", "Ca_int", "SCLK", "Ti_%", "filename", "RTT"},
	[][]string{
		[]string{"23", "1.5", "5", "11111", "4", "fileA.msa", "44"},
		[]string{"70", "3.4", "32", "12345", "4.21", "fileB.msa", "45"},
	},
}

result, err := convertQuantificationData(data, []string{"PMC", "RTT", "SCLK", "filename"})
fmt.Printf("%v|%v\n", result, err)

Output:

{[Ca_% Ca_int Ti_%] [F I F] [{23 44 11111 fileA.msa [1.5 5 4]} {70 45 12345 fileB.msa [3.4 32 4.21]}]}|<nil>
Example (DecodeMapFileNameColumn) 
rt, det, err := decodeMapFileNameColumn("file.txt")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_A")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_A_MyRoiID")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Dwell_B")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_C")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("LongRead_B")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Scotland_something_00012.msa")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Scotland_something_00012_10keV_33.msa")
fmt.Printf("%v|%v|%v\n", rt, det, err)

rt, det, err = decodeMapFileNameColumn("Normal_A_0123456789_873495_455.msa")
fmt.Printf("%v|%v|%v\n", rt, det, err)

Output:

||decodeMapFileNameColumn: Invalid READTYPE in filename: "file.txt"
Normal|A|<nil>
Normal|A|<nil>
Dwell|B|<nil>
||decodeMapFileNameColumn: Invalid DETECTOR_ID in filename: "Normal_C"
||decodeMapFileNameColumn: Invalid READTYPE in filename: "LongRead_B"
||decodeMapFileNameColumn: Invalid READTYPE in filename: "Scotland_something_00012.msa"
||decodeMapFileNameColumn: Invalid READTYPE in filename: "Scotland_something_00012_10keV_33.msa"
Normal|A|<nil>
Example (FilterListItems) 
// Should just filter indexes that are valid
idxToIgnoreMap := map[int]bool{
	-9: true,
	1:  true,
	2:  true,
	5:  true,
	6:  true,
}

fmt.Println(filterListItems([]string{"snowboarding", "is", "awesome", "says", "Peter", "Nemere"}, idxToIgnoreMap))

Output:

[snowboarding says Peter]
Example (GetElements) 
fmt.Printf("%v", getElements([]string{"PMC", "SCLK", "Ca_%", "Ti_%", "Ca_int", "Ti_int", "livetime", "Mg_%", "chisq"}))

Output:

[Ca Ti Mg]
Example (GetInterestingColIndexes) 
header := []string{"PMC", "K_%", "Ca_%", "Fe_%", "K_int", "Ca_int", "Fe_int", "K_err", "Ca_err", "Fe_err", "total_counts", "livetime", "chisq", "eVstart", "eV/ch", "res", "iter", "filename", "Events", "Triggers", "SCLK", "RTT"}
interesting, err := getInterestingColIndexes(header, []string{"PMC", "filename", "SCLK", "RTT"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)
interesting, err = getInterestingColIndexes(header, []string{"K_%", "total_counts"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)

// Bad cases
interesting, err = getInterestingColIndexes(header, []string{"PMC", "TheFileName", "SCLK", "RTT"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)
header[5] = "SCLK"
interesting, err = getInterestingColIndexes(header, []string{"PMC", "TheFileName", "SCLK", "RTT"})
fmt.Printf("\"%v\" \"%v\"\n", interesting, err)

// 22 header items...

Output:

"map[PMC:0 RTT:21 SCLK:20 filename:17]" "<nil>"
"map[K_%:1 total_counts:10]" "<nil>"
"map[]" "CSV column missing: TheFileName"
"map[]" "Duplicate CSV column: SCLK"
Example (MakeColumnTypeList) 
data := csvData{[]string{"a", "b", "c", "d", "e"}, [][]string{[]string{"1.11111", "2", "3.1415962", "5", "6"}}}
result, err := makeColumnTypeList(data, map[int]bool{2: true, 3: true})
fmt.Printf("%v|%v\n", result, err)
result, err = makeColumnTypeList(data, map[int]bool{})
fmt.Printf("%v|%v\n", result, err)

// Bad type
data = csvData{[]string{"a", "b", "c", "d", "e"}, [][]string{[]string{"1.11111", "Wanaka", "3.1415962", "5"}}}
result, err = makeColumnTypeList(data, map[int]bool{2: true, 3: true})
fmt.Printf("%v|%v\n", result, err)

// Skipping the string 1 should make it work...
result, err = makeColumnTypeList(data, map[int]bool{1: true, 3: true})
fmt.Printf("%v|%v\n", result, err)

Output:

[F I I]|<nil>
[F I F I I]|<nil>
[F]|Failed to parse "Wanaka" as float or int at col 1/row 0
[F F]|<nil>
Example (MakeIndividualPMCListFileContents_AB) 
fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", false, false, map[int32]bool{}))

Output:

5x11dataset.bin
15|Normal|A
15|Normal|B
7|Normal|A
7|Normal|B
388|Normal|A
388|Normal|B
 <nil>
Example (MakeIndividualPMCListFileContents_AB_Dwell) 
fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", false, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
15|Normal|A,15|Dwell|A
15|Normal|B,15|Dwell|B
7|Normal|A
7|Normal|B
388|Normal|A
388|Normal|B
 <nil>
Example (MakeIndividualPMCListFileContents_Combined) 
fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", true, false, map[int32]bool{}))

Output:

5x11dataset.bin
15|Normal|A,15|Normal|B
7|Normal|A,7|Normal|B
388|Normal|A,388|Normal|B
 <nil>
Example (MakeIndividualPMCListFileContents_Combined_Dwell) 
fmt.Println(makeIndividualPMCListFileContents([]int32{15, 7, 388}, "5x11dataset.bin", true, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
15|Normal|A,15|Normal|B,15|Dwell|A,15|Dwell|B
7|Normal|A,7|Normal|B
388|Normal|A,388|Normal|B
 <nil>
Example (MakeQuantJobPMCLists) 
fmt.Println(makeQuantJobPMCLists([]int32{1, 2, 3, 4, 5, 6, 7, 8}, 3))
fmt.Println(makeQuantJobPMCLists([]int32{1, 2, 3, 4, 5, 6, 7, 8, 9}, 3))
fmt.Println(makeQuantJobPMCLists([]int32{1, 2, 3, 4, 5, 6, 7, 8, 9, 10}, 3))

Output:

[[1 2 3] [4 5 6] [7 8]]
[[1 2 3] [4 5 6] [7 8 9]]
[[1 2 3] [4 5 6] [7 8 9] [10]]
Example (MakeQuantedLocation) 
// Should just filter indexes that are valid
fmt.Println(makeQuantedLocation([]string{"Ca_%", "PMC", "Ti_%", "RTT", "filename", "Ca_int"}, []string{"1.11111", "2", "3.1415962", "5", "FileA.msa", "6"}, map[int]bool{1: true, 3: true, 4: true}))

Output:

{2 5 0 FileA.msa [1.11111 3.1415962 6]} <nil>
Example (MakeROIPMCListFileContents_AB) 
fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", false, false, map[int32]bool{}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,15|Normal|A,388|Normal|A
roi1-id:7|Normal|B,15|Normal|B,388|Normal|B
roi2-id:7|Normal|A,450|Normal|A
roi2-id:7|Normal|B,450|Normal|B
 <nil>
Example (MakeROIPMCListFileContents_AB_Dwells) 
fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", false, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,15|Normal|A,15|Dwell|A,388|Normal|A
roi1-id:7|Normal|B,15|Normal|B,15|Dwell|B,388|Normal|B
roi2-id:7|Normal|A,450|Normal|A
roi2-id:7|Normal|B,450|Normal|B
 <nil>
Example (MakeROIPMCListFileContents_Combined) 
fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", true, false, map[int32]bool{}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,7|Normal|B,15|Normal|A,15|Normal|B,388|Normal|A,388|Normal|B
roi2-id:7|Normal|A,7|Normal|B,450|Normal|A,450|Normal|B
 <nil>
Example (MakeROIPMCListFileContents_Combined_Dwells) 
fmt.Println(makeROIPMCListFileContents(testROIs, "5x11dataset.bin", true, true, map[int32]bool{15: true}))

Output:

5x11dataset.bin
roi1-id:7|Normal|A,7|Normal|B,15|Normal|A,15|Normal|B,15|Dwell|A,15|Dwell|B,388|Normal|A,388|Normal|B
roi2-id:7|Normal|A,7|Normal|B,450|Normal|A,450|Normal|B
 <nil>
Example (MatchPMCsWithDataset) 
l := &logger.StdOutLogger{}
data := csvData{[]string{"X", "Y", "Z", "filename", "Ca_%"}, [][]string{[]string{"1", "0.40", "0", "Roastt_Laguna_Salinas_28kV_230uA_03_03_2020_111.msa", "4.5"}}}

exp, err := readDatasetFile("./testdata/LagunaSalinasdataset.bin")
fmt.Printf("Test file read: %v\n", err)
fmt.Printf("%v, header[%v]=%v, data[%v]=%v\n", matchPMCsWithDataset(&data, exp, true, l), len(data.header)-1, data.header[5], len(data.data[0])-1, data.data[0][5])

data = csvData{[]string{"X", "Y", "Z", "filename", "Ca_%"}, [][]string{[]string{"1", "930.40", "0", "Roastt_Laguna_Salinas_28kV_230uA_03_03_2020_111.msa", "4.5"}}}
fmt.Println(matchPMCsWithDataset(&data, exp, true, l))

data = csvData{[]string{"X", "Y", "Z", "filename", "Ca_%"}, [][]string{[]string{"1", "0.40", "0", "Roastt_Laguna_Salinas_28kV_230uA_03_03_2020_116.msa", "4.5"}}}
fmt.Printf("%v, header[%v]=%v, data[%v]=%v\n", matchPMCsWithDataset(&data, exp, false, l), len(data.header)-1, data.header[5], len(data.data[0])-1, data.data[0][5])

Output:

Test file read: <nil>
<nil>, header[5]=PMC, data[5]=111
matchPMCsWithDataset Failed to match 1.00,930.40,0.00 to a PMC in dataset file
<nil>, header[5]=PMC, data[5]=116
Example (ParseFloatColumnValue) 
fVal, err := parseFloatColumnValue("3.1415926")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("-3.15")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("1.234e02")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("nan")
fmt.Printf("%v|%v\n", fVal, err)

fVal, err = parseFloatColumnValue("-nan")
fmt.Printf("%v|%v\n", fVal, err)

Output:

3.1415925|<nil>
-3.15|<nil>
123.4|<nil>
0|strconv.ParseFloat: parsing "": invalid syntax
NaN|<nil>
NaN|<nil>
Example (ProcessQuantROIsToPMCs_Combined_CSVRowCountROICountMismatch) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT, filename
15, 5.1, 400, 7890, Normal_A_roi1-id
7, 6.1, 405, 7800, Normal_A_roi1-id
12, 6.7, 407, 7700, Normal_A_roi1-id
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

PMC 12 in CSV: JobData/abc123/output/node001.pmcs_result.csv doesn't exist in ROI: roi1
Example (ProcessQuantROIsToPMCs_Combined_DownloadError) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	nil,
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Failed to read map CSV: JobData/abc123/output/node001.pmcs_result.csv
Example (ProcessQuantROIsToPMCs_Combined_InvalidPMC) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, filename, RTT
15, 5.1, 400, Normal_A_roi1-id, 7890
Qwerty, 6.1, 405, Normal_A_roi1-id, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Failed to process map CSV: JobData/abc123/output/node001.pmcs_result.csv, invalid PMC Qwerty at line 4
Example (ProcessQuantROIsToPMCs_Combined_NoFileNameCol) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, RTT
15, 5.1, 400, 7890
7, 6.1, 405, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Map csv: JobData/abc123/output/node001.pmcs_result.csv, does not contain a filename column (used to match up ROIs)
Example (ProcessQuantROIsToPMCs_Combined_OK) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, filename, CaO_int, RTT
15, 5.1, Normal_A_roi1-id, 400, 7890
7, 6.1, Normal_B_roi2-id, 405, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", true, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

<nil>
The custom header
PMC, CaO_%, filename, CaO_int, RTT
7, 5.1, Normal_A_roi1-id, 400, 7890
15, 5.1, Normal_A_roi1-id, 400, 7890
388, 5.1, Normal_A_roi1-id, 400, 7890
7, 6.1, Normal_B_roi2-id, 405, 7800
450, 6.1, Normal_B_roi2-id, 405, 7800
Example (ProcessQuantROIsToPMCs_SeparateAB_InvalidFileName) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, filename, RTT
15, 5.1, 400, Normal_A_roi1-id, 7890
15, 5.2, 401, Normal_B, 7890
7, 6.1, 405, Normal_A, 7800
7, 6.2, 406, Normal_B, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", false, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

Invalid file name read: Normal_B from map CSV: JobData/abc123/output/node001.pmcs_result.csv, line 4
Example (ProcessQuantROIsToPMCs_SeparateAB_OK) 
var mockS3 awsutil.MockS3Client
defer mockS3.FinishTest()

const jobsBucket = "jobs-bucket"

// Some of our files are empty, not there, have content
// and they're meant to end up combined into one response...
mockS3.ExpGetObjectInput = []s3.GetObjectInput{
	{
		Bucket: aws.String(jobsBucket), Key: aws.String("JobData/abc123/output/node001.pmcs_result.csv"),
	},
}
mockS3.QueuedGetObjectOutput = []*s3.GetObjectOutput{
	{
		Body: io.NopCloser(bytes.NewReader([]byte(`Header row1
PMC, CaO_%, CaO_int, filename, RTT
15, 5.1, 400, Normal_A_roi1-id, 7890
15, 5.2, 401, Normal_B_roi1-id, 7890
7, 6.1, 405, Normal_A_roi2-id, 7800
7, 6.2, 406, Normal_B_roi2-id, 7800
`))),
	},
}

fs := fileaccess.MakeS3Access(&mockS3)
outputCSV, err := processQuantROIsToPMCs(fs, jobsBucket, "JobData/abc123", "The custom header", "node001.pmcs", false, testROIs)

fmt.Printf("%v\n", err)
fmt.Println(outputCSV)

Output:

<nil>
The custom header
PMC, CaO_%, CaO_int, filename, RTT
7, 5.1, 400, Normal_A_roi1-id, 7890
7, 5.2, 401, Normal_B_roi1-id, 7890
15, 5.1, 400, Normal_A_roi1-id, 7890
15, 5.2, 401, Normal_B_roi1-id, 7890
388, 5.1, 400, Normal_A_roi1-id, 7890
388, 5.2, 401, Normal_B_roi1-id, 7890
7, 6.1, 405, Normal_A_roi2-id, 7800
7, 6.2, 406, Normal_B_roi2-id, 7800
450, 6.1, 405, Normal_A_roi2-id, 7800
450, 6.2, 406, Normal_B_roi2-id, 7800
Example (ReadCSV) 
csv := `something header
more header
col 1,"col, 2",  col_3
"value one",123, 456
value two,444,555
`
d, err := readCSV(csv, 2)
fmt.Printf("%v|%v", d, err)

Output:

{[col 1 col, 2 col_3] [[value one 123 456] [value two 444 555]]}|<nil>
Example (ValidateParameters) 
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10 -f"))
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10.55 -o \"filename.whatever\" -f -Fe,1"))
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10;ls -al;echo -f"))
fmt.Printf("%v\n", validateParameters("-b,0,50,2,10&&rm -rf ~/; -f"))

Output:

<nil>
<nil>
Invalid parameters passed: -b,0,50,2,10;ls -al;echo -f
Invalid parameters passed: -b,0,50,2,10&&rm -rf ~/; -f

Index

Examples

Constants

View Source 
const JobParamsFileName = "params.json"

JobParamsFileName - File name of job params file

View Source 
const QuantModeABManualUpload = "ABManual"
View Source 
const QuantModeABMultiQuant = "ABMultiQuant"
View Source 
const QuantModeCombinedManualUpload = "ABManual"
View Source 
const QuantModeCombinedMultiQuant = "CombinedMultiQuant"

Variables

This section is empty.

Functions

func ConvertQuantificationCSV 

func ConvertQuantificationCSV(logger logger.ILogger, data string, expectMetaColumns []string, exprPB *protos.Experiment, matchPMCByCoord bool, detectorIDOverride string, detectorDuplicateAB bool) ([]byte, []string, error)

ConvertQuantificationCSV - converts from incoming string CSV data to serialised binary data. exprPB if nil means we wont match to dataset PMCs Returns the serialised quantification bytes and the elements that were quantified

func CreateJob 

func CreateJob(createParams *protos.QuantCreateParams, requestorUserId string, svcs *services.APIServices, sessUser *wsHelpers.SessionUser, wg *sync.WaitGroup, sendUpdate func(*protos.JobStatus)) (*protos.JobStatus, error)

CreateJob - creates a new quantification job

func FormCombinedCSV 

func FormCombinedCSV(quantIDs []string, dataPerDetectorPerPMC map[string]map[int32]quantItem, allColumns map[string]bool) string

func FormMultiQuantSummary 

func FormMultiQuantSummary(dataPerDetectorPerPMC map[string]map[int32]quantItem, allColumns map[string]bool, totalPMCCount int) *protos.QuantCombineSummary

func ImportQuantCSV 

func ImportQuantCSV(
	hctx wsHelpers.HandlerContext,
	scanId string,
	importUser *protos.UserInfo,
	csvBody string,
	csvOrigin string,
	idPrefix string,
	quantName string,
	quantModeEnum string,
	comments string) (string, error)

func IsValidCreateParam 

func IsValidCreateParam(createParams *protos.QuantCreateParams, hctx wsHelpers.HandlerContext) error

Validates the create parameters. Side-effect of modifying PmcsEncoded to just be an array of decoded PMCs

func ListUserQuants 

func ListUserQuants(searchParams *protos.SearchParams, hctx wsHelpers.HandlerContext) ([]*protos.QuantificationSummary, map[string]*protos.OwnershipItem, error)

func MultiQuantCombinedCSV 

func MultiQuantCombinedCSV(
	name string,
	scanId string,
	roiZStack []*protos.QuantCombineItem,
	exprPB *protos.Experiment,
	hctx wsHelpers.HandlerContext) (combinedQuantData, error)

func MultiQuantCompare 

func MultiQuantCompare(reqRoiId string, roiPMCs []int32, quantIds []string, exprPB *protos.Experiment, hctx wsHelpers.HandlerContext) ([]*protos.QuantComparisonTable, error)

func RunAutoQuantifications 

func RunAutoQuantifications(scanId string, svcs *services.APIServices)

Types

type QuantJobUpdater 

type QuantJobUpdater struct {
	// contains filtered or unexported fields
}

func MakeQuantJobUpdater 

func MakeQuantJobUpdater(
	params *protos.QuantCreateParams,
	session *melody.Session,

	notifier services.INotifier,
	db *mongo.Database,
) QuantJobUpdater

func (*QuantJobUpdater) SendQuantJobUpdate 

func (i *QuantJobUpdater) SendQuantJobUpdate(status *protos.JobStatus)

Source Files

View all Source files

Directories

Path Synopsis
Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.
 Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.

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