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Merge ElucidataInc#1345 from saifulbkhan/fix_adduct_settings
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[Fix] Adduct settings load and reset fail
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@saif-el
saif-el authored Feb 27, 2021
2 parents 99ac14e + 0eb4559 commit 813ac49
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Showing 3 changed files with 183 additions and 8 deletions.
16 changes: 8 additions & 8 deletions src/core/libmaven/mavenparameters.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -674,11 +674,11 @@ bool MavenParameters::loadSettings(const char* data)

pugi::xml_node pnode = xmlDoc.child("Settings");

for(pugi::xml_node_iterator it = pnode.begin(); it != pnode.end(); ++it) {

setIsotopeDialogSettings(it->name(), it->text().get());
setPeakDetectionSettings(it->name(), it->text().get());
setOptionsDialogSettings(it->name(), it->text().get());
for (pugi::xml_node_iterator it = pnode.begin(); it != pnode.end(); ++it) {
setIsotopeDialogSettings(it->name(), it->text().get());
setAdductsDialogSettings(it->name(), it->text().get());
setPeakDetectionSettings(it->name(), it->text().get());
setOptionsDialogSettings(it->name(), it->text().get());
}

return true;
Expand All @@ -696,12 +696,12 @@ void MavenParameters::reset(const std::list<string>& keys)

pugi::xml_node pnode = xmlDoc.child("Settings");

for(pugi::xml_node_iterator it = pnode.begin(); it != pnode.end(); ++it) {

if( std::find(keys.begin(), keys.end(), it->name()) != keys.end() ) {
for (pugi::xml_node_iterator it = pnode.begin(); it != pnode.end(); ++it) {
if (std::find(keys.begin(), keys.end(), it->name()) != keys.end()) {
setOptionsDialogSettings(it->name(), it->text().get());
setPeakDetectionSettings(it->name(), it->text().get());
setIsotopeDialogSettings(it->name(), it->text().get());
setAdductsDialogSettings(it->name(), it->text().get());
}
}
}
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171 changes: 171 additions & 0 deletions tests/test-scripts/settings.xml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,171 @@
<?xml version="1.0"?>
<Settings>
<C13LabelBPE>1</C13LabelBPE>
<C13LabelIsoWidget>1</C13LabelIsoWidget>
<C13Labeled_BPE>1</C13Labeled_BPE>
<C13Labeled_IsoWidget>1</C13Labeled_IsoWidget>
<D2LabelBPE>0</D2LabelBPE>
<D2LabelIsoWidget>0</D2LabelIsoWidget>
<D2Labeled_BPE>0</D2Labeled_BPE>
<D2Labeled_IsoWidget>0</D2Labeled_IsoWidget>
<N15LabelBPE>0</N15LabelBPE>
<N15LabelIsoWidget>1</N15LabelIsoWidget>
<N15Labeled_BPE>0</N15Labeled_BPE>
<N15Labeled_IsoWidget>0</N15Labeled_IsoWidget>
<S34LabelBPE>0</S34LabelBPE>
<S34LabelIsoWidget>0</S34LabelIsoWidget>
<S34Labeled_BPE>0</S34Labeled_BPE>
<S34Labeled_IsoWidget>0</S34Labeled_IsoWidget>
<abundanceThreshold>0.5</abundanceThreshold>
<activeTableName>KNOWNS (1)</activeTableName>
<adductPercentCorrelation>90</adductPercentCorrelation>
<adductSearchWindow>0.5</adductSearchWindow>
<alignment_algorithm>0</alignment_algorithm>
<alignment_good_peak_count>1</alignment_good_peak_count>
<alignment_limit_group_count>1000</alignment_limit_group_count>
<alignment_min_peak_intensity>5000.000000</alignment_min_peak_intensity>
<alignment_min_peak_width>3</alignment_min_peak_width>
<alignment_min_signal_noise_ratio>2</alignment_min_signal_noise_ratio>
<alignment_peak_detection>0</alignment_peak_detection>
<alignment_peak_grouping_window>10</alignment_peak_grouping_window>
<amuQ1>0.5</amuQ1>
<amuQ3>0.5</amuQ3>
<aslsAsymmetry>8</aslsAsymmetry>
<aslsBaselineMode>0</aslsBaselineMode>
<aslsSmoothness>2</aslsSmoothness>
<automatedDetection>0</automatedDetection>
<baselineQuantile>80</baselineQuantile>
<baselineSmoothing>5</baselineSmoothing>
<baselineSmoothingWindow>7</baselineSmoothingWindow>
<baseline_quantile>80</baseline_quantile>
<baseline_smoothing>5</baseline_smoothing>
<centroidScans>0</centroidScans>
<chargeMax>0</chargeMax>
<chargeMin>1</chargeMin>
<compoundExtractionWindow>5</compoundExtractionWindow>
<compoundMassCutoffWindow>5</compoundMassCutoffWindow>
<compoundRTWindow>1</compoundRTWindow>
<compoundRtWindow>1</compoundRtWindow>
<considerDeltaRT>0</considerDeltaRT>
<correctC13IsotopeAbundance>0</correctC13IsotopeAbundance>
<databaseSearch>1</databaseSearch>
<dbDetection>1</dbDetection>
<deltaRTCheck>0</deltaRTCheck>
<deltaRTWeight>10</deltaRTWeight>
<distXWeight>10</distXWeight>
<distYWeight>10</distYWeight>
<eicMaxGroups>10</eicMaxGroups>
<eicSmoothingAlgorithm>0</eicSmoothingAlgorithm>
<eicSmoothingWindow>10</eicSmoothingWindow>
<eicType>0</eicType>
<eic_smoothingAlgorithm>0</eic_smoothingAlgorithm>
<eic_smoothingWindow>10</eic_smoothingWindow>
<filterAdductsAgainstParent>0</filterAdductsAgainstParent>
<filterIsotopesAgainstParent>1</filterIsotopesAgainstParent>
<filterline>0</filterline>
<fragAnnotationLimit>1</fragAnnotationLimit>
<fragmentTolerance>20</fragmentTolerance>
<grouping_maxRtWindow>0.25</grouping_maxRtWindow>
<identificationDatabase>-1</identificationDatabase>
<identificationMatchRt>0</identificationMatchRt>
<identificationRtWindow>1</identificationRtWindow>
<instrumentType>0</instrumentType>
<intensityQuantile>0</intensityQuantile>
<intensityWeight>10</intensityWeight>
<ionizationMode>0</ionizationMode>
<ionizationType>0</ionizationType>
<isIsotopeEqualPeakFilter>0</isIsotopeEqualPeakFilter>
<isotopeC13Correction>0</isotopeC13Correction>
<isotopeFilterEqualPeak>0</isotopeFilterEqualPeak>
<isotopeMinPeakQuality>0</isotopeMinPeakQuality>
<isotopeMinSignalBaselineDifference>0</isotopeMinSignalBaselineDifference>
<isotopicMinSignalBaselineDifference>0</isotopicMinSignalBaselineDifference>
<limitGroupsPerCompound>10</limitGroupsPerCompound>
<linkIsotopeRtRange>1</linkIsotopeRtRange>
<mainWindowCharge>1</mainWindowCharge>
<mainWindowMassResolution>5.000000</mainWindowMassResolution>
<mainWindowPeakQuantitation>0</mainWindowPeakQuantitation>
<mainWindowSelectedDbName>KNOWNS</mainWindowSelectedDbName>
<massCutoffMerge>20</massCutoffMerge>
<massCutoffType>ppm</massCutoffType>
<massDomainResolution>20</massDomainResolution>
<matchFragmentation>0</matchFragmentation>
<matchFragmentationOptions>0</matchFragmentationOptions>
<matchRt>0</matchRt>
<maxIntensity>9999999999</maxIntensity>
<maxIsotopeScanDiff>5</maxIsotopeScanDiff>
<maxMz>999999999</maxMz>
<maxNaturalAbundanceErr>100</maxNaturalAbundanceErr>
<maxNaturalAbundanceError>100</maxNaturalAbundanceError>
<maxRt>999999999</maxRt>
<maxRtDiffBetweenPeaks>0.25</maxRtDiffBetweenPeaks>
<minFragMatch>3</minFragMatch>
<minFragMatchScore>0</minFragMatchScore>
<minGoodGroupCount>1</minGoodGroupCount>
<minGoodPeakCount>1</minGoodPeakCount>
<minGroupIntensity>5000</minGroupIntensity>
<minGroupQuality>0.5</minGroupQuality>
<minIntensity>50000</minIntensity>
<minIsotopeParentCorrelation>0.2</minIsotopeParentCorrelation>
<minIsotopicCorrelation>0.2</minIsotopicCorrelation>
<minIsotopicPeakQuality>0</minIsotopicPeakQuality>
<minMz>0</minMz>
<minNoNoiseObs>3</minNoNoiseObs>
<minPeakQuality>0</minPeakQuality>
<minPeakWidth>3</minPeakWidth>
<minQuality>0.5</minQuality>
<minRt>0</minRt>
<minSignalBaselineDifference>0</minSignalBaselineDifference>
<minSignalBaselineRatio>2</minSignalBaselineRatio>
<minSignalBlankRatio>2</minSignalBlankRatio>
<modelTypes>-1</modelTypes>
<mustHaveFragmentation>0</mustHaveFragmentation>
<mzMax>1e+09</mzMax>
<mzMin>0</mzMin>
<obi_warp_bin_size>0.600000</obi_warp_bin_size>
<obi_warp_factor_diag>2.000000</obi_warp_factor_diag>
<obi_warp_factor_gap>1.000000</obi_warp_factor_gap>
<obi_warp_gap_extend>3.400000</obi_warp_gap_extend>
<obi_warp_gap_init>0.200000</obi_warp_gap_init>
<obi_warp_local>0</obi_warp_local>
<obi_warp_no_standard_normal>0</obi_warp_no_standard_normal>
<obi_warp_reference_sample>Select Randomly</obi_warp_reference_sample>
<obi_warp_response>20.000000</obi_warp_response>
<obi_warp_score>cor</obi_warp_score>
<obi_warp_show_advance_params>0</obi_warp_show_advance_params>
<overlapWeight>10</overlapWeight>
<parentAdductRequired>0</parentAdductRequired>
<parentIsotopeRequired>1</parentIsotopeRequired>
<peakClassifierFile>C:/Program Files (x86)/El-MAVEN_peakML/El-MAVEN/bin\default.model</peakClassifierFile>
<peakMlCuration>1</peakMlCuration>
<peakQuantitation>0</peakQuantitation>
<peakWidthQuantile>0</peakWidthQuantile>
<poly_fit_num_iterations>10</poly_fit_num_iterations>
<poly_fit_polynomial_degree>5</poly_fit_polynomial_degree>
<q1Accuracy>0.5</q1Accuracy>
<q3Accuracy>0.5</q3Accuracy>
<qualityQuantile>0</qualityQuantile>
<qualityWeight>10</qualityWeight>
<quantileIntensity>0</quantileIntensity>
<quantileQuality>0</quantileQuality>
<quantileSignalBaselineRatio>0</quantileSignalBaselineRatio>
<quantileSignalBlankRatio>0</quantileSignalBlankRatio>
<reportIsotopes>1</reportIsotopes>
<reportIsotopesOptions>1</reportIsotopesOptions>
<rtMax>1e+09</rtMax>
<rtMin>0</rtMin>
<rtStep>10</rtStep>
<scanFilterMinIntensity>0</scanFilterMinIntensity>
<scanFilterMinQuantile>0</scanFilterMinQuantile>
<scanFilterMsLevel>0</scanFilterMsLevel>
<scanFilterPolarity>0</scanFilterPolarity>
<scoringAlgo>0</scoringAlgo>
<searchAdducts>0</searchAdducts>
<sigBaselineRatio>2</sigBaselineRatio>
<sigBlankRatio>2</sigBlankRatio>
<signalBaselineRatioQuantile>0</signalBaselineRatioQuantile>
<signalBlankRatioQuantile>0</signalBlankRatioQuantile>
<timeDomainResolution>10</timeDomainResolution>
<uploadMultiprocessing>1</uploadMultiprocessing>
<useOverlap>1</useOverlap>
</Settings>
4 changes: 4 additions & 0 deletions tests/test-scripts/test_gen_reports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
bin_path = path.abspath(path.join(path.dirname(__file__), '..', '..', 'bin'))
peakdetector_path = path.join(bin_path, "peakdetector")
samples_path = path.join(bin_path, "methods", "091215_120*.mzXML")
settings_path = path.join(path.dirname(__file__), "settings.xml")


def download_script():
Expand Down Expand Up @@ -115,6 +116,7 @@ def test_regular_lcms_reports(output_dir):
reports = generate_reports(output_dir,
project_path,
[peakdetector_path,
"-x", settings_path,
"-c", "1",
"-d", dummy_db(),
"-f", "0000",
Expand All @@ -140,6 +142,7 @@ def test_labeled_lcms_reports(output_dir):
reports = generate_reports(output_dir,
project_path,
[peakdetector_path,
"-x", settings_path,
"-c", "1",
"-d", dummy_db(),
"-f", "0001",
Expand All @@ -165,6 +168,7 @@ def test_feature_detection_reports(output_dir):
reports = generate_reports(output_dir,
project_path,
[peakdetector_path,
"-x", settings_path,
"-e", "1",
"-i", "1500000",
"-I", "1.0",
Expand Down

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