Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies
Request successful!

  0%|          | 0/1681 [00:00<?, ?it/s]
  0%|          | 1/1681 [00:01<44:32,  1.59s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  0%|          | 2/1681 [00:06<1:40:05,  3.58s/it]
  0%|          | 3/1681 [00:07<1:10:44,  2.53s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  0%|          | 4/1681 [00:15<2:10:14,  4.66s/it]Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS168
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9657
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX TripleTOF 4600: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
DERIVED_FILES
Control 1.mzXML
FILES
DERIVED_FILES
Control 2.mzXML
FILES
DERIVED_FILES
Control 3.mzXML
FILES
DERIVED_FILES
Experiment 1.mzXML
FILES
DERIVED_FILES
Experiment 2.mzXML
FILES
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Experiment 3.mzXML
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IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
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IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 6 rows!
Added 6 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS194
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9823
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
ChromatographyAndPhase: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
NCBITaxonomy:
  : missing value
MassSpectrometer:
  QExactive: missing value
  QTRAP5500: missing value
  QTRAP6500+: missing value
UBERONBodyPartName:
  : missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
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DGTG_cox14 1-s.mzXML
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FC_Kon A.mzML
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FC_cox14 1.mzML
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FC_cox14 2.mzML
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FC_cox14 4.mzML
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FC_cox14 5.mzML
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FC_cox14 6.mzML
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FC_cox14 7.mzML
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FC_cox14 8.mzML
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FC_wt 1.mzML
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FC_wt 2.mzML
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FC_wt 3.mzML
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FC_wt 4.mzML
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FC_wt 5.mzML
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FC_wt 6.mzML
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FC_wt 7.mzML
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FC_wt 8.mzML
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lpds_Kon A.mzML
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lpds_cox14 1.mzML
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lpds_cox14 2.mzML
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lpds_cox14 4.mzML
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lpds_cox14 6.mzML
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lpds_cox14 7.mzML
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pPE_cox14 1.mzML
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pPE_cox14 2.mzML
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pPE_cox14 3.mzML
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pPE_cox14 4.mzML
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pPE_cox14 5.mzML
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pPE_cox14 6.mzML
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pPE_cox14 7.mzML
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pPE_cox14 8.mzML
FILES
pPE_wt 1.mzML
FILES
pPE_wt 2.mzML
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pPE_wt 3.mzML
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pPE_wt 4.mzML
FILES
pPE_wt 5.mzML
FILES
pPE_wt 6.mzML
FILES
pPE_wt 7.mzML
FILES
pPE_wt 8.mzML
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  extension
IGNORED:  Assay_DI Instrument
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Accession Number.4
IGNORED:  filename_lower
IGNORED:  Samples_Source Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Derivatization
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
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IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
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IGNORED:  Samples_Genotype
IGNORED:  Assay_Metabolite Assignment File
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IGNORED:  Assay_MS Assay Name
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IGNORED:  Assay_Protocol REF.3
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IGNORED:  Samples_Sample type
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 6
Returning 66 rows!
Added 66 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9835
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
YearOfAnalysis:/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  0%|          | 5/1681 [00:20<2:06:19,  4.52s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  0%|          | 6/1681 [00:24<2:02:30,  4.39s/it]
  1970: missing value
MassSpectrometer:
  Thermo Scientific Orbitrap Exploris 120: missing value
IonizationSourceAndPolarity:
  electrospray ionization: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
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ALP1_neg.raw
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RAW_FILES
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IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
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IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 38 rows!
Added 38 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS10035
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
YearOfAnalysis:
  1970: missing value
MassSpectrometer:
  Waters Xevo TQ: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
RAW_FILES
20230828_Shao_102.raw
FILES
RAW_FILES
20230828_Shao_103.raw
FILES
RAW_FILES
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FILES
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IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Samples_Glutamine
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Induction
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Samples_Drug
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 30 rows!
Added 30 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS10062
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
YearOfAnalysis:
  1970: missing value
MassSpectrometer:
  Thermo Scientific Q Exactive HF: missing value/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  0%|          | 7/1681 [00:29<2:09:37,  4.65s/it]
  0%|          | 8/1681 [00:30<1:39:54,  3.58s/it]
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
22P11650003_OCTML_NEG.raw
FILES
22P11650003_OCTML_POS.raw
FILES
22P11650007_OCTML_NEG.raw
FILES
22P11650007_OCTML_POS.raw
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22P11650008_OCTML_NEG.raw
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22P11650008_OCTML_POS.raw
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22P11650011_OCTML_NEG.raw
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22P11650012_OCTML_NEG.raw
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22P11650027_OCTML_POS.raw
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22P11650028_OCTML_NEG.raw
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22P11650028_OCTML_POS.raw
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22P11650031_OCTML_NEG.raw
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22P11650031_OCTML_POS.raw
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22P11650032_OCTML_NEG.raw
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22P11650032_OCTML_POS.raw
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22P11650035_OCTML_NEG.raw
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22P11650036_OCTML_NEG.raw
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22P11650036_OCTML_POS.raw
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22P11650039_OCTML_NEG.raw
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22P11650042_OCTML_NEG.raw
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22P11650042_OCTML_POS.raw
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22P11650043_OCTML_NEG.raw
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22P11650043_OCTML_POS.raw
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22P11650046_OCTML_NEG.raw
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22P11650046_OCTML_POS.raw
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22P11650047_OCTML_NEG.raw
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22P11650047_OCTML_POS.raw
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22P11650052_OCTML_NEG.raw
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DB_OCTML_POS_05.raw
FILES
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QC_OCTML_NEG_MSMS1.raw
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QC_OCTML_NEG_MSMS2.raw
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QC_OCTML_POS_06.raw
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QC_OCTML_POS_12.raw
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QC_OCTML_POS_MSMS1.raw
FILES
QC_OCTML_POS_MSMS2.raw
FILES
QC_OCTML_POS_MSMS3.raw
FILES
QC_OCTML_POS_MSMS4.raw
FILES
QC_OCTML_POS_MSMS5.raw
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Samples_Treatment
IGNORED:  Assay_Column model
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
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Number of rows removed due to not enough metadata: 0
Returning 94 rows!
Added 94 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9836
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS10083
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
YearOfAnalysis:
  1970: missing value
MassSpectrometer:
  Thermo Scientific Q Exactive HF: missing value
ENVOEnvironmentBiome:
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ENVOEnvironmentMaterial:
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FILES
22P11650002_OCTML_NEG.raw
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22P11650002_OCTML_POS.raw
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22P11650006_OCTML_NEG.raw
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22P11650006_OCTML_POS.raw
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22P11650010_OCTML_NEG.raw
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22P11650014_OCTML_NEG.raw
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22P11650014_OCTML_POS.raw
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22P11650018_OCTML_POS.raw
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22P11650022_OCTML_NEG.raw
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22P11650034_OCTML_NEG.raw
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22P11650034_OCTML_POS.raw
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22P11650038_OCTML_NEG.raw
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22P11650038_OCTML_POS.raw
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22P11650041_OCTML_NEG.raw
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22P11650041_OCTML_POS.raw
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22P11650045_OCTML_NEG.raw
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22P11650045_OCTML_POS.raw
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DB_OCTML_NEG_05.raw
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DB_OCTML_NEG_06.raw
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DB_OCTML_POS_01.raw
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DB_OCTML_POS_03.raw
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QC_OCTML_NEG_13.raw
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QC_OCTML_NEG_14.raw
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QC_OCTML_NEG_MSMS1.raw
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QC_OCTML_NEG_MSMS2.raw
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QC_OCTML_NEG_MSMS3.raw
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QC_OCTML_NEG_MSMS4.raw
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QC_OCTML_NEG_MSMS5.raw
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QC_OCTML_POS_06.raw
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QC_OCTML_POS_07.raw
FILES
QC_OCTML_POS_08.raw
FILES
QC_OCTML_POS_09.raw
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QC_OCTML_POS_10.raw
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QC_OCTML_POS_11.raw
FILES
QC_OCTML_POS_12.raw
FILES
QC_OCTML_POS_13.raw
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QC_OCTML_POS_14.raw
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QC_OCTML_POS_MSMS1.raw
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QC_OCTML_POS_MSMS2.raw
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QC_OCTML_POS_MSMS3.raw
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QC_OCTML_POS_MSMS5.raw
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Samples_Treatment
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
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IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 9/1681 [00:35<1:48:52,  3.91s/it]
  1%|          | 10/1681 [00:37<1:35:56,  3.44s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 11/1681 [00:43<1:54:13,  4.10s/it]
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
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IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
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Number of rows removed due to not enough metadata: 0
Returning 68 rows!
Added 68 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9853
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9914
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
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DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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  nan: missing value
ENVOEnvironmentMaterial:
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FILES
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mouse_C0plusD0_SOX4_OE_TET2_KO.mzML
FILES
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MetaboMSnPos
Pool_pos_Met_3.mzML
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MetaboMSnPos
Pool_pos_Met_4.mzML
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Samples_Cell
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
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IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
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IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Samples_Genotype
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 30 rows!
Added 30 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9929
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
YearOfAnalysis:
  1970: missing value
MassSpectrometer:
  Thermo Scientific Q Exactive Plus: missing value
FILES
DERIVED_FILES
IL_NEG.mzXML
FILES
DERIVED_FILES
IL_POS.mzXML
FILES
DERIVED_FILES
UIL_NEG.mzXML
FILES
DERIVED_FILES
UIL_POS.mzXML
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
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IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Accession Number.4
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IGNORED:  Samples_Source Name
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IGNORED:  Assay_Guard column/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 12/1681 [00:47<1:59:10,  4.28s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 13/1681 [00:52<2:01:33,  4.37s/it]
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Derivatization
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
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IGNORED:  Samples_Infection
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Number of rows removed due to not enough metadata: 4
Returning 0 rows!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9930
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
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Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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FILES
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Number of rows removed due to not enough metadata: 6
Returning 0 rows!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9938
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive HF-X: missing value
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  nan: missing value
ENVOEnvironmentMaterial:
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HF-1_CN3_FZTM230053815-1A.mzML
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HF-1_CN3_FZTM230053816-1A.mzML
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HF-1_CN3_FZTM230053817-1A.mzML
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HF-1_CN3_FZTM230053818-1A.mzML
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HF-1_CN3_FZTM230053819-1A.mzML
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HF-1_CN3_FZTM230053820-1A.mzML
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HF-1_CN3_FZTM230053821-1A.mzML
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HF-1_CP2_FZTM230053806-1A.mzML
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HF-1_CP2_FZTM230053807-1A.mzML
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HF-1_CP2_FZTM230053808-1A.mzML
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HF-1_CP2_FZTM230053809-1A.mzML
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HF-1_CP2_FZTM230053811-1A.mzML
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HF-1_CP2_FZTM230053812-1A.mzML
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HF-1_CP2_FZTM230053813-1A.mzML
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DERIVED_FILES
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HF-1_CP3_FZTM230053814-1A.mzML
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DERIVED_FILES
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HF-1_CP3_FZTM230053815-1A.mzML
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HF-1_CP3_FZTM230053816-1A.mzML
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HF-1_CP3_FZTM230053817-1A.mzML
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HF-1_CP3_FZTM230053819-1A.mzML
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DERIVED_FILES
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HF-1_CP3_FZTM230053820-1A.mzML
FILES
DERIVED_FILES
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IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
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IGNORED:  Assay_Data Transformation Name
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IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
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IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
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IGNORED:  Samples_Term Accession Number.4
IGNORED:  filename_lower
IGNORED:  Samples_Source Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Derivatization
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  Assay_MS Assay Name
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IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 14/1681 [00:57<2:03:21,  4.44s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 15/1681 [01:01<1:58:40,  4.27s/it]
  1%|          | 16/1681 [01:03<1:43:12,  3.72s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 17/1681 [01:07<1:42:38,  3.70s/it]
  1%|          | 18/1681 [01:09<1:29:06,  3.21s/it]
Returning 32 rows!
Added 32 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS9948
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific ISQ: missing value
IonizationSourceAndPolarity:
  electron ionization (positive): missing value
ChromatographyAndPhase:
  : missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
ATL1.raw
FILES
ATL2.raw
FILES
ATL3.raw
FILES
ATL4.raw
FILES
ATL5.raw
FILES
ATL6.raw
FILES
Con1.raw
FILES
Con2.raw
FILES
Con3.raw
FILES
Con4.raw
FILES
Con5.raw
FILES
Con6.raw
FILES
Mod1.raw
FILES
Mod2.raw
FILES
Mod3.raw
FILES
Mod4.raw
FILES
Mod5.raw
FILES
Mod6.raw
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IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 18 rows!
Added 18 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1014
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS10284
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
BMSC-0Gy-1.raw
FILES
BMSC-0Gy-2.raw
FILES
BMSC-0Gy-3.raw
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BMSC-0Gy-4.raw
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FILES
QC-2.raw
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QC-3.raw
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IGNORED:  Samples_Term Source REF.3
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IGNORED:  Samples_Term Accession Number
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IGNORED:  Samples_Term Source REF.2
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IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 11 rows!
Added 11 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1033
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1040
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Agilent 6550 iFunnel Q-TOF: missing value
FILES
AGPKZVBTJJNPAG-WHFBIAKZSA-N_STSL_0101_Isoleucine_0002fmol_180425_S2_LC02_MS02_52.mzML
FILES
AGPKZVBTJJNPAG-WHFBIAKZSA-N_STSL_0101_Isoleucine_0008fmol_180425_S2_LC02_MS02_53.mzML
FILES
AGPKZVBTJJNPAG-WHFBIAKZSA-N_STSL_0101_Isoleucine_0031fmol_180425_S2_LC02_MS02_54.mzML
FILES
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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Number of rows removed due to not enough metadata: 978
Returning 0 rows!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1041
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
NCBITaxonomy:
  : missing value
MassSpectrometer:
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UBERONBodyPartName:
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ENVOEnvironmentBiome:
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ENVOEnvironmentMaterial:
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20161020_Hypotop_232.mzXML/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|          | 20/1681 [01:38<3:55:36,  8.51s/it]
  1%|          | 21/1681 [01:40<3:02:16,  6.59s/it]
  1%|▏         | 22/1681 [01:41<2:18:59,  5.03s/it]
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IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Samples_Timepoint
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Disease
IGNORED:  Samples_Term Source REF.3
IGNORED:  Samples_Term Source REF.4
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 256 rows!
Added 256 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1044
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1045
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS10498
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX TripleTOF 4600: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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IGNORED:  Samples_Variant
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IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|▏         | 23/1681 [01:46<2:19:16,  5.04s/it]
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
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IGNORED:  Samples_Term Source REF.5
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IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 74 rows!
Added 74 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS105
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Agilent 5975C MSD: missing value
  LECO Pegasus: missing value
IonizationSourceAndPolarity:
  electron ionization (positive): missing value
ChromatographyAndPhase:
  : missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
GC-SIM-MS_01.CDF
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GC-qMS_32.CDF
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GC-qMS_33.CDF
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GC-qMS_34.CDF
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GC-qMS_35.CDF
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GC-qMS_36.CDF
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GC-qMS_37.CDF
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GC-qMS_38.CDF
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GC-qMS_39.CDF
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GC-qMS_40.CDF
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GC-qMS_42.CDF
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GC-qMS_43.CDF
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GC-qMS_44.CDF
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GC-qMS_45.CDF
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GC-qMS_46.CDF
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GC-qMS_47.CDF
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GC-qMS_48.CDF
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GC-qMS_49.CDF
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GC-qMS_50.CDF
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GC-qMS_51.CDF
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GC-qMS_52.CDF
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GC-qMS_53.CDF
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GC-qMS_54.CDF
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GC-qMS_56.CDF
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GC-qMS_57.CDF
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GC-qMS_58.CDF
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GC-qMS_59.CDF
FILES
GC-qMS_60.CDF
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GC-qMS_61.CDF
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GC-qMS_62.CDF
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GC-qMS_72.CDF
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GC-qMS_73.CDF
FILES
GC-qMS_74.CDF
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GC-qMS_75.CDF
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GC-qMS_76.CDF
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GC-qMS_77.CDF
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GC-qMS_78.CDF
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GC-qMS_79.CDF
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GC-qMS_80.CDF
FILES
GC-qMS_81.CDF
FILES
GC-qMS_82.CDF
FILES
GC-qMS_83.CDF
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GC-qMS_84.CDF
FILES
GC-qMS_85.CDF
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GC-qMS_86.CDF
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GC-qMS_87.CDF
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GC-qMS_88.CDF
FILES
GC-qMS_89.CDF
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|▏         | 24/1681 [01:54<2:46:55,  6.04s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  1%|▏         | 25/1681 [02:00<2:41:56,  5.87s/it]
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Samples_Disease
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Batch
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Assay_Term Accession Number.5
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  Assay_Term Source REF.5
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 267 rows!
Added 267 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1066
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
NCBITaxonomy:
  : missing value
MassSpectrometer:
  Thermo Scientific Q Exactive Plus: missing value
UBERONBodyPartName:
  : missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
000_DaLi_H9M9_Blank_01_neg_05.mzML
FILES
000_DaLi_H9M9_Blank_01_neg_06_HILIC.mzML
FILES
000_DaLi_H9M9_Blank_01_pos_06.mzML
FILES
000_DaLi_H9M9_Blank_01_pos_06_HILIC.mzML
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014_DaLi_H9M9_H_C_R1_neg_20_HILIC.mzML
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014_DaLi_H9M9_H_C_R1_pos_20_HILIC.mzML
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017_DaLi_H9M9_BC_MCT_R1_neg_22.mzML
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017_DaLi_H9M9_BC_MCT_R1_neg_23_HILIC.mzML
FILES
017_DaLi_H9M9_BC_MCT_R1_pos_23.mzML
FILES
017_DaLi_H9M9_BC_MCT_R1_pos_23_HILIC.mzML
FILES
019_DaLi_H9M9_H_LCT_R1_neg_24.mzML
FILES
019_DaLi_H9M9_H_LCT_R1_neg_25_HILIC.mzML
FILES
019_DaLi_H9M9_H_LCT_R1_pos_25.mzML
FILES
019_DaLi_H9M9_H_LCT_R1_pos_25_HILIC.mzML
FILES
032_DaLi_H9M9_BC_C_R1_neg_37.mzML
FILES
032_DaLi_H9M9_BC_C_R1_neg_38_HILIC.mzML
FILES
032_DaLi_H9M9_BC_C_R1_pos_38.mzML
FILES
032_DaLi_H9M9_BC_C_R1_pos_38_HILIC.mzML
FILES
033_DaLi_H9M9_H_MCT_R1_neg_38.mzML
FILES
033_DaLi_H9M9_H_MCT_R1_neg_39_HILIC.mzML
FILES
033_DaLi_H9M9_H_MCT_R1_pos_39.mzML
FILES
033_DaLi_H9M9_H_MCT_R1_pos_39_HILIC.mzML
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
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IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
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IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Term Source REF.6
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IGNORED:  Assay_Protocol REF.2
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IGNORED:  Assay_Term Accession Number.5
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IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 28 rows!
Added 28 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS10690
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
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FILES
FLP003_p001.raw
FILES
FLP003_p002.raw
FILES
FLP003_p003.raw
FILES
FLP003_p004.raw
FILES
FLP003_p005.raw
FILES
FLP003_p006.raw
FILES
FLP003_p007.raw
FILES
FLP003_p008.raw
FILES
FLP003_p009.raw
FILES
FLP003_p010.raw
FILES
FLP003_p011.raw
FILES
FLP003_p012.raw
FILES
FLP003_p013.raw
FILES
FLP003_p014.raw
FILES
FLP003_p015.raw
IGNORED:  Samples_Variant
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IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  Samples_Replicate
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Samples_Mutation
IGNORED:  Assay_Protocol REF.1
IGNORED:  Assay_Autosampler model/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 26/1681 [02:04<2:29:21,  5.42s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 27/1681 [02:09<2:20:29,  5.10s/it]
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
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IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
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IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 15 rows!
Added 15 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1073
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive Plus: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
neg_mock-1_a.raw
FILES
neg_mock-1_b.raw
FILES
neg_mock-2_a.raw
FILES
neg_mock-2_b.raw
FILES
neg_mock-3_a.raw
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neg_mock-3_b.raw
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neg_sub-1_a.raw
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neg_sub-1_b.raw
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neg_sub-2_a.raw
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neg_sub-2_b.raw
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neg_sub-3_a.raw
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neg_sub-3_b.raw
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neg_wt-1_a.raw
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neg_wt-1_b.raw
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neg_wt-2_a.raw
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neg_wt-2_b.raw
FILES
neg_wt-3_a.raw
FILES
neg_wt-3_b.raw
FILES
pos_mock-1_a.raw
FILES
pos_mock-1_b.raw
FILES
pos_mock-2_a.raw
FILES
pos_mock-2_b.raw
FILES
pos_mock-3_a.raw
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pos_mock-3_b.raw
FILES
pos_sub-1_a.raw
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pos_sub-1_b.raw
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pos_sub-2_b.raw
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pos_sub-3_a.raw
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pos_sub-3_b.raw
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pos_wt-1_a.raw
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pos_wt-1_b.raw
FILES
pos_wt-2_a.raw
FILES
pos_wt-2_b.raw
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pos_wt-3_a.raw
FILES
pos_wt-3_b.raw
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
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IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
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IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Samples_Virus
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  Samples_Replicate
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
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IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
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IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
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IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 36 rows!
Added 36 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1079
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
ChromatographyAndPhase: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
NCBITaxonomy:
  : missing value
MassSpectrometer:
  LECO Pegasus 4D: missing value
UBERONBodyPartName:
  : missing value
ENVOEnvironmentBiome:
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ENVOEnvironmentMaterial:
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FILES
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1A_t0_1.cdf
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QC4_2.cdf/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 28/1681 [02:17<2:43:18,  5.93s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 29/1681 [02:21<2:30:02,  5.45s/it]
FILES
QC4_3.cdf
FILES
QC5_1.cdf
FILES
QC5_2.cdf
FILES
QC5_3.cdf
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QC6_1.cdf
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QC_A_3.cdf
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QC_B_1.cdf
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QC_B_2.cdf
FILES
QC_B_3.cdf
IGNORED:  Samples_Protocol REF
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Assay_Term Source REF.6
IGNORED:  Assay_Term Accession Number.10
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Term Source REF.8
IGNORED:  Assay_Term Accession Number.6
IGNORED:  Samples_Lysate
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Data Transformation Name
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Source REF.7
IGNORED:  Assay_Term Source REF.9
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Column type 2
IGNORED:  Assay_Post Extraction
IGNORED:  Assay_Protocol REF.4
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Term Source REF.2
IGNORED:  filename_lower
IGNORED:  Samples_Source Name
IGNORED:  Assay_Guard column
IGNORED:  Assay_Protocol REF
IGNORED:  Assay_Term Source REF.5
IGNORED:  Assay_Term Accession Number.9
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.8
IGNORED:  Assay_Derivatization
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  extension
IGNORED:  Assay_Term Accession Number.2
IGNORED:  filepath
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Accession Number.5
IGNORED:  Samples_Term Source REF.5
IGNORED:  Assay_Column model 2
IGNORED:  Samples_Organism
IGNORED:  Is Descendant
IGNORED:  Is Organ
IGNORED:  Assay_Column type 1
IGNORED:  Assay_MS Assay Name
IGNORED:  keep
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Scan m/z range
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Assay_Normalization Name
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.2
IGNORED:  Samples_Plasmid
IGNORED:  Assay_Term Accession Number
IGNORED:  row_id
IGNORED:  base
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Assay_Column model 1
IGNORED:  Samples_Dialysis
IGNORED:  Assay_Term Source REF.3
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Source REF.6
IGNORED:  Is Multicellular
IGNORED:  Assay_Term Source REF.10
IGNORED:  Samples_Term Source REF
IGNORED:  Assay_Term Accession Number.7
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 152 rows!
Added 152 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS108
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
Lut_A_220d.raw
FILES
Lut_A_221a.raw
FILES
Lut_A_221e.raw
FILES
Lut_A_222f.raw
FILES
Lut_A_223a.raw
FILES
Lut_A_223b.raw
FILES
Lut_A_223e.raw
FILES
Lut_A_223f.raw
FILES
Lut_A_224a.raw
FILES
Lut_A_224d.raw
FILES
Lut_A_224e.raw
FILES
Lut_A_291d.raw
FILES
Lut_B_222g.raw
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Lut_B_222i.raw
FILES
Lut_B_223d.raw
FILES
Lut_B_223i.raw
FILES
Lut_B_223j.raw
FILES
Lut_B_224b.raw
FILES
Lut_B_224f.raw
FILES
Lut_B_290e.raw
FILES
Lut_B_290f.raw
FILES
Lut_B_290g.raw
FILES
Lut_B_291e.raw
FILES
Lut_B_291g.raw
FILES
Lut_C_221f.raw
FILES
Lut_C_221i.raw
FILES
Lut_C_221j.raw
FILES
Lut_C_223h.raw
FILES
Lut_C_223l.raw
FILES
Lut_C_223m.raw
FILES
Lut_C_223n.raw
FILES
Lut_C_224h.raw
FILES
Lut_C_224i.raw
FILES
Lut_C_224j.raw
FILES
Lut_C_224k.raw
FILES
Lut_C_290h.raw
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Phytohormones
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Samples_Unit.1
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  Samples_Carotenoids
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 36 rows!
Added 36 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS109
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
A-car_A_220g.raw
FILES
A-car_A_220h.raw
FILES
A-car_A_221f.raw
FILES
A-car_A_223j.raw
FILES
A-car_A_223n.raw
FILES
A-car_A_224b.raw
FILES
A-car_A_224h.raw
FILES
A-car_A_224j.raw
FILES
A-car_A_290a.raw
FILES
A-car_A_290e.raw
FILES
A-car_A_290f.raw
FILES
A-car_A_290h.raw
FILES
A-car_B_220e.raw
FILES
A-car_B_220f.raw
FILES
A-car_B_221e.raw
FILES
A-car_B_221i.raw
FILES
A-car_B_221j.raw
FILES
A-car_B_222f.raw
FILES
A-car_B_222i.raw
FILES
A-car_B_223b.raw
FILES
A-car_B_223i.raw
FILES
A-car_B_224a.raw
FILES
A-car_B_224c.raw
FILES
A-car_B_290g.raw
FILES
A-car_C_220a.raw
FILES
A-car_C_220d.raw
FILES
A-car_C_222g.raw
FILES
A-car_C_223a.raw
FILES
A-car_C_223c.raw
FILES
A-car_C_223h.raw
FILES
A-car_C_224d.raw
FILES
A-car_C_224e.raw
FILES
A-car_C_224f.raw
FILES
A-car_C_224g.raw
FILES
A-car_C_291e.raw
FILES
A-car_C_291g.raw
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 30/1681 [02:25<2:20:33,  5.11s/it]
  2%|▏         | 31/1681 [02:27<1:52:10,  4.08s/it]
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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 33/1681 [02:32<1:37:12,  3.54s/it]
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Phytohormones
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Samples_Unit.1
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  Samples_Carotenoids
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 36 rows!
Added 36 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1093
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1103
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1104
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific ISQ: missing value
  Thermo Scientific Q Exactive: missing value
IonizationSourceAndPolarity:
  electron ionization (positive): missing value
ChromatographyAndPhase:
  : missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
DS_180824_ISQ_04.mzXML
FILES
DS_180824_ISQ_06.mzXML
FILES
DS_180824_ISQ_07.mzXML
FILES
DS_180824_ISQ_08.mzXML
FILES
DS_180824_ISQ_09.mzXML
FILES
DS_180824_ISQ_10.mzXML
FILES
DS_180824_ISQ_11.mzXML
FILES
DS_180824_ISQ_12.mzXML
FILES
DS_180824_ISQ_13.mzXML
FILES
DS_180824_ISQ_14.mzXML
FILES
DS_180824_ISQ_15.mzXML
FILES
DS_180824_ISQ_16.mzXML
FILES
DS_180824_ISQ_17.mzXML
FILES
DS_180824_ISQ_18.mzXML
FILES
DS_180824_ISQ_19.mzXML
FILES
DS_180824_ISQ_20.mzXML
FILES
DS_180824_ISQ_21.raw
FILES
DS_180918_08.raw
FILES
DS_180919_03.mzXML
FILES
DS_180919_05.mzXML
FILES
DS_180919_06.mzXML
FILES
DS_180919_07.mzXML
FILES
DS_180919_08.mzXML
FILES
DS_180919_09.mzXML
FILES
DS_180919_10.mzXML
FILES
DS_180919_12.mzXML
FILES
DS_180919_13.mzXML
FILES
DS_180919_14.mzXML
FILES
DS_180919_15.mzXML
FILES
DS_180919_16.mzXML
FILES
DS_180919_17.mzXML
FILES
DS_180919_18.mzXML
FILES
DS_180919_19.mzXML
FILES
DS_181212_03.raw
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Samples_Salinity
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Assay_Term Accession Number.5
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Samples_MSD Analyser
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  Assay_Term Source REF.5
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 34 rows!
Added 34 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1115
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX TripleTOF 6600: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
F0_1_neg.wiff
FILES
F0_1_pos.wiff
FILES
F0_2_neg.wiff
FILES
F0_2_pos.wiff
FILES
F0_3_neg.wiff
FILES
F0_3_pos.wiff
FILES
F12_1_neg.wiff
FILES
F12_1_pos.wiff
FILES
F12_2_neg.wiff
FILES
F12_2_pos.wiff
FILES
F12_3_neg.wiff
FILES
F12_3_pos.wiff
FILES
F24_1_neg.wiff
FILES
F24_1_pos.wiff
FILES
F24_2_neg.wiff
FILES
F24_2_pos.wiff
FILES
F24_3_neg.wiff
FILES
F24_3_pos.wiff
FILES
F48_1_neg.wiff
FILES
F48_1_pos.wiff
FILES
F48_2_neg.wiff
FILES
F48_2_pos.wiff
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F48_3_neg.wiff
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F48_3_pos.wiff
FILES
QC01_neg.wiff
FILES
QC01_pos.wiff
FILES
QC02_neg.wiff
FILES
QC02_pos.wiff
FILES
QC03_neg.wiff
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QC03_pos.wiff
FILES
QC04_neg.wiff
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QC04_pos.wiff
FILES
TQC01_neg.wiff
FILES
TQC01_pos.wiff
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X0_1_neg.wiff
FILES
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X0_2_neg.wiff
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X0_2_pos.wiff
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X0_3_neg.wiff
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X12_1_neg.wiff
FILES
X12_1_pos.wiff
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X12_2_neg.wiff
FILES
X12_2_pos.wiff
FILES
X12_3_neg.wiff
FILES
X12_3_pos.wiff
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X18_1_neg.wiff
FILES
X18_1_pos.wiff
FILES
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FILES
X18_2_pos.wiff
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X18_3_neg.wiff
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X18_3_pos.wiff
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X24_1_neg.wiff
FILES
X24_1_pos.wiff
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X24_2_pos.wiff
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X24_3_neg.wiff
FILES
X24_3_pos.wiff
FILES
X6_1_neg.wiff
FILES/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 34/1681 [02:37<1:49:09,  3.98s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 35/1681 [02:42<1:51:04,  4.05s/it]
  2%|▏         | 36/1681 [02:43<1:27:42,  3.20s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 37/1681 [02:46<1:30:23,  3.30s/it]
X6_1_pos.wiff
FILES
X6_2_neg.wiff
FILES
X6_2_pos.wiff
FILES
X6_3_neg.wiff
FILES
X6_3_pos.wiff
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IGNORED:  Samples_Viral exposure
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 67 rows!
Added 67 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS11229
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Agilent 5975C inert XL MSD: missing value
IonizationSourceAndPolarity:
  electron ionization (positive): missing value
ChromatographyAndPhase:
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FILES
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py-S1-test02.D
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 1 rows!
Added 1 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS11250
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1127
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX API 4000: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
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FILES
F10-1.mzML
FILES
F10-2.mzML
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F10-3.mzML
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F6-1.mzML
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F6-2.mzML
FILES
F6-3.mzML
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F7-1.mzML
FILES
F7-2.mzML
FILES
F7-3.mzML
FILES
F8-1.mzML
FILES
F8-2.mzML
FILES
F8-3.mzML
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F9-1.mzML
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F9-2.mzML
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F9-3.mzML
IGNORED:  Samples_Variant
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IGNORED:  Assay_Normalization Name
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IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
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IGNORED:  Assay_Protocol REF.2
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
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Number of rows removed due to not enough metadata: 0
Returning 15 rows!
Added 15 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1133
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 38/1681 [02:54<2:06:26,  4.62s/it]
  2%|▏         | 39/1681 [02:55<1:36:37,  3.53s/it]
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
NCBITaxonomy:
  : missing value
MassSpectrometer:
  Agilent 6520A Q-TOF: missing value
UBERONBodyPartName:
  : missing value
ENVOEnvironmentBiome:
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ENVOEnvironmentMaterial:
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FILES
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IGNORED:  Samples_Variant
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IGNORED:  Samples_Term Source REF.3
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IGNORED:  Assay_Term Source REF
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 168 rows!
Added 168 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS114
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1140
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX TripleTOF 5600: missing value
ENVOEnvironmentBiome:
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ENVOEnvironmentMaterial:
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FILES
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IGNORED:  Assay_Labeled Extract Name
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IGNORED:  filename_lower
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IGNORED:  Samples_Source Name
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IGNORED:  Samples_Unit
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IGNORED:  Assay_Term Accession Number.1/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 40/1681 [03:00<1:49:12,  3.99s/it]
  2%|▏         | 41/1681 [03:02<1:30:43,  3.32s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  2%|▏         | 42/1681 [03:08<1:52:58,  4.14s/it]
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
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IGNORED:  Assay_Term Source REF.3
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Number of rows removed due to not enough metadata: 0
Returning 17 rows!
Added 17 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS11419
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1167
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
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DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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Number of rows removed due to not enough metadata: 0
Returning 62 rows!
Added 62 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1168
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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IGNORED:  row_id/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  3%|▎         | 43/1681 [03:14<2:06:07,  4.62s/it]
  3%|▎         | 44/1681 [03:17<1:53:19,  4.15s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  3%|▎         | 45/1681 [03:25<2:27:33,  5.41s/it]
  3%|▎         | 46/1681 [03:27<1:58:23,  4.34s/it]
IGNORED:  Assay_Term Accession Number
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IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
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Number of rows removed due to not enough metadata: 0
Returning 80 rows!
Added 80 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1183
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1187
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
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ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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  Agilent 7200 Q-TOF: missing value
IonizationSourceAndPolarity:
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FILES
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IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Samples_Genotype
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Samples_Location
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Weight
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 23
Returning 120 rows!
Added 120 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1206
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1188
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  3%|▎         | 47/1681 [03:33<2:11:56,  4.84s/it]
  3%|▎         | 48/1681 [03:35<1:48:19,  3.98s/it]
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
FRAG_NEG.mzml
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FRAG_POS.mzml
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KM_1.mzxml
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KM_10.mzxml
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KM_10_neg.mzxml
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pooled_8.mzxml
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pooled_8_neg.mzxml
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pooled_9.mzxml
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pooled_9_neg.mzxml
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  Samples_Replicate
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Samples_IFN response
IGNORED:  Samples_Organism
IGNORED:  Assay_Sample Name
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Time
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF.6
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 12
Returning 58 rows!
Added 58 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1198
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1210
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Agilent 7010 Triple Quadrupole: missing value
  Thermo Scientific TSQ Vantage: missing value
  Thermo Scientific Q Exactive HF: missing value
IonizationSourceAndPolarity:
  electron ionization (positive): missing value
ChromatographyAndPhase:
  : missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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FILES
E82-2-1-DI.mzML/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:166: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = df.apply(lambda x: age_category(x['AgeInYears']) if x['NCBITaxonomy'] == "9606|Homo sapiens" else value['missing'], axis=1)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:190: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['TaxonID'] = df['NCBITaxonomy'].apply(lambda x: x.split('|')[0] if '|' in x else 'missing value')
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:188: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['USI'] = 'mzspec:' + df['MassiveID'] + ':' + df['filename']

  3%|▎         | 49/1681 [03:46<2:48:52,  6.21s/it]
FILES
E82-2-1.mzML
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E82-2-2.mzML
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E83-1-1-DI.mzML
FILES
E83-1-1.mzML
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Number of rows removed due to not enough metadata: 16
Returning 275 rows!
Added 275 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1219
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Q Exactive Plus: missing value
ENVOEnvironmentBiome:
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  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Number of rows removed due to not enough metadata: 0
Returning 92 rows!
Added 92 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1221
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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TermsofPosition: ADDED!
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Country: ADDED!
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LatitudeandLongitude: ADDED!
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WT_NR_01.d/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Returning 44 rows!
Added 44 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1257
Request successful!
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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Returning 250 rows!
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Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1259
Request successful!
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Country: ADDED!
HumanPopulationDensity: ADDED!
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qiita_sample_name: ADDED!
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intestine/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Number of rows removed due to not enough metadata: 0
Returning 252 rows!
Added 252 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1264
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1266
Request successful!
SampleCollectionMethod: ADDED!
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TermsofPosition: ADDED!
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Country: ADDED!
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/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  3%|▎         | 55/1681 [04:30<3:13:42,  7.15s/it]
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Number of rows removed due to not enough metadata: 0
Returning 80 rows!
Added 80 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1267
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1274
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS103
Request successful!
SampleCollectionMethod: ADDED!
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IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
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IGNORED:  Assay_Term Source REF.4/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  3%|▎         | 58/1681 [04:39<2:05:00,  4.62s/it]
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
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Number of rows removed due to not enough metadata: 0
Returning 96 rows!
Added 96 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1282
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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FILES
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GC-MS
01_GC.cdf
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RAW_FILES/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▎         | 59/1681 [04:46<2:23:32,  5.31s/it]
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Number of rows removed due to not enough metadata: 0
Returning 176 rows!
Added 176 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1286
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
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IonizationSourceAndPolarity:
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ChromatographyAndPhase:
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ENVOEnvironmentBiome:
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IGNORED:  Assay_Post Extraction/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▎         | 60/1681 [04:53<2:40:21,  5.94s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▎         | 61/1681 [04:58<2:30:48,  5.59s/it]
IGNORED:  Samples_Term Source REF.2
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Number of rows removed due to not enough metadata: 23
Returning 68 rows!
Added 68 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1302
Request successful!
SampleCollectionMethod: ADDED!
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Country: ADDED!
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Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1309
Request successful!
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IGNORED:  Samples_Term Source REF.5/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▎         | 62/1681 [05:06<2:52:24,  6.39s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▎         | 63/1681 [05:12<2:46:18,  6.17s/it]
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
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Number of rows removed due to not enough metadata: 0
Returning 86 rows!
Added 86 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1311
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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DepthorAltitudeMeters: ADDED!
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Number of rows removed due to not enough metadata: 42
Returning 0 rows!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1319
Request successful!
SampleCollectionMethod: ADDED!
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Country: ADDED!
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/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:190: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['TaxonID'] = df['NCBITaxonomy'].apply(lambda x: x.split('|')[0] if '|' in x else 'missing value')
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:188: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['USI'] = 'mzspec:' + df['MassiveID'] + ':' + df['filename']

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IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Samples_NT_code
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Samples_Drug concentration
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Samples_Drug
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 115
Returning 140 rows!
Added 140 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1320
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1334
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
ChromatographyAndPhase: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Agilent 6545 Q-TOF: missing value
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IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  extension
IGNORED:  Assay_DI Instrument
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▍         | 66/1681 [05:30<2:33:17,  5.69s/it]
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Accession Number.4
IGNORED:  filename_lower
IGNORED:  Samples_Source Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Derivatization
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  Assay_MS Assay Name
IGNORED:  keep
IGNORED:  Assay_Protocol REF.3
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Lipid
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 55
Returning 0 rows!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS135
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Q Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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IGNORED:  Assay_Term Accession Number.17
IGNORED:  Assay_Term Source REF.15
IGNORED:  Samples_Protocol REF
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Assay_Raw data file format
IGNORED:  Assay_Term Source REF.6/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:97: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = value['missing']
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:166: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df[key] = df.apply(lambda x: age_category(x['AgeInYears']) if x['NCBITaxonomy'] == "9606|Homo sapiens" else value['missing'], axis=1)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:190: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['TaxonID'] = df['NCBITaxonomy'].apply(lambda x: x.split('|')[0] if '|' in x else 'missing value')
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:188: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['USI'] = 'mzspec:' + df['MassiveID'] + ':' + df['filename']

  4%|▍         | 67/1681 [05:37<2:45:38,  6.16s/it]
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  4%|▍         | 69/1681 [05:40<1:45:52,  3.94s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▍         | 70/1681 [05:45<1:47:30,  4.00s/it]
IGNORED:  Samples_Term Source REF.7
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Number of rows removed due to not enough metadata: 0
Returning 120 rows!
Added 120 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1355
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1359
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1463
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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ChromatographyAndPhase:
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Number of rows removed due to not enough metadata: 0
Returning 34 rows!
Added 34 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS136
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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Country: ADDED!
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IGNORED:  Samples_AgeAtBloodDraw
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IGNORED:  Assay_Term Accession Number.11
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IGNORED:  Samples_gender
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IGNORED:  Assay_Term Source REF.20
IGNORED:  Assay_Term Source REF.7
IGNORED:  Assay_Native spectrum identifier format
IGNORED:  Assay_Term Source REF.9
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IGNORED:  Assay_Protocol REF/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▍         | 71/1681 [07:57<19:02:34, 42.58s/it]
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IGNORED:  keep
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IGNORED:  Assay_Data file content
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IGNORED:  Assay_Instrument software
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IGNORED:  Assay_Term Accession Number.12
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  Assay_Data Transformation software version
IGNORED:  Assay_Protocol REF.3
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IGNORED:  Samples_Term Source REF
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IGNORED:  Assay_Term Source REF.12
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IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 6186 rows!
Added 6186 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1369
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive HF: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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QExHF03_HPLC_0000179.mzML
FILES
QExHF03_HPLC_0000180.mzML
FILES
QExHF03_HPLC_0000181.mzML
FILES
QExHF03_HPLC_0000182.mzML
FILES
QExHF03_HPLC_0000183.mzML
FILES
QExHF03_HPLC_0000184.mzML
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Samples_Treatment
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
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IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Run order
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
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IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Samples_Concentration
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:190: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['TaxonID'] = df['NCBITaxonomy'].apply(lambda x: x.split('|')[0] if '|' in x else 'missing value')
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:188: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['USI'] = 'mzspec:' + df['MassiveID'] + ':' + df['filename']

  4%|▍         | 72/1681 [08:05<14:21:47, 32.14s/it]
  4%|▍         | 73/1681 [08:07<10:22:26, 23.23s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▍         | 74/1681 [08:14<8:07:11, 18.19s/it] 
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 7
Returning 78 rows!
Added 78 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1370
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1371
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
ChromatographyAndPhase: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Waters Xevo G2-XS QTof: missing value
IonizationSourceAndPolarity:
   (negative): missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
IKHH29.mzxml
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MK312.mzxml
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MK76.mzxml
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MK83.mzxml
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MK91.mzxml
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MK99.mzxml
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  extension
IGNORED:  Assay_DI Instrument
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
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IGNORED:  Samples_Disease
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.3
IGNORED:  Samples_Term Source REF.4
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
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IGNORED:  Samples_Term Source REF.5
IGNORED:  Samples_Term Accession Number.4
IGNORED:  filename_lower
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IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 130 rows!
Added 130 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1375
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
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TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
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Country: ADDED!
HumanPopulationDensity: ADDED!
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DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Agilent 6495A Triple Quadrupole: missing value
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FILES
100_PLASMA_H044_B-2.mzML
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101_PLASMA_H047_B-1.mzML
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34_PLASMA_H047_A-2.mzML
FILES/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  4%|▍         | 75/1681 [08:20<6:27:18, 14.47s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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IGNORED:  Samples_Variant
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IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Samples_Ethnic group
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Samples_age
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Samples_Term Source REF.7
IGNORED:  Assay_Protocol REF.2
IGNORED:  Samples_Term Accession Number.7
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Samples_gender
IGNORED:  Samples_Organism
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 145 rows!
Added 145 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1376
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive HF: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
QExHF03_HPLC_0000546.mzML
FILES
QExHF03_HPLC_0000547.mzML
FILES
QExHF03_HPLC_0000548.mzML
FILES
QExHF03_HPLC_0000549.mzML
FILES
QExHF03_HPLC_0000550.mzML
FILES
QExHF03_HPLC_0000551.mzML
FILES
QExHF03_HPLC_0000552.mzML
FILES
QExHF03_HPLC_0000553.mzML
FILES
QExHF03_HPLC_0000554.mzML
FILES
QExHF03_HPLC_0000555.mzML
FILES
QExHF03_HPLC_0000556.mzML
FILES
QExHF03_HPLC_0000557.mzML
FILES
QExHF03_HPLC_0000558.mzML
FILES
QExHF03_HPLC_0000559.mzML
FILES
QExHF03_HPLC_0000560.mzML
FILES
QExHF03_HPLC_0000561.mzML
FILES
QExHF03_HPLC_0000562.mzML
FILES
QExHF03_HPLC_0000563.mzML
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Accession Number.4
IGNORED:  filename_lower
IGNORED:  Samples_Source Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Derivatization
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  Assay_MS Assay Name
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Sample role
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 18 rows!
Added 18 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1381
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX QTRAP 6500: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
QTrap007483_031618-Blank ext.mzML
FILES
QTrap007484_031618-STD ext.mzML
FILES
QTrap007485_031618-Unst1.mzML
FILES
QTrap007486_031618-Unst1.mzML
FILES
QTrap007487_031618-Unst1.mzML
FILES
QTrap007488_031618-Unst2.mzML
FILES
QTrap007489_031618-Unst2.mzML
FILES
QTrap007490_031618-Unst2.mzML
FILES
QTrap007491_031618-Unst3.mzML
FILES
QTrap007492_031618-Unst3.mzML
FILES
QTrap007493_031618-Unst3.mzML
FILES
QTrap007494_031618-Unst4.mzML
FILES
QTrap007495_031618-Unst4.mzML
FILES
QTrap007496_031618-Unst4.mzML
FILES
QTrap007497_031618-Unst6.mzML
FILES
QTrap007498_031618-Unst6.mzML
FILES
QTrap007499_031618-Unst6.mzML
FILES
QTrap007503_031618-Blank ext.mzML
FILES
QTrap007504_031618-STD ext.mzML
FILES
QTrap007505_031618-0.01Thr1.mzML
FILES
QTrap007506_031618-0.01Thr1.mzML
FILES
QTrap007507_031618-0.01Thr1.mzML
FILES
QTrap007508_031618-0.01Thr2.mzML
FILES
QTrap007509_031618-0.01Thr2.mzML
FILES
QTrap007510_031618-0.01Thr2.mzML
FILES
QTrap007511_031618-0.01Thr3.mzML
FILES
QTrap007512_031618-0.01Thr3.mzML
FILES
QTrap007513_031618-0.01Thr3.mzML
FILES
QTrap007514_031618-0.01Thr4.mzML
FILES
QTrap007515_031618-0.01Thr4.mzML
FILES
QTrap007516_031618-0.01Thr4.mzML
FILES
QTrap007517_031618-0.01Thr6.mzML
FILES
QTrap007518_031618-0.01Thr6.mzML
FILES
QTrap007519_031618-0.01Thr6.mzML
FILES
QTrap007523_031618-Blank ext.mzML
FILES
QTrap007524_031618-STD ext.mzML
FILES
QTrap007525_031618-1Thr1.mzML
FILES
QTrap007526_031618-1Thr1.mzML
FILES
QTrap007527_031618-1Thr1.mzML
FILES
QTrap007528_031618-1Thr2.mzML
FILES
QTrap007529_031618-1Thr2.mzML
FILES
QTrap007530_031618-1Thr2.mzML
FILES
QTrap007531_031618-1Thr3.mzML
FILES
QTrap007532_031618-1Thr3.mzML
FILES
QTrap007533_031618-1Thr3.mzML
FILES
QTrap007534_031618-1Thr4.mzML
FILES
QTrap007535_031618-1Thr4.mzML
FILES
QTrap007536_031618-1Thr4.mzML
FILES
QTrap007537_031618-1Thr6.mzML
FILES
QTrap007538_031618-1Thr6.mzML
FILES
QTrap007539_031618-1Thr6.mzML
FILES
QTrap007543_031618-Blank ext.mzML
FILES
QTrap007544_031618-STD ext.mzML
FILES
QTrap007545_031618-1CRP1.mzML
FILES
QTrap007546_031618-1CRP1.mzML
FILES
QTrap007547_031618-1CRP1.mzML
FILES
QTrap007548_031618-1CRP2.mzML
FILES
QTrap007549_031618-1CRP2.mzML
FILES
QTrap007550_031618-1CRP2.mzML
FILES
QTrap007551_031618-1CRP3.mzML
FILES
QTrap007552_031618-1CRP3.mzML
FILES
QTrap007553_031618-1CRP3.mzML
FILES
QTrap007554_031618-1CRP4.mzML
FILES
QTrap007555_031618-1CRP4.mzML
FILES
QTrap007556_031618-1CRP4.mzML
FILES
QTrap007557_031618-1CRP6.mzML
FILES
QTrap007558_031618-1CRP6.mzML
FILES
QTrap007559_031618-1CRP6.mzML
FILES
QTrap007563_031718-Blank ext.mzML
FILES
QTrap007564_031718-STD ext.mzML
FILES
QTrap007565_031718-5CRP1.mzML
FILES
QTrap007566_031718-5CRP1.mzML
FILES
QTrap007567_031718-5CRP1.mzML
FILES
QTrap007568_031718-5CRP2.mzML
FILES
QTrap007569_031718-5CRP2.mzML
FILES
QTrap007570_031718-5CRP2.mzML
FILES
QTrap007571_031718-5CRP3.mzML
FILES
QTrap007572_031718-5CRP3.mzML
FILES
QTrap007573_031718-5CRP3.mzML
FILES
QTrap007574_031718-5CRP4.mzML
FILES
QTrap007575_031718-5CRP4.mzML
FILES
QTrap007576_031718-5CRP4.mzML
FILES
QTrap007577_031718-5CRP6.mzML
FILES
QTrap007578_031718-5CRP6.mzML
FILES
QTrap007579_031718-5CRP6.mzML
FILES
QTrap007603_031718-buffer ext.mzML
FILES
QTrap007604_031718-buffer ext.mzML
FILES
QTrap007605_031718-buffer ext.mzML
FILES
QTrap007607_032118-Blank ext.mzML
FILES
QTrap007608_032118-STD ext.mzML
FILES
QTrap007609_032118-Unst1_SN.mzML
FILES
QTrap007610_032118-Unst1_SN.mzML
FILES
QTrap007611_032118-Unst1_SN.mzML
FILES
QTrap007612_032118-Unst2_SN.mzML
FILES
QTrap007613_032118-Unst2_SN.mzML
FILES
QTrap007614_032118-Unst2_SN.mzML
FILES
QTrap007615_032118-Unst3_SN.mzML
FILES
QTrap007616_032118-Unst3_SN.mzML
FILES
QTrap007617_032118-Unst3_SN.mzML
FILES
QTrap007618_032118-Unst4_SN.mzML
FILES
QTrap007619_032118-Unst4_SN.mzML
FILES
QTrap007620_032118-Unst4_SN.mzML
FILES
QTrap007621_032118-Unst6_SN.mzML
FILES
QTrap007622_032118-Unst6_SN.mzML
FILES
QTrap007623_032118-Unst6_SN.mzML
FILES
QTrap007627_032118-Blank ext.mzML
FILES
QTrap007628_032118-STD ext.mzML
FILES
QTrap007629_032118-0.01Thr1_SN.mzML
FILES
QTrap007630_032118-0.01Thr1_SN.mzML
FILES
QTrap007631_032118-0.01Thr1_SN.mzML
FILES
QTrap007632_032118-0.01Thr2_SN.mzML
FILES
QTrap007633_032118-0.01Thr2_SN.mzML
FILES
QTrap007634_032118-0.01Thr2_SN.mzML
FILES
QTrap007635_032118-0.01Thr3_SN.mzML
FILES
QTrap007636_032118-0.01Thr3_SN.mzML
FILES
QTrap007637_032118-0.01Thr3_SN.mzML
FILES
QTrap007638_032118-0.01Thr4_SN.mzML
FILES
QTrap007639_032118-0.01Thr4_SN.mzML
FILES
QTrap007640_032118-0.01Thr4_SN.mzML
FILES
QTrap007641_032118-0.01Thr6_SN.mzML
FILES
QTrap007642_032118-0.01Thr6_SN.mzML
FILES
QTrap007643_032118-0.01Thr6_SN.mzML
FILES
QTrap007647_032118-Blank ext.mzML
FILES
QTrap007648_032118-STD ext.mzML
FILES
QTrap007649_032118-1Thr1_SN.mzML
FILES
QTrap007650_032118-1Thr1_SN.mzML
FILES
QTrap007651_032118-1Thr1_SN.mzML
FILES
QTrap007652_032118-1Thr2_SN.mzML
FILES
QTrap007653_032118-1Thr2_SN.mzML
FILES
QTrap007654_032118-1Thr2_SN.mzML
FILES
QTrap007655_032118-1Thr3_SN.mzML
FILES
QTrap007656_032118-1Thr3_SN.mzML
FILES
QTrap007657_032118-1Thr3_SN.mzML
FILES
QTrap007658_032118-1Thr4_SN.mzML
FILES
QTrap007659_032118-1Thr4_SN.mzML
FILES
QTrap007660_032118-1Thr4_SN.mzML
FILES
QTrap007661_032118-1Thr6_SN.mzML
FILES
QTrap007662_032118-1Thr6_SN.mzML
FILES
QTrap007663_032118-1Thr6_SN.mzML
FILES
QTrap007667_032118-Blank ext.mzML
FILES
QTrap007668_032118-STD ext.mzML
FILES
QTrap007669_032118-1CRP1_SN.mzML
FILES
QTrap007670_032118-1CRP1_SN.mzML
FILES
QTrap007671_032118-1CRP1_SN.mzML
FILES
QTrap007672_032118-1CRP2_SN.mzML
FILES
QTrap007673_032118-1CRP2_SN.mzML
FILES
QTrap007674_032118-1CRP2_SN.mzML
FILES
QTrap007675_032118-1CRP3_SN.mzML
FILES
QTrap007676_032118-1CRP3_SN.mzML
FILES
QTrap007677_032118-1CRP3_SN.mzML
FILES
QTrap007678_032118-1CRP4_SN.mzML
FILES
QTrap007679_032118-1CRP4_SN.mzML
FILES
QTrap007680_032118-1CRP4_SN.mzML
FILES
QTrap007681_032118-1CRP6_SN.mzML
FILES
QTrap007682_032118-1CRP6_SN.mzML
FILES
QTrap007683_032118-1CRP6_SN.mzML
FILES
QTrap007687_032218-Blank ext.mzML
FILES
QTrap007688_032218-STD ext.mzML
FILES
QTrap007689_032218-5CRP1_SN.mzML
FILES
QTrap007690_032218-5CRP1_SN.mzML
FILES
QTrap007691_032218-5CRP1_SN.mzML
FILES
QTrap007692_032218-5CRP2_SN.mzML
FILES
QTrap007693_032218-5CRP2_SN.mzML
FILES
QTrap007694_032218-5CRP2_SN.mzML
FILES
QTrap007695_032218-5CRP3_SN.mzML
FILES
QTrap007696_032218-5CRP3_SN.mzML
FILES
QTrap007697_032218-5CRP3_SN.mzML
FILES
QTrap007698_032218-5CRP4_SN.mzML
FILES
QTrap007699_032218-5CRP4_SN.mzML
FILES
QTrap007700_032218-5CRP4_SN.mzML
FILES
QTrap007701_032218-5CRP6_SN.mzML
FILES
QTrap007702_032218-5CRP6_SN.mzML
FILES
QTrap007703_032218-5CRP6_SN.mzML
FILES
QTrap007727_032218-buffer ext.mzML
FILES
QTrap007728_032218-buffer ext.mzML
FILES
QTrap007729_032218-buffer ext.mzML
FILES
QTrap007730_032318-0.01Thr4.mzML
FILES
QTrap007731_032318-5CRP6.mzML
FILES
QTrap007732_032318-1CRP6_SN.mzML
FILES
QTrap007733_032318-5CRP6_SN.mzML
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Samples_Variant
IGNORED:  Samples_Treatment
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Samples_Sample extract
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  5%|▍         | 77/1681 [08:32<4:40:24, 10.49s/it]/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  5%|▍         | 78/1681 [08:38<4:04:52,  9.17s/it]
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Samples_Concentration
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 20
Returning 160 rows!
Added 160 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1382
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive HF: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
QExHF03_HPLC_0000193.mzML
FILES
QExHF03_HPLC_0000194.mzML
FILES
QExHF03_HPLC_0000195.mzML
FILES
QExHF03_HPLC_0000196.mzML
FILES
QExHF03_HPLC_0000197.mzML
FILES
QExHF03_HPLC_0000198.mzML
FILES
QExHF03_HPLC_0000199.mzML
FILES
QExHF03_HPLC_0000200.mzML
FILES
QExHF03_HPLC_0000201.mzML
FILES
QExHF03_HPLC_0000202.mzML
FILES
QExHF03_HPLC_0000203.mzML
FILES
QExHF03_HPLC_0000204.mzML
FILES
QExHF03_HPLC_0000205.mzML
FILES
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QExHF03_HPLC_0000228.mzML
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QExHF03_HPLC_0000229.mzML
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Number of rows removed due to not enough metadata: 4
Returning 30 rows!
Added 30 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1383
Request successful!
SampleCollectionMethod: ADDED!
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IGNORED:  Assay_Term Accession Number.3/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  5%|▍         | 79/1681 [08:42<3:20:07,  7.50s/it]
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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  5%|▍         | 81/1681 [08:49<2:30:29,  5.64s/it]
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Number of rows removed due to not enough metadata: 0
Returning 15 rows!
Added 15 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1388
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1390
Request successful!
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Returning 66 rows!
Added 66 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1396
Request successful!
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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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IGNORED:  Samples_Variant
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IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Disease
IGNORED:  Samples_Term Source REF.3
IGNORED:  Samples_Term Source REF.4
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Autosampler model
IGNORED:  Assay_Protocol REF.2
IGNORED:  Samples_UNIT
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Time point
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Assay_Ion source
IGNORED:  Assay_Guard column
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Is Multicellular
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 47
Returning 644 rows!
Added 644 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1399
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Waters SYNAPT G2 HDMS System: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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IGNORED:  Samples_Protocol REF
IGNORED:  Samples_Drug 1 concentration
IGNORED:  Samples_Term Source REF.3
IGNORED:  Samples_Term Accession Number.12
IGNORED:  Assay_Term Source REF
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IGNORED:  Is Fluid
IGNORED:  Assay_Extract Name
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IGNORED:  Assay_Term Accession Number.4/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  5%|▍         | 83/1681 [09:14<3:58:04,  8.94s/it]
  5%|▍         | 84/1681 [09:16<2:59:56,  6.76s/it]
IGNORED:  Samples_Treatment
IGNORED:  Assay_Data Transformation Name
IGNORED:  Samples_Sample Name
IGNORED:  Samples_Timepoint
IGNORED:  Samples_Term Accession Number
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IGNORED:  Samples_Term Source REF.12
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IGNORED:  filepath
IGNORED:  Samples_Term Accession Number.9
IGNORED:  Samples_Term Accession Number.8
IGNORED:  Samples_Term Accession Number.11
IGNORED:  Assay_Protocol REF.2
IGNORED:  Samples_Term Accession Number.7
IGNORED:  Samples_Term Source REF.5
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Samples_Term Source REF.8
IGNORED:  Is Descendant
IGNORED:  Is Organ
IGNORED:  Assay_MS Assay Name
IGNORED:  keep
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Scan m/z range
IGNORED:  Assay_Column model
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Gene knockout
IGNORED:  Samples_Term Source REF.9
IGNORED:  Assay_Normalization Name
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Unit.2
IGNORED:  Samples_Term Source REF.2
IGNORED:  Samples_Replicate
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  base
IGNORED:  Samples_Term Source REF.10
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Samples_Genotype
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_Label
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Source REF.6
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF.11
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 16
Returning 204 rows!
Added 204 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS14
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1402
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific LTQ Orbitrap XL: missing value
  Q Exactive Plus: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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20170721_QEX_control_rep2_130min.mzML/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Number of rows removed due to not enough metadata: 0
Returning 252 rows!
Added 252 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1410
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1411
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1416
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1432
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Bruker solariX FTMS: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
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/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)
/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:188: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`
  df['USI'] = 'mzspec:' + df['MassiveID'] + ':' + df['filename']

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Number of rows removed due to not enough metadata: 0
Returning 20 rows!
Added 20 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1435
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS144
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
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Returning 72 rows!
Added 72 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS145
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
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BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
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Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
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QXA07POSLAT20180416_WEIZ0218VW_MOUSE_MUSCLE2_04.mzML/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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Number of rows removed due to not enough metadata: 0
Returning 192 rows!
Added 192 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1452
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1455
Request successful!
SampleCollectionMethod: ADDED!
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TermsofPosition: ADDED!
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Country: ADDED!
HumanPopulationDensity: ADDED!
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qiita_sample_name: ADDED!
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IGNORED:  Samples_Source Name/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

  6%|▌         | 94/1681 [09:55<2:18:06,  5.22s/it]
IGNORED:  Assay_Guard column
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Returning 11 rows!
Added 11 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1464
Request successful!
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RAW_FILES/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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IGNORED:  Assay_Batch
IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
IGNORED:  Assay_Column model
IGNORED:  extension
IGNORED:  Assay_Data Transformation Name
IGNORED:  Assay_Term Source REF.4
IGNORED:  Assay_Mass analyzer
IGNORED:  Samples_Organism part
IGNORED:  Samples_Sample Name
IGNORED:  Assay_Term Accession Number.2
IGNORED:  Assay_Normalization Name
IGNORED:  filepath
IGNORED:  Samples_Protocol REF
IGNORED:  Assay_Term Source REF.1
IGNORED:  Samples_Term Source REF.4
IGNORED:  Samples_Term Source REF.3
IGNORED:  Assay_Term Source REF
IGNORED:  Samples_Term Accession Number
IGNORED:  Assay_Post Extraction
IGNORED:  Samples_Batch
IGNORED:  Samples_Term Source REF.2
IGNORED:  row_id
IGNORED:  Assay_Term Accession Number
IGNORED:  Assay_Protocol REF.4
IGNORED:  base
IGNORED:  Assay_Labeled Extract Name
IGNORED:  Assay_Protocol REF.1
IGNORED:  Samples_Term Accession Number.3
IGNORED:  Assay_Protocol REF.2
IGNORED:  Assay_Term Source REF.2
IGNORED:  Samples_Phenotype
IGNORED:  Assay_Term Accession Number.5
IGNORED:  Samples_Term Source REF.5
IGNORED:  filename_lower
IGNORED:  Samples_Term Accession Number.4
IGNORED:  Samples_Source Name
IGNORED:  Assay_Sample Name
IGNORED:  Samples_Organism
IGNORED:  Samples_Unit
IGNORED:  Assay_Ion source
IGNORED:  Assay_Term Accession Number.1
IGNORED:  Is Fluid
IGNORED:  Samples_Collection Number
IGNORED:  Assay_Extract Name
IGNORED:  Assay_Scan polarity
IGNORED:  Assay_Term Source REF.3
IGNORED:  Is Descendant
IGNORED:  Assay_Protocol REF
IGNORED:  Is Organ
IGNORED:  Assay_Metabolite Assignment File
IGNORED:  Assay_MS Assay Name
IGNORED:  Assay_Label
IGNORED:  Assay_Term Source REF.5
IGNORED:  keep
IGNORED:  Assay_Column type
IGNORED:  Assay_Protocol REF.3
IGNORED:  Samples_Term Accession Number.5
IGNORED:  Samples_Term Source REF.6
IGNORED:  Samples_Sample type
IGNORED:  Assay_Chromatography Instrument
IGNORED:  Samples_Term Accession Number.1
IGNORED:  Assay_Term Accession Number.3
IGNORED:  Assay_Term Accession Number.4
IGNORED:  Assay_Scan m/z range
IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 519 rows!
Added 519 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1474
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Orbitrap Fusion: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
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WT_T0_1_neg.mzXML/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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IGNORED:  Samples_Variant
IGNORED:  Samples_Term Accession Number.2
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IGNORED:  Assay_Column model
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IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Derivatization
Number of rows removed due to not enough metadata: 0
Returning 84 rows!
Added 84 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1488
Request successful!
Added 0 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1490
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  Thermo Scientific Q Exactive: missing value
ENVOEnvironmentBiome:
  nan: missing value
ENVOEnvironmentMaterial:
  nan: missing value
FILES
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IGNORED:  Samples_Term Accession Number.2
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IGNORED:  Samples_Term Accession Number.9
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IGNORED:  Samples_Term Source REF.9
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IGNORED:  Samples_Term Source REF.10
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IGNORED:  Assay_Protocol REF.1
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IGNORED:  Assay_Ion source
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IGNORED:  Assay_Metabolite Assignment File
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IGNORED:  Is Multicellular
IGNORED:  Samples_Term Source REF
IGNORED:  Samples_specimen mass
IGNORED:  Samples_Term Accession Number.6
IGNORED:  Samples_Term Source REF.1
IGNORED:  Assay_Sample Name
Number of rows removed due to not enough metadata: 0
Returning 12 rows!
Added 12 samples.
Requested: https://www.ebi.ac.uk:443/metabolights/ws/studies/public/study/MTBLS1503
Request successful!
SampleCollectionMethod: ADDED!
SampleExtractionMethod: ADDED!
InternalStandardsUsed: ADDED!
SubjectIdentifierAsRecorded: ADDED!
BiologicalSex: ADDED!
TermsofPosition: ADDED!
HealthStatus: ADDED!
DOIDCommonName: ADDED!
ComorbidityListDOIDIndex: ADDED!
SampleCollectionDateandTime: ADDED!
Country: ADDED!
HumanPopulationDensity: ADDED!
LatitudeandLongitude: ADDED!
DepthorAltitudeMeters: ADDED!
qiita_sample_name: ADDED!
MassSpectrometer:
  AB SCIEX TripleTOF 6600: missing value
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IGNORED:  row_id/app/workflows/PublicDataset_ReDU_Metadata_Workflow/bin/read_and_validate_redu_from_github.py:30: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  uberon_ontology_table['Label'] = uberon_ontology_table['Label'].astype(str)

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