updated matchms_metadata_merge tool and testdata

RECETOX · Nov 22, 2023 · 53af14e · 53af14e
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commit 53af14e
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Showing 4 changed files with 19 additions and 18 deletions.
diff --git a/tools/matchms/matchms_metadata_merge.xml b/tools/matchms/matchms_metadata_merge.xml
@@ -28,6 +28,7 @@ import matchms
 import numpy as np
 
 matchms.set_matchms_logger_level('ERROR')
+matchms.Metadata.set_key_replacements({})
 
 spectra = list(matchms.importing.load_from_msp('${spectral_library}', False))
 

diff --git a/tools/matchms/test-data/metadata_merge/input.msp b/tools/matchms/test-data/metadata_merge/input.msp
@@ -2,7 +2,7 @@ INCHI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10
 INSTRUMENTTYPE: LC-ESI-QQ
 COLLISIONENERGY: 40
 FORMULA: C10H15N5O10P2
-COMPOUND_NAME: ADP
+NAME: ADP
 PRECURSORMZ: 428.31
 IONMODE: positive
 NUM PEAKS: 2
@@ -14,7 +14,7 @@ INCHI: InChI=1S/C6H6O4/c7-2-4-1-5(8)6(9)3-10-4/h1,3,7,9H,2H2
 INSTRUMENTTYPE: LC-ESI-ITFT
 COLLISIONENERGY: 60 % (nominal)
 FORMULA: C6H6O4
-COMPOUND_NAME: Kojic acid
+NAME: Kojic acid
 PRECURSORTYPE: [M-H]-
 PRECURSORMZ: 141.0193
 IONMODE: negative
@@ -25,7 +25,7 @@ INCHI: InChI=1S/C18H22N2/c1-19-12-14-20(15-13-19)18(16-8-4-2-5-9-16)17-10-6-3-7-
 INSTRUMENTTYPE: LC-ESI-ITFT
 COLLISIONENERGY: 85% (nominal)
 FORMULA: C18H22N2
-COMPOUND_NAME: Cyclizine
+NAME: Cyclizine
 PRECURSORTYPE: [M+H]+
 PRECURSORMZ: 267.1856
 IONMODE: positive

diff --git a/tools/matchms/test-data/metadata_merge/metadata.csv b/tools/matchms/test-data/metadata_merge/metadata.csv
@@ -1,4 +1,4 @@
-compound_name,inchikey,SMILES
+Name,inchikey,SMILES
 ADP,XTWYTFMLZFPYCI-UHFFFAOYSA-N,C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
 Kojic acid,BEJNERDRQOWKJM-UHFFFAOYSA-N,C1=C(OC=C(C1=O)O)CO
 Cyclizine,,CN1CCN(CC1)C(C2=CC=CC=C2)C3=CC=CC=C3
diff --git a/tools/matchms/test-data/metadata_merge/output.msp b/tools/matchms/test-data/metadata_merge/output.msp
@@ -1,10 +1,10 @@
 INCHI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)
+INSTRUMENTTYPE: LC-ESI-QQ
+COLLISIONENERGY: 40
 FORMULA: C10H15N5O10P2
-COMPOUND_NAME: ADP
+NAME: ADP
+PRECURSORMZ: 428.31
 IONMODE: positive
-INSTRUMENT_TYPE: LC-ESI-QQ
-COLLISION_ENERGY: 40
-PRECURSOR_MZ: 428.31
 INCHIKEY: XTWYTFMLZFPYCI-UHFFFAOYSA-N
 SMILES: C1=NC2=C(C(=N1)N)N=CN2C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O
 NUM PEAKS: 2
@@ -13,25 +13,25 @@ NUM PEAKS: 2
 
 INCHIKEY: BEJNERDRQOWKJM-UHFFFAOYSA-N
 INCHI: InChI=1S/C6H6O4/c7-2-4-1-5(8)6(9)3-10-4/h1,3,7,9H,2H2
+INSTRUMENTTYPE: LC-ESI-ITFT
+COLLISIONENERGY: 60 % (nominal)
 FORMULA: C6H6O4
-COMPOUND_NAME: Kojic acid
+NAME: Kojic acid
+PRECURSORTYPE: [M-H]-
+PRECURSORMZ: 141.0193
 IONMODE: negative
-INSTRUMENT_TYPE: LC-ESI-ITFT
-COLLISION_ENERGY: 60 % (nominal)
-ADDUCT: [M-H]-
-PRECURSOR_MZ: 141.0193
 SMILES: C1=C(OC=C(C1=O)O)CO
 NUM PEAKS: 1
 141.0194    999.0
 
 INCHI: InChI=1S/C18H22N2/c1-19-12-14-20(15-13-19)18(16-8-4-2-5-9-16)17-10-6-3-7-11-17/h2-11,18H,12-15H2,1H3
+INSTRUMENTTYPE: LC-ESI-ITFT
+COLLISIONENERGY: 85% (nominal)
 FORMULA: C18H22N2
-COMPOUND_NAME: Cyclizine
+NAME: Cyclizine
+PRECURSORTYPE: [M+H]+
+PRECURSORMZ: 267.1856
 IONMODE: positive
-INSTRUMENT_TYPE: LC-ESI-ITFT
-COLLISION_ENERGY: 85% (nominal)
-ADDUCT: [M+H]+
-PRECURSOR_MZ: 267.1856
 INCHIKEY: nan
 SMILES: CN1CCN(CC1)C(C2=CC=CC=C2)C3=CC=CC=C3
 NUM PEAKS: 3