Merge branch 'hotfix-2.1.7' into main

MassBank · Nov 26, 2020 · acc67fb · acc67fb
2 parents 73d3eb0 + 6673178
commit acc67fb
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diff --git a/MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql b/MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql
@@ -250,57 +250,59 @@ CREATE TABLE LAST_UPDATE (
 	VERSION VARCHAR(100)
 );
 
-create view spectra_data as select
-       RECORD.ACCESSION as spectrum_id,
-       RECORD.RECORD_TITLE as spectrum_name,
-       RECORD.DATE as date,
-       RECORD.AUTHORS as authors,
-       RECORD.LICENSE as license,
-       RECORD.COPYRIGHT as copyright,
-       RECORD.PUBLICATION as publication,
-       RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as msLevel,
-       RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
-       RECORD.PK_SPLASH as splash,
-       RECORD.CH as compound_id,
-       (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'BASE_PEAK') as precursorIntensity,
-       (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'PRECURSOR_M/Z') as precursorMz,
-       (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'PRECURSOR_TYPE') as adduct,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'IONIZATION') as ionization,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'IONIZATION_VOLTAGE') as ionizationVoltage,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'FRAGMENTATION_MODE') as fragmentationMode,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'COLLISION_ENERGY') as collisionEnergyText,
-       (select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
-       INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
-       (select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
-       INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
+create view msms_spectrum as select
+      RECORD.ACCESSION as spectrum_id,
+      RECORD.RECORD_TITLE as spectrum_name,
+      RECORD.DATE as date,
+      RECORD.AUTHORS as authors,
+      RECORD.LICENSE as license,
+      RECORD.COPYRIGHT as copyright,
+      RECORD.PUBLICATION as publication,
+      RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as ms_level,
+      RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
+      RECORD.PK_SPLASH as splash,
+      RECORD.CH as compound_id,
+      (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'BASE_PEAK') as precursor_intensity,
+      (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'PRECURSOR_M/Z') as precursor_mz_text,
+      (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'PRECURSOR_TYPE') as adduct,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'IONIZATION') as ionization,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'IONIZATION_VOLTAGE') as ionization_voltage,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'FRAGMENTATION_MODE') as fragmentation_mode,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'COLLISION_ENERGY') as collision_energy_text,
+      (select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
+      INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
+      (select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
+      INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
 from RECORD;
 
+create view msms_spectrum_peak as select
+      PEAK.RECORD as spectrum_id,
+      PEAK.PK_PEAK_MZ as mz,
+      PEAK.PK_PEAK_INTENSITY as intensity
+from PEAK;
+
 create view compound as select
-       COMPOUND.ID as compound_id,
-       COMPOUND.CH_FORMULA as formula,
-       COMPOUND.CH_EXACT_MASS as exactmass,
-       COMPOUND.CH_SMILES as smiles,
-       COMPOUND.CH_IUPAC as inchi,
-       (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
-       and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
-       (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
-       and CH_LINK.DATABASE_NAME = 'CAS') as cas,
-       (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
-       and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem,
-       NAME.CH_NAME as compound_name
-from COMPOUND
-join COMPOUND_NAME on (COMPOUND.ID = COMPOUND_NAME.COMPOUND)
-join NAME on (COMPOUND_NAME.NAME = NAME.ID);
+      COMPOUND.ID as compound_id,
+      COMPOUND.CH_FORMULA as formula,
+      COMPOUND.CH_EXACT_MASS as exactmass,
+      COMPOUND.CH_SMILES as smiles,
+      COMPOUND.CH_IUPAC as inchi,
+      (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
+      and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
+      (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
+      and CH_LINK.DATABASE_NAME = 'CAS') as cas,
+      (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
+      and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem
+from COMPOUND;
 
-create view peaks as select
-       PEAK.RECORD as spectrum_id,
-       PEAK.PK_PEAK_MZ as mz,
-       PEAK.PK_PEAK_INTENSITY as intensity
-from PEAK;
+create view synonym as select
+      COMPOUND_NAME.COMPOUND as compound_id,
+      NAME.CH_NAME as synonym
+from NAME join COMPOUND_NAME on (COMPOUND_NAME.NAME = NAME.ID);
diff --git a/modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql b/modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql
@@ -254,57 +254,59 @@ CREATE TABLE LAST_UPDATE (
 	VERSION VARCHAR(100)
 );
 
-create view spectra_data as select
-       RECORD.ACCESSION as spectrum_id,
-       RECORD.RECORD_TITLE as spectrum_name,
-       RECORD.DATE as date,
-       RECORD.AUTHORS as authors,
-       RECORD.LICENSE as license,
-       RECORD.COPYRIGHT as copyright,
-       RECORD.PUBLICATION as publication,
-       RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as msLevel,
-       RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
-       RECORD.PK_SPLASH as splash,
-       RECORD.CH as compound_id,
-       (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'BASE_PEAK') as precursorIntensity,
-       (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'PRECURSOR_M/Z') as precursorMz,
-       (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'PRECURSOR_TYPE') as adduct,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'IONIZATION') as ionization,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'IONIZATION_VOLTAGE') as ionizationVoltage,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'FRAGMENTATION_MODE') as fragmentationMode,
-       (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
-       and SUBTAG = 'COLLISION_ENERGY') as collisionEnergyText,
-       (select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
-       INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
-       (select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
-       INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
+create view msms_spectrum as select
+      RECORD.ACCESSION as spectrum_id,
+      RECORD.RECORD_TITLE as spectrum_name,
+      RECORD.DATE as date,
+      RECORD.AUTHORS as authors,
+      RECORD.LICENSE as license,
+      RECORD.COPYRIGHT as copyright,
+      RECORD.PUBLICATION as publication,
+      RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as ms_level,
+      RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
+      RECORD.PK_SPLASH as splash,
+      RECORD.CH as compound_id,
+      (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'BASE_PEAK') as precursor_intensity,
+      (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'PRECURSOR_M/Z') as precursor_mz_text,
+      (select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'PRECURSOR_TYPE') as adduct,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'IONIZATION') as ionization,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'IONIZATION_VOLTAGE') as ionization_voltage,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'FRAGMENTATION_MODE') as fragmentation_mode,
+      (select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
+      and SUBTAG = 'COLLISION_ENERGY') as collision_energy_text,
+      (select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
+      INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
+      (select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
+      INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
 from RECORD;
 
+create view msms_spectrum_peak as select
+      PEAK.RECORD as spectrum_id,
+      PEAK.PK_PEAK_MZ as mz,
+      PEAK.PK_PEAK_INTENSITY as intensity
+from PEAK;
+
 create view compound as select
-       COMPOUND.ID as compound_id,
-       COMPOUND.CH_FORMULA as formula,
-       COMPOUND.CH_EXACT_MASS as exactmass,
-       COMPOUND.CH_SMILES as smiles,
-       COMPOUND.CH_IUPAC as inchi,
-       (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
-       and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
-       (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
-       and CH_LINK.DATABASE_NAME = 'CAS') as cas,
-       (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
-       and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem,
-       NAME.CH_NAME as compound_name
-from COMPOUND
-join COMPOUND_NAME on (COMPOUND.ID = COMPOUND_NAME.COMPOUND)
-join NAME on (COMPOUND_NAME.NAME = NAME.ID);
+      COMPOUND.ID as compound_id,
+      COMPOUND.CH_FORMULA as formula,
+      COMPOUND.CH_EXACT_MASS as exactmass,
+      COMPOUND.CH_SMILES as smiles,
+      COMPOUND.CH_IUPAC as inchi,
+      (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
+      and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
+      (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
+      and CH_LINK.DATABASE_NAME = 'CAS') as cas,
+      (select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
+      and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem
+from COMPOUND;
 
-create view peaks as select
-       PEAK.RECORD as spectrum_id,
-       PEAK.PK_PEAK_MZ as mz,
-       PEAK.PK_PEAK_INTENSITY as intensity
-from PEAK;
+create view synonym as select
+      COMPOUND_NAME.COMPOUND as compound_id,
+      NAME.CH_NAME as synonym
+from NAME join COMPOUND_NAME on (COMPOUND_NAME.NAME = NAME.ID);