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Merge branch 'hotfix-2.1.7' into main
2 parents 73d3eb0 + 6673178 commit acc67fb

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‎MassBank-Project/MassBank-lib/src/main/resources/create_massbank_scheme.sql

Lines changed: 52 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -250,57 +250,59 @@ CREATE TABLE LAST_UPDATE (
250250
VERSION VARCHAR(100)
251251
);
252252

253-
create view spectra_data as select
254-
RECORD.ACCESSION as spectrum_id,
255-
RECORD.RECORD_TITLE as spectrum_name,
256-
RECORD.DATE as date,
257-
RECORD.AUTHORS as authors,
258-
RECORD.LICENSE as license,
259-
RECORD.COPYRIGHT as copyright,
260-
RECORD.PUBLICATION as publication,
261-
RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as msLevel,
262-
RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
263-
RECORD.PK_SPLASH as splash,
264-
RECORD.CH as compound_id,
265-
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
266-
and SUBTAG = 'BASE_PEAK') as precursorIntensity,
267-
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
268-
and SUBTAG = 'PRECURSOR_M/Z') as precursorMz,
269-
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
270-
and SUBTAG = 'PRECURSOR_TYPE') as adduct,
271-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
272-
and SUBTAG = 'IONIZATION') as ionization,
273-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
274-
and SUBTAG = 'IONIZATION_VOLTAGE') as ionizationVoltage,
275-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
276-
and SUBTAG = 'FRAGMENTATION_MODE') as fragmentationMode,
277-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
278-
and SUBTAG = 'COLLISION_ENERGY') as collisionEnergyText,
279-
(select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
280-
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
281-
(select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
282-
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
253+
create view msms_spectrum as select
254+
RECORD.ACCESSION as spectrum_id,
255+
RECORD.RECORD_TITLE as spectrum_name,
256+
RECORD.DATE as date,
257+
RECORD.AUTHORS as authors,
258+
RECORD.LICENSE as license,
259+
RECORD.COPYRIGHT as copyright,
260+
RECORD.PUBLICATION as publication,
261+
RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as ms_level,
262+
RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
263+
RECORD.PK_SPLASH as splash,
264+
RECORD.CH as compound_id,
265+
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
266+
and SUBTAG = 'BASE_PEAK') as precursor_intensity,
267+
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
268+
and SUBTAG = 'PRECURSOR_M/Z') as precursor_mz_text,
269+
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
270+
and SUBTAG = 'PRECURSOR_TYPE') as adduct,
271+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
272+
and SUBTAG = 'IONIZATION') as ionization,
273+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
274+
and SUBTAG = 'IONIZATION_VOLTAGE') as ionization_voltage,
275+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
276+
and SUBTAG = 'FRAGMENTATION_MODE') as fragmentation_mode,
277+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
278+
and SUBTAG = 'COLLISION_ENERGY') as collision_energy_text,
279+
(select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
280+
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
281+
(select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
282+
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
283283
from RECORD;
284284

285+
create view msms_spectrum_peak as select
286+
PEAK.RECORD as spectrum_id,
287+
PEAK.PK_PEAK_MZ as mz,
288+
PEAK.PK_PEAK_INTENSITY as intensity
289+
from PEAK;
290+
285291
create view compound as select
286-
COMPOUND.ID as compound_id,
287-
COMPOUND.CH_FORMULA as formula,
288-
COMPOUND.CH_EXACT_MASS as exactmass,
289-
COMPOUND.CH_SMILES as smiles,
290-
COMPOUND.CH_IUPAC as inchi,
291-
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
292-
and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
293-
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
294-
and CH_LINK.DATABASE_NAME = 'CAS') as cas,
295-
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
296-
and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem,
297-
NAME.CH_NAME as compound_name
298-
from COMPOUND
299-
join COMPOUND_NAME on (COMPOUND.ID = COMPOUND_NAME.COMPOUND)
300-
join NAME on (COMPOUND_NAME.NAME = NAME.ID);
292+
COMPOUND.ID as compound_id,
293+
COMPOUND.CH_FORMULA as formula,
294+
COMPOUND.CH_EXACT_MASS as exactmass,
295+
COMPOUND.CH_SMILES as smiles,
296+
COMPOUND.CH_IUPAC as inchi,
297+
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
298+
and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
299+
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
300+
and CH_LINK.DATABASE_NAME = 'CAS') as cas,
301+
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
302+
and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem
303+
from COMPOUND;
301304

302-
create view peaks as select
303-
PEAK.RECORD as spectrum_id,
304-
PEAK.PK_PEAK_MZ as mz,
305-
PEAK.PK_PEAK_INTENSITY as intensity
306-
from PEAK;
305+
create view synonym as select
306+
COMPOUND_NAME.COMPOUND as compound_id,
307+
NAME.CH_NAME as synonym
308+
from NAME join COMPOUND_NAME on (COMPOUND_NAME.NAME = NAME.ID);

‎modules/sql/docker-entrypoint-initdb.d/01-init-massbank.sql

Lines changed: 52 additions & 50 deletions
Original file line numberDiff line numberDiff line change
@@ -254,57 +254,59 @@ CREATE TABLE LAST_UPDATE (
254254
VERSION VARCHAR(100)
255255
);
256256

257-
create view spectra_data as select
258-
RECORD.ACCESSION as spectrum_id,
259-
RECORD.RECORD_TITLE as spectrum_name,
260-
RECORD.DATE as date,
261-
RECORD.AUTHORS as authors,
262-
RECORD.LICENSE as license,
263-
RECORD.COPYRIGHT as copyright,
264-
RECORD.PUBLICATION as publication,
265-
RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as msLevel,
266-
RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
267-
RECORD.PK_SPLASH as splash,
268-
RECORD.CH as compound_id,
269-
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
270-
and SUBTAG = 'BASE_PEAK') as precursorIntensity,
271-
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
272-
and SUBTAG = 'PRECURSOR_M/Z') as precursorMz,
273-
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
274-
and SUBTAG = 'PRECURSOR_TYPE') as adduct,
275-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
276-
and SUBTAG = 'IONIZATION') as ionization,
277-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
278-
and SUBTAG = 'IONIZATION_VOLTAGE') as ionizationVoltage,
279-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
280-
and SUBTAG = 'FRAGMENTATION_MODE') as fragmentationMode,
281-
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
282-
and SUBTAG = 'COLLISION_ENERGY') as collisionEnergyText,
283-
(select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
284-
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
285-
(select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
286-
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
257+
create view msms_spectrum as select
258+
RECORD.ACCESSION as spectrum_id,
259+
RECORD.RECORD_TITLE as spectrum_name,
260+
RECORD.DATE as date,
261+
RECORD.AUTHORS as authors,
262+
RECORD.LICENSE as license,
263+
RECORD.COPYRIGHT as copyright,
264+
RECORD.PUBLICATION as publication,
265+
RECORD.AC_MASS_SPECTROMETRY_MS_TYPE as ms_level,
266+
RECORD.AC_MASS_SPECTROMETRY_ION_MODE as polarity,
267+
RECORD.PK_SPLASH as splash,
268+
RECORD.CH as compound_id,
269+
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
270+
and SUBTAG = 'BASE_PEAK') as precursor_intensity,
271+
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
272+
and SUBTAG = 'PRECURSOR_M/Z') as precursor_mz_text,
273+
(select VALUE from MS_FOCUSED_ION where RECORD = RECORD.ACCESSION
274+
and SUBTAG = 'PRECURSOR_TYPE') as adduct,
275+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
276+
and SUBTAG = 'IONIZATION') as ionization,
277+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
278+
and SUBTAG = 'IONIZATION_VOLTAGE') as ionization_voltage,
279+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
280+
and SUBTAG = 'FRAGMENTATION_MODE') as fragmentation_mode,
281+
(select VALUE from AC_MASS_SPECTROMETRY where RECORD = RECORD.ACCESSION
282+
and SUBTAG = 'COLLISION_ENERGY') as collision_energy_text,
283+
(select INSTRUMENT.AC_INSTRUMENT from INSTRUMENT where
284+
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument,
285+
(select INSTRUMENT.AC_INSTRUMENT_TYPE from INSTRUMENT where
286+
INSTRUMENT.ID = RECORD.AC_INSTRUMENT) as instrument_type
287287
from RECORD;
288288

289+
create view msms_spectrum_peak as select
290+
PEAK.RECORD as spectrum_id,
291+
PEAK.PK_PEAK_MZ as mz,
292+
PEAK.PK_PEAK_INTENSITY as intensity
293+
from PEAK;
294+
289295
create view compound as select
290-
COMPOUND.ID as compound_id,
291-
COMPOUND.CH_FORMULA as formula,
292-
COMPOUND.CH_EXACT_MASS as exactmass,
293-
COMPOUND.CH_SMILES as smiles,
294-
COMPOUND.CH_IUPAC as inchi,
295-
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
296-
and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
297-
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
298-
and CH_LINK.DATABASE_NAME = 'CAS') as cas,
299-
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
300-
and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem,
301-
NAME.CH_NAME as compound_name
302-
from COMPOUND
303-
join COMPOUND_NAME on (COMPOUND.ID = COMPOUND_NAME.COMPOUND)
304-
join NAME on (COMPOUND_NAME.NAME = NAME.ID);
296+
COMPOUND.ID as compound_id,
297+
COMPOUND.CH_FORMULA as formula,
298+
COMPOUND.CH_EXACT_MASS as exactmass,
299+
COMPOUND.CH_SMILES as smiles,
300+
COMPOUND.CH_IUPAC as inchi,
301+
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
302+
and CH_LINK.DATABASE_NAME = 'INCHIKEY') as inchikey,
303+
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
304+
and CH_LINK.DATABASE_NAME = 'CAS') as cas,
305+
(select DATABASE_ID from CH_LINK where CH_LINK.COMPOUND = COMPOUND.ID
306+
and CH_LINK.DATABASE_NAME = 'PUBCHEM') as pubchem
307+
from COMPOUND;
305308

306-
create view peaks as select
307-
PEAK.RECORD as spectrum_id,
308-
PEAK.PK_PEAK_MZ as mz,
309-
PEAK.PK_PEAK_INTENSITY as intensity
310-
from PEAK;
309+
create view synonym as select
310+
COMPOUND_NAME.COMPOUND as compound_id,
311+
NAME.CH_NAME as synonym
312+
from NAME join COMPOUND_NAME on (COMPOUND_NAME.NAME = NAME.ID);

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