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setup in the ci pipeline the lambdaminer database
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@rmassei
rmassei committed Feb 14, 2025
1 parent 707eca8 commit 79723b1
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22 changes: 22 additions & 0 deletions .github/lambdaminer/Dockerfile
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# SPDX-FileCopyrightText: 2024 Helmholtz Centre for Environmental Research GmbH - UFZ
#
# SPDX-License-Identifier: LicenseRef-UFZ-GPL-3.0-or-later

# Use an official PostgreSQL image as the base image
FROM postgres:13

# Set environment variables
ENV POSTGRES_DB lmdb
ENV POSTGRES_USER lmdb_adm
ENV POSTGRES_PASSWORD BJSeVYMK6QaDE3eVfJEB

# Copy scripts and data
COPY ddl /home/lmdb/ddl
COPY data /home/lmdb/data
COPY journal /home/lmdb/journal

# Copy the build script into the initdb entrypoint for automatic execution
COPY build.sql /docker-entrypoint-initdb.d/

# Expose the default PostgreSQL port
EXPOSE 5400
51 changes: 51 additions & 0 deletions .github/lambdaminer/build.sql
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-- SPDX-FileCopyrightText: 2024 Helmholtz Centre for Environmental Research GmbH - UFZ
--
-- SPDX-License-Identifier: LicenseRef-UFZ-GPL-3.0-or-later

/*
* This script builds the Lambda-Miner Database
*/

\i /home/lmdb/ddl/lmdb_schema.sql
\i /home/lmdb/ddl/lmdb_privileges.sql

/*
* Data
*/

-- Reference data
\i /home/lmdb/data/reference_data/element.sql
\i /home/lmdb/data/reference_data/feature.sql
\i /home/lmdb/data/reference_data/feature_chemical_formula.sql
\i /home/lmdb/data/reference_data/evaluation_rule.sql
\i /home/lmdb/data/reference_data/evaluation_config.sql
\i /home/lmdb/data/reference_data/eval_config_eval_rule.sql
\i /home/lmdb/data/reference_data/chemical_formula_config.sql
\i /home/lmdb/data/reference_data/element_cformula_config.sql
\i /home/lmdb/data/reference_data/sample_preparation.sql
\i /home/lmdb/data/reference_data/user_role.sql

-- Test data

\i /home/lmdb/data/test_data/instrument.sql
\i /home/lmdb/data/test_data/location.sql
\i /home/lmdb/data/test_data/ufz_user.sql
\i /home/lmdb/data/test_data/ufz_user_role.sql
\i /home/lmdb/data/test_data/project.sql
\i /home/lmdb/data/test_data/ufz_user_project.sql
\i /home/lmdb/data/test_data/calibration_method.sql
\i /home/lmdb/data/test_data/sample.sql
\i /home/lmdb/data/test_data/measurement.sql
\i /home/lmdb/data/test_data/peak.sql
\i /home/lmdb/data/test_data/chemical_formula_assignment.sql
\i /home/lmdb/data/test_data/measurement_cformula_config.sql
\i /home/lmdb/data/test_data/eval_config_cfa.sql
\i /home/lmdb/data/test_data/measurement_evaluation_config.sql

/*
* Journal (recent changes)
*/

\i /home/lmdb/journal/240325-0_drop-table-ufz-user-role.sql
\i /home/lmdb/journal/240508-0_new-calibration-function.sql
\i /home/lmdb/journal/240521-0_geo-distance-function.sql
36 changes: 36 additions & 0 deletions .github/lambdaminer/data/reference_data/chemical_formula_config.sql
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-- SPDX-FileCopyrightText: 2024 Helmholtz Centre for Environmental Research GmbH - UFZ
--
-- SPDX-License-Identifier: LicenseRef-UFZ-GPL-3.0-or-later

--
-- Data for Name: chemical_formula_config; Type: TABLE DATA; Schema: public; Owner: lmdb_adm
--

INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (127, false, 'CFC_LC-MS_NOM_N2S1', 0.00000000, 750.00000000, -1.00000000, 1.00000000, 0.000, 1.000, 0.300, 2.500, 0.000, 0.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (1, false, 'Standard_CFC', 0.00000000, 750.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, NULL, NULL, 'even', false, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (125, false, 'CFC_LC-MS_NOM_small', 0.00000000, 750.00000000, -1.00000000, 1.00000000, 0.000, 1.000, 0.300, 2.500, 0.000, 0.500, NULL, NULL, NULL, NULL, 0.000, 25.000, NULL, NULL, 'even', false, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (123, false, 'CFC_LC-MS_NOM_large', 0.00000000, 900.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, NULL, NULL, 'even', false, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (128, false, 'CFC_LC-MS_NOM_N5S3', 0.00000000, 1000.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (130, true, 'CFC_ESI_NOM_N5S3', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (126, false, 'CFC_NOM_N5S3', 0.00000000, 750.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', false, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (132, false, 'CFC_ESI_NOM_N5S3_pos', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (129, false, 'CFC_LDI_NOM_N5S3', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 50.000, -10.000, 30.000, 'even', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (133, false, 'CFC_APPI_even_N3S3', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 50.000, -10.000, 30.000, 'even', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (140, false, 'CFC_APPI_odd_N3S3', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 50.000, -10.000, 30.000, 'odd', true, 'small');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (194, false, 'CFC_LDI_NOM_N5S3P1', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 50.000, -10.000, 30.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (197, false, 'CFC_LC-MS_DBP_N2S1Cl5P2', 0.00000000, 1000.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (141, false, 'CFC_LC-MS_DBP_N2S1Cl5', 0.00000000, 1000.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (142, false, 'CFC_ESI_OBP_N5S3_18O', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -15.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (143, false, 'CFC_LC-MS_CBZ-BR_N3S1D5', 0.00000000, 1000.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 2.500, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (193, false, 'CFC_ESI_NOM_N8S3', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (176, false, 'CFC_LC-MS_NOM_N2S1D9', 0.00000000, 1000.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 3.000, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (178, false, 'CFC_LC_CBZ-BR_N3S1D10', 0.00000000, 1000.00000000, -2.00000000, 2.00000000, 0.000, 1.200, 0.300, 2.500, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (122, false, 'CFC_CHNO_CN-Isotopes_Teickner_MA', 0.00000000, 600.00000000, -0.50000000, 0.50000000, 0.000, 1.000, 0.500, 2.500, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 20.000, -10.000, 10.000, 'even', false, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (177, false, 'CFC_DI_CBZ-BR_N3S1D10', 0.00000000, 1000.00000000, -1.00000000, 1.00000000, 0.000, 1.200, 0.300, 2.500, 0.000, 1.500, NULL, NULL, NULL, NULL, 0.000, 25.000, -10.000, 10.000, 'even', true, 'big');
INSERT INTO public.chemical_formula_config (chemical_formula_config_id, default_config, label, mass_range_min, mass_range_max, fault_tolerance_min, fault_tolerance_max, oc_ratio_min, oc_ratio_max, hc_ratio_min, hc_ratio_max, nc_ratio_min, nc_ratio_max, sc_ratio_min, sc_ratio_max, pc_ratio_min, pc_ratio_max, dbe_min, dbe_max, dbe_o_min, dbe_o_max, electron_config, active, library) VALUES (200, false, 'CFC_LC_MS_NOM_N5S3_21D', 0.00000000, 1000.00000000, -0.50000000, 0.50000000, 0.000, 1.200, 0.000, 2.500, 0.000, 1.400, NULL, NULL, NULL, NULL, 0.000, 30.000, -10.000, 30.000, 'even', true, 'big');

--
-- Name: chemical_formula_config_chemical_formula_config_id_seq; Type: SEQUENCE SET; Schema: public; Owner: lmdb_adm
--

SELECT pg_catalog.setval('public.chemical_formula_config_chemical_formula_config_id_seq', 200, true);
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