diff --git a/screening/source/sql/imaging/postgresql/016/data.sql b/screening/source/sql/imaging/postgresql/016/data.sql deleted file mode 100644 index f08222c48c2932180be40863f775e14dac5267bc..0000000000000000000000000000000000000000 --- a/screening/source/sql/imaging/postgresql/016/data.sql +++ /dev/null @@ -1,275 +0,0 @@ --- Note that these data has to be loaded manually into the openBIS Core database. - --- TODO: this sql should be converted to a generic sql without refering to technical ids. --- Now the ids should be updated if some new records will be added in the generic data. - --- --- PostgreSQL database dump --- - -SET statement_timeout = 0; -SET client_encoding = 'UTF8'; -SET standard_conforming_strings = off; -SET check_function_bodies = false; -SET client_min_messages = warning; -SET escape_string_warning = off; - -SET search_path = public, pg_catalog; - --- --- Data for Name: controlled_vocabularies; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY controlled_vocabularies (id, code, description, registration_timestamp, pers_id_registerer, is_managed_internally, is_internal_namespace, dbin_id, modification_timestamp, is_chosen_from_list, source_uri) FROM stdin; -2 PLATE_GEOMETRY The geometry or dimensions of a plate 2008-06-17 16:38:30.723292+02 1 t t 1 2009-11-27 16:02:26.451046+01 t \N -3 MICROSCOPE Microscope used in an experiment. 2009-11-29 23:55:18.978884+01 1 f f 1 2009-12-17 01:50:54.68+01 t \N -\. - - --- --- Data for Name: controlled_vocabulary_terms; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY controlled_vocabulary_terms (id, code, registration_timestamp, covo_id, pers_id_registerer, label, description, ordinal) FROM stdin; -3 384_WELLS_16X24 2008-06-17 16:38:30.723292+02 2 1 384 Wells, 16x24 \N 1 -4 96_WELLS_8X12 2008-06-17 16:38:31.101031+02 2 1 96 Wells, 8x12 \N 2 -5 1536_WELLS_32X48 2008-06-17 16:38:31.101031+02 2 1 1536 Wells, 32x48 \N 3 -6 BD_PATHWAY_855 2009-11-29 23:55:18.978884+01 3 1 \N \N 1 -7 MD_IMAGEXPRESS_MICROLIVE 2009-11-29 23:55:18.978884+01 3 1 \N \N 2 -8 MD_IMAGEXPRESS_MICRO_2 2009-11-29 23:55:18.978884+01 3 1 \N \N 3 -\. - - --- --- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY data_set_types (id, code, description, dbin_id, modification_timestamp) FROM stdin; -3 HCS_IMAGE_ANALYSIS_DATA Data derived from analysis of HCS images 1 2009-11-27 16:02:26.451046+01 -2 HCS_IMAGE HCS raw images acquired by microscopes 1 2009-11-27 16:02:26.451046+01 -4 HCS_ANALYSIS_PER_GENE Image analysis data aggregated per gene. 1 2009-12-16 16:59:50.743029+01 -\. - - --- --- Data for Name: material_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY material_types (id, code, description, dbin_id, modification_timestamp) FROM stdin; -1 VIRUS Virus 1 2009-11-27 16:02:26.451046+01 -2 CELL_LINE Cell Line or Cell Culture. The growing of cells under controlled conditions. 1 2009-11-27 16:02:26.451046+01 -3 GENE Gene 1 2009-11-27 16:02:26.451046+01 -4 SIRNA siRNA nucleotide 1 2009-11-27 16:02:26.451046+01 -5 CONTROL Control of a control layout 1 2009-11-27 16:02:26.451046+01 -6 BACTERIUM Bacterium 1 2009-11-27 16:02:26.451046+01 -7 COMPOUND Compound 1 2009-11-27 16:02:26.451046+01 -\. - - --- --- Data for Name: property_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY property_types (id, code, description, label, daty_id, registration_timestamp, pers_id_registerer, covo_id, is_managed_internally, is_internal_namespace, dbin_id, maty_prop_id) FROM stdin; -3 NUCLEOTIDE_SEQUENCE A sequence of nucleotides Nucleotide Sequence 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N -4 REFSEQ NCBI Reference Sequence code, applicable to sequences of type: DNA, RNA, protein RefSeq 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N -13 MICROSCOPE Microscope 7 2009-11-29 23:57:05.85618+01 1 3 f f 1 \N -7 INHIBITOR_OF Inhibitor Of Inhibitor Of 8 2009-11-27 16:02:45.060699+01 1 \N f f 1 3 -11 SIRNA siRNA siRNA 8 2009-11-29 23:56:19.39967+01 1 \N f f 1 4 -12 CONTROL Control Control 8 2009-11-29 23:56:37.355313+01 1 \N f f 1 5 -6 PLATE_GEOMETRY Plate Geometry Plate Geometry 7 2008-06-17 16:38:30.723292+02 1 2 t t 1 \N -15 NUMBER_OF_CHANNEL Channels 3 2009-12-17 10:56:17.239319+01 1 \N f f 1 \N -16 LIBRARY_ID Library id Id from the master plate library 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N -\. - - --- --- Data for Name: data_set_type_property_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, section, ordinal) FROM stdin; -\. - - --- --- Data for Name: experiment_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY experiment_types (id, code, description, dbin_id, modification_timestamp) FROM stdin; -2 COMPOUND_HCS Compound High Content Screening 1 2009-11-27 16:02:26.451046+01 -1 SIRNA_HCS Small Interfering RNA High Content Screening 1 2009-11-27 16:02:26.451046+01 -\. - - --- --- Data for Name: experiment_type_property_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY experiment_type_property_types (id, exty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, section, ordinal) FROM stdin; -1 1 1 t t 1 2008-06-17 16:38:49.023295+02 \N 1 -2 2 1 t t 1 2008-06-17 16:38:49.301922+02 \N 1 -5 1 13 f f 1 2009-12-17 10:54:01.261178+01 \N 2 -\. - - --- --- Data for Name: file_format_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY file_format_types (id, code, description, dbin_id) FROM stdin; -7 PNG \N 1 -8 CSV files with values separated by comma or semicolon 1 -9 JPG \N 1 -\. - - --- --- Data for Name: filters; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY filters (id, dbin_id, name, description, registration_timestamp, pers_id_registerer, modification_timestamp, expression, is_public, grid_id) FROM stdin; -9 1 Infection index \N 2009-12-16 21:19:19.012657+01 1 2009-12-16 22:41:56.863+01 float(row.col('colIndex_5')) > float(${threshold}) t data-set-reporting-gridplate-image-analysis-merger -8 1 Total number of cells \N 2009-12-16 21:18:05.161964+01 1 2009-12-16 22:42:31.707+01 int(row.col('colIndex_3')) > int(${threshold}) t data-set-reporting-gridplate-image-analysis-merger -7 1 Number of infected cells \N 2009-12-16 21:17:40.765083+01 1 2009-12-16 22:42:46.052+01 int(row.col('colIndex_4')) > int(${threshold}) t data-set-reporting-gridplate-image-analysis-merger -\. - - --- --- Data for Name: material_type_property_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY material_type_property_types (id, maty_id, prty_id, is_mandatory, registration_timestamp, pers_id_registerer, is_managed_internally, section, ordinal) FROM stdin; -10 4 7 t 2009-11-27 16:02:45.060699+01 1 f \N 4 -9 5 1 f 2008-02-28 13:03:03.358532+01 1 f \N 1 -8 4 1 f 2008-02-28 13:03:03.358532+01 1 f \N 3 -6 4 3 t 2008-02-28 13:03:03.358532+01 1 f \N 1 -12 4 16 f 2008-02-28 13:03:03.358532+01 1 f \N 1 -5 3 1 f 2008-02-28 13:03:03.358532+01 1 f \N 2 -3 7 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1 -2 6 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1 -1 1 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1 -\. - - --- --- Data for Name: sample_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix) FROM stdin; -3 PLATE Cell Plate 1 t 2 0 2009-11-27 16:02:26.451046+01 f S -7 SIRNA_WELL \N 1 f 0 1 2009-11-27 19:42:03.483115+01 f O -8 CONTROL_WELL \N 1 f 0 1 2009-11-27 19:42:25.791288+01 f C -9 LIBRARY \N 1 f 0 0 2009-11-27 19:42:25.791288+01 f L -\. - - --- --- Data for Name: sample_type_property_types; Type: TABLE DATA; Schema: public; Owner: - --- - -COPY sample_type_property_types (id, saty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, is_displayed, section, ordinal) FROM stdin; -8 7 11 f f 1 2009-11-29 23:57:38.268212+01 t \N 1 -9 8 12 f f 1 2009-11-29 23:57:49.098187+01 t \N 1 -10 3 6 f f 1 2009-11-30 01:28:20.972263+01 t \N 1 -\. - --- --- PostgreSQL database dump complete --- - --------------------------------------------------- --- update sequences values --------------------------------------------------- - -select setval('controlled_vocabulary_id_seq', 100); -select setval('cvte_id_seq', 100); -select setval('property_type_id_seq', 100); -select setval('file_format_type_id_seq', 100); -select setval('filter_id_seq', 100); -select setval('experiment_type_id_seq', 100); -select setval('sample_type_id_seq', 100); -select setval('data_set_type_id_seq', 100); -select setval('material_type_id_seq', 100); -select setval('etpt_id_seq', 100); -select setval('stpt_id_seq', 100); -select setval('mtpt_id_seq', 100); - - --------------------------------------------------- --- create a gene property and assign it to sirna well --------------------------------------------------- - -insert into property_types( - id, - code, description, label, - daty_id, - pers_id_registerer, - dbin_id, - maty_prop_id) -values( - nextval('PROPERTY_TYPE_ID_SEQ'), - 'GENE','Inhibited gene','Gene', - (select id from data_types where code = 'MATERIAL'), - (select id from persons where user_id ='system'), - (select id from database_instances where is_original_source = 'T'), - (select id from material_types where code = 'GENE') - ); - -insert into sample_type_property_types( - id, - saty_id, - prty_id, - is_mandatory, - pers_id_registerer, - ordinal -) values( - nextval('stpt_id_seq'), - (select id from sample_types where code = 'SIRNA_WELL'), - (select id from property_types where code = 'GENE'), - false, - (select id from persons where user_id ='system'), - (select max(ordinal)+1 from sample_type_property_types - where saty_id = (select id from sample_types where code = 'SIRNA_WELL')) - ); - - --------------------------------------------------- --- Create gene property: gene_symbols --------------------------------------------------- - - - insert into property_types - (id - ,code - ,description - ,label - ,daty_id - ,pers_id_registerer - ,dbin_id) - values - (nextval('PROPERTY_TYPE_ID_SEQ') - ,'GENE_SYMBOLS' - ,'Gene symbols' - ,'Gene symbols' - ,(select id from data_types where code ='VARCHAR') - ,(select id from persons where user_id ='system') - ,(select id from database_instances where is_original_source = 'T') - ); - - insert into material_type_property_types( - id, - maty_id, - prty_id, - is_mandatory, - pers_id_registerer, - ordinal - ) values( - nextval('mtpt_id_seq'), - (select id from material_types where code = 'GENE'), - (select id from property_types where code = 'GENE_SYMBOLS'), - false, - (select id from persons where user_id ='system'), - (select max(ordinal)+1 from material_type_property_types - where maty_id = (select id from material_types where code = 'GENE')) - ); - diff --git a/screening/source/sql/imaging/postgresql/016/upload-screening-metadata.sh b/screening/source/sql/imaging/postgresql/016/upload-screening-metadata.sh deleted file mode 100755 index 1a8a1969f1ef9d83fafdeb766696b9c5eef14fe7..0000000000000000000000000000000000000000 --- a/screening/source/sql/imaging/postgresql/016/upload-screening-metadata.sh +++ /dev/null @@ -1,2 +0,0 @@ -DB=$1 -psql -U postgres -d openbis_$DB -f data.sql