init review script
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5_GEONATURE/EXPORT/flore_export_sinp_with_metadata 2.py
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177
5_GEONATURE/EXPORT/flore_export_sinp_with_metadata 2.py
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from pycen import con_gn
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sql = '''
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DROP VIEW IF EXISTS gn_exports.v_synthese_sinp_with_metadata_flora_for_gn2pg_bis;
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CREATE VIEW gn_exports.v_synthese_sinp_with_metadata_flora_for_gn2pg_bis AS
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WITH af_actors AS (
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SELECT cafa.id_acquisition_framework
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FROM gn_meta.cor_acquisition_framework_actor cafa
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LEFT JOIN utilisateurs.bib_organismes borg ON cafa.id_organism = borg.id_organisme
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WHERE borg.uuid_organisme = '5a433bd0-2070-25d9-e053-2614a8c026f8'::uuid
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), af AS (
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SELECT taf.id_acquisition_framework
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FROM gn_meta.t_acquisition_frameworks taf
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JOIN af_actors ON af_actors.id_acquisition_framework = taf.id_acquisition_framework
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GROUP BY taf.id_acquisition_framework
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), ds AS (
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SELECT tds.id_dataset,
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tds.dataset_name AS nom_jdd,
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tds.id_acquisition_framework
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FROM gn_meta.t_datasets tds
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GROUP BY tds.id_dataset, tds.dataset_name
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), geo AS (
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SELECT "left"(geo_1.area_code::text, 2) AS departement,
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geo_1.area_code AS commune,
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s_1.id_synthese,
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st_transform(s_1.the_geom_local, 4326) AS st_transform
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FROM ref_geo.l_areas geo_1
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JOIN gn_synthese.synthese s_1 ON st_intersects(s_1.the_geom_4326, st_transform(geo_1.geom, 4326))
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WHERE geo_1.id_type = 25
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)
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SELECT
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ds.nom_jdd AS nom_jdd,
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s.unique_id_sinp_grp AS id_sinp_releve,
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occ.id_releve_occtax AS identifiant_releve,
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NULL::text AS code_perso_releve,
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s.unique_id_sinp AS id_sinp_observation,
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s.entity_source_pk_value AS identifiant_observation,
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geo.departement,
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geo.commune,
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NULL::text AS lieu_dit,
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CASE
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WHEN "position"(sp.srtext::text, 'GEOGCS'::text) = 1 THEN "substring"(replace(sp.srtext::text, 'GEOGCS["'::text, ''::text), 1, "position"(replace(sp.srtext::text, 'GEOGCS["'::text, ''::text), '",'::text) - 1)
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WHEN "position"(sp.srtext::text, 'PROJCS'::text) = 1 THEN "substring"(replace(sp.srtext::text, 'PROJCS["'::text, ''::text), 1, "position"(replace(sp.srtext::text, 'PROJCS["'::text, ''::text), '",'::text) - 1)
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WHEN "position"(sp.srtext::text, 'GEOCCS'::text) = 1 THEN "substring"(replace(sp.srtext::text, 'GEOCCS["'::text, ''::text), 1, "position"(replace(sp.srtext::text, 'GEOCCS["'::text, ''::text), '",'::text) - 1)
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WHEN "position"(sp.srtext::text, 'COMPD_CS'::text) = 1 THEN "substring"(replace(sp.srtext::text, 'COMPD_CS["'::text, ''::text), 1, "position"(replace(sp.srtext::text, 'COMPD_CS["'::text, ''::text), '",'::text) - 1)
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ELSE 'Non défini'::text
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END AS sys_coord,
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st_srid(s.the_geom_4326) AS "SRID",
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st_astext(s.the_geom_4326) AS localisation_wkt,
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st_x(st_centroid(s.the_geom_4326)) AS coord_x,
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st_y(st_centroid(s.the_geom_4326)) AS coord_y,
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s."precision" AS precision,
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NULL::text AS nature_objet,
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s.altitude_min AS alti_min,
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s.altitude_max AS alti_max,
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NULL::text AS pente,
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NULL::text AS exposition,
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NULL::text AS comm_geol,
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NULL::text AS milieu,
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s.observers AS observateurs,
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s.date_min AS date_debut,
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s.date_max AS date_fin,
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NULL::text AS comm_context,
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n2.mnemonique AS type_regroupement,
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s.grp_method AS meth_regroupement,
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NULL::text AS surface,
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(s."additional_data"::json#>>'{strate_flore}') ||
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ref_nomenclatures.get_nomenclature_label((s."additional_data"::json#>>'{id_nomenclature_strate_flore}')::int)
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AS strate_vegetation,
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(s."additional_data"::json#>>'{heigth_herbace}')::text || (s."additional_data"::json#>>'{heigth_arbust}')::text
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|| (s."additional_data"::json#>>'{heigth_arbore}')::text || (s."additional_data"::json#>>'{heigth_ssarbust}')::text
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AS hauteur_strate,
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(s."additional_data"::json#>>'{rcvmt_herbace}')::text || (s."additional_data"::json#>>'{rcvmt_arbust}')::text
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|| (s."additional_data"::json#>>'{rcvmt_arbore}')::text || (s."additional_data"::json#>>'{rcvmt_ssarbust}')::text
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AS recouvrement_strate,
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s.cd_hab AS cdhab,
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NULL::text AS cdhab_v,
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NULL::text AS code_eur,
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NULL::text AS code_eunis,
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NULL::text AS code_cahab,
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NULL::text AS code_cb,
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NULL::text AS id_microhab,
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n21.regne AS regne,
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s.nom_cite AS nom_cite,
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s.cd_nom as cd_nom,
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(s."additional_data"::json#>>'{effectif_textuel}')::text ||
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ref_nomenclatures.get_nomenclature_label((s."additional_data"::json#>>'{id_nomenclature_braunblanq_abdom}')::int)::text
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AS abondance,
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NULL::text AS sociabilite,
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n11.mnemonique AS sexe,
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n7.mnemonique AS naturalite,
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NULL::text AS comm_description,
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n15.mnemonique AS statut_observation,
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n12.mnemonique AS objet_denombrement,
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n13.mnemonique AS type_denombrement,
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s.count_min AS nombre_min,
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s.count_max AS nombre_max,
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n17.label_default AS statut_source,
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NULL::text AS reference_biblio,
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NULL::text AS page,
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n8.mnemonique AS preuve_existence,
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s.digital_proof AS preuve_numerique,
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s.non_digital_proof AS preuve_non_numerique,
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NULL::text AS nom_collection,
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NULL::text AS ref_collection,
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s.determiner AS determinateur,
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NULL::text AS niv_val,
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NULL::text AS niveau_diffusion,
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n16.mnemonique AS floutage_dee,
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NULL::text AS methode_observation,
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CASE WHEN ts.name_source like 'MONITORING_%%'
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THEN split_part(ts.name_source,'_',2)
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ELSE 'RELEVE FLORE'::text
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END AS protocole,
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n6.mnemonique AS etat_biologique,
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n5.mnemonique AS statut_biologique,
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n10.mnemonique AS stade_vie,
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n19.mnemonique AS methode_determination,
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n3.mnemonique AS comportement,
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s.additional_data - '{effectif_textuel,strate_flore,code_atlas,id_nomenclature_braunblanq_abdom,id_nomenclature_strate_flore}'::text[] AS donnees_additionnelles
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FROM gn_synthese.synthese s
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JOIN ds ON ds.id_dataset = s.id_dataset
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JOIN af ON ds.id_acquisition_framework = af.id_acquisition_framework
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JOIN geo ON s.id_synthese = geo.id_synthese
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JOIN spatial_ref_sys sp ON st_srid(s.the_geom_4326) = sp.auth_srid
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LEFT JOIN ref_habitats.habref h ON h.cd_hab = s.cd_hab
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LEFT JOIN pr_occtax.t_releves_occtax occ ON occ.unique_id_sinp_grp = s.unique_id_sinp_grp
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LEFT JOIN ref_nomenclatures.t_nomenclatures n1 ON s.id_nomenclature_geo_object_nature = n1.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n2 ON s.id_nomenclature_grp_typ = n2.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n3 ON s.id_nomenclature_behaviour = n3.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n4 ON s.id_nomenclature_obs_technique = n4.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n5 ON s.id_nomenclature_bio_status = n5.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n6 ON s.id_nomenclature_bio_condition = n6.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n7 ON s.id_nomenclature_naturalness = n7.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n8 ON s.id_nomenclature_exist_proof = n8.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n9 ON s.id_nomenclature_diffusion_level = n9.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n10 ON s.id_nomenclature_life_stage = n10.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n11 ON s.id_nomenclature_sex = n11.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n12 ON s.id_nomenclature_obj_count = n12.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n13 ON s.id_nomenclature_type_count = n13.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n14 ON s.id_nomenclature_sensitivity = n14.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n15 ON s.id_nomenclature_observation_status = n15.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n16 ON s.id_nomenclature_blurring = n16.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n17 ON s.id_nomenclature_source_status = n17.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n18 ON s.id_nomenclature_info_geo_type = n18.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n19 ON s.id_nomenclature_determination_method = n19.id_nomenclature
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LEFT JOIN ref_nomenclatures.t_nomenclatures n20 ON s.id_nomenclature_valid_status = n20.id_nomenclature
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LEFT JOIN taxonomie.taxref n21 ON s.cd_nom = n21.cd_nom
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JOIN gn_synthese.cor_area_synthese cas ON cas.id_synthese = s.id_synthese
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-- ADD CEN_38
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JOIN gn_synthese.t_sources ts ON ts.id_source = s.id_source
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WHERE n21.regne::text = 'Plantae'::text
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-- exclision CA ([SICEN] Données anciennes,[TEST] : migration sicen,[SICEN] Hors Etude)
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AND ds.id_acquisition_framework NOT IN (53,65,66,1,2,6)
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-- exclision JDD `Observations opportunistes du CEN Isère importé depuis Faune Isère`
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AND ds.id_dataset NOT IN (185,377,236)
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-- exclision CA (`Gestion de l'Espace Naturel Sensible du Méandre des Oves`, `Gestion de la Réserve Naturelle Nationale de l'Ile de la Platière`, `Gestion des Natura 2000 FR 8201749 « Milieux alluviaux et aquatiques de l’Île de la Platière » et FR 8212012 « Île de la Platière »`, `RNN Platière`
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--AND (ts.id_module = 7 AND ds.id_acquisition_framework IN (7,38,39,42,44,45,46,48,55,57,58,60)
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AND (
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unaccent(observers) LIKE ANY (array['%%Conservatoire d%%Espaces Naturels Isere%%', '%%Conservatoire d%%Espaces Naturels d%%Isere%%', '%%CEN Isere%%', '%%Association des Amis de l%%Ile de la Platiere%%'])
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OR observers NOT LIKE '%%(%%)%%'
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)
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AND unaccent(observers) NOT LIKE ALL(array[
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'%%Sympetrum%%','%%Departement%%','%%Rhone%%','%%Oxalis%%',
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'%%LPO%%','%%GRPLS%%','%%Parvi%%','%%CD Isere%%','%%Personnel%%','%%Independant%%'
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'%%DELOCHE Denis%%'
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])
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AND observers NOT IN ('', 'Benoit Dodelin',', ')
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-- statut_validation = 'Certain - très probable'
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-- AND n20.cd_nomenclature = '1'
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ORDER BY s.id_synthese;
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'''
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with con_gn.begin() as cnx:
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cnx.execute(sql)
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