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intégration du taxref V8 - Fix #34
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@gildeluermoz
gildeluermoz committed Jan 13, 2016
1 parent dff04b4 commit 4f40d52
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Showing 7 changed files with 65 additions and 55 deletions.
82 changes: 41 additions & 41 deletions data/2154/synthese_2154.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -3795,14 +3795,14 @@ CREATE TABLE taxref (
cd_taxsup integer,
cd_ref integer,
lb_nom character varying(100),
lb_auteur character varying(150),
lb_auteur character varying(250),
nom_complet character varying(255),
nom_valide character varying(255),
nom_vern character varying(255),
nom_vern_eng character varying(255),
group1_inpn character varying(255),
group2_inpn character varying(255),
nom_complet_html character varying(255)
nom_vern character varying(1000),
nom_vern_eng character varying(500),
group1_inpn character varying(50),
group2_inpn character varying(50),
nom_complet_html character varying(500)
);


Expand Down Expand Up @@ -4693,39 +4693,40 @@ CREATE TABLE bib_taxref_statuts (

CREATE TABLE import_taxref (
regne character varying(20),
phylum character varying(50),
classe character varying(50),
ordre character varying(50),
famille character varying(50),
group1_inpn character varying(50),
group2_inpn character varying(50),
cd_nom integer NOT NULL,
cd_taxsup integer,
cd_ref integer,
rang character varying(10),
lb_nom character varying(100),
lb_auteur character varying(250),
nom_complet character varying(255),
nom_valide character varying(255),
nom_vern character varying(500),
nom_vern_eng character varying(500),
habitat character varying(10),
fr character varying(10),
gf character varying(10),
mar character varying(10),
gua character varying(10),
sm character varying(10),
sb character varying(10),
spm character varying(10),
may character varying(10),
epa character varying(10),
reu character varying(10),
taaf character varying(10),
pf character varying(10),
nc character varying(10),
wf character varying(10),
cli character varying(10),
url text
phylum character varying(50),
classe character varying(50),
ordre character varying(50),
famille character varying(50),
group1_inpn character varying(50),
group2_inpn character varying(50),
cd_nom integer NOT NULL,
cd_taxsup integer,
cd_ref integer,
rang character varying(10),
lb_nom character varying(100),
lb_auteur character varying(250),
nom_complet character varying(255),
nom_complet_html character varying(500),
nom_valide character varying(255),
nom_vern character varying(1000),
nom_vern_eng character varying(500),
habitat character varying(10),
fr character varying(10),
gf character varying(10),
mar character varying(10),
gua character varying(10),
sm character varying(10),
sb character varying(10),
spm character varying(10),
may character varying(10),
epa character varying(10),
reu character varying(10),
taaf character varying(10),
pf character varying(10),
nc character varying(10),
wf character varying(10),
cli character varying(10),
url text
);


Expand Down Expand Up @@ -9699,5 +9700,4 @@ GRANT ALL ON TABLE v_observateurs TO geonatuser;

--
-- PostgreSQL database dump complete
--

--
1 change: 0 additions & 1 deletion data/inpn/.gitignore
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Binary file added data/inpn/ESPECES_REGLEMENTEES.zip
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Binary file added data/inpn/TAXREF_INPN_v8.0.zip
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Binary file removed data/inpn/data_inpn_v7.tar.gz
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17 changes: 9 additions & 8 deletions data/inpn/data_inpn_v7_synthese.sql → data/inpn/data_inpn_v8_synthese.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,7 @@ INSERT INTO bib_taxref_statuts (id_statut, nom_statut) VALUES ('Y', 'Introduite
INSERT INTO bib_taxref_statuts (id_statut, nom_statut) VALUES ('Z', 'Endémique éteinte');
INSERT INTO bib_taxref_statuts (id_statut, nom_statut) VALUES ('0', 'Non renseigné');
INSERT INTO bib_taxref_statuts (id_statut, nom_statut) VALUES ('Q', 'Mentionné par erreur');
INSERT INTO bib_taxref_statuts (id_statut, nom_statut) VALUES (' ', 'Non précisé');

-------------------------------------------------------------
------------Insertion des données taxref -------------
Expand All @@ -76,14 +77,14 @@ INSERT INTO bib_taxref_statuts (id_statut, nom_statut) VALUES ('Q', 'Mentionné
---import taxref--
TRUNCATE TABLE import_taxref;
COPY import_taxref (regne, phylum, classe, ordre, famille, group1_inpn, group2_inpn,
cd_nom, cd_taxsup, cd_ref, rang, lb_nom, lb_auteur, nom_complet,
cd_nom, cd_taxsup, cd_ref, rang, lb_nom, lb_auteur, nom_complet, nom_complet_html,
nom_valide, nom_vern, nom_vern_eng, habitat, fr, gf, mar, gua,
sm, sb, spm, may, epa, reu, taaf, pf, nc, wf, cli, url)
FROM '/home/synthese/geonature/data/inpn/taxref_v70.txt'
FROM '/home/synthese/geonature/data/inpn/TAXREFv80.txt'
WITH CSV HEADER
DELIMITER E'\t';
DELIMITER E'\t' encoding 'LATIN1';

---selection des taxons faune uniquement--
---selection des taxons faune-flore-fonge uniquement--
TRUNCATE TABLE taxref CASCADE;
INSERT INTO taxref
SELECT cd_nom, fr as id_statut, habitat::int as id_habitat, rang as id_rang, regne, phylum, classe,
Expand All @@ -104,9 +105,9 @@ cd_protection, article, intitule, protection, arrete, fichier,
fg_afprot, niveau, cd_arrete, url, date_arrete, rang_niveau,
lb_article, type_protection
)
FROM '/home/synthese/geonature/data/inpn/taxref_PROTECTION_ESPECES_TYPES_70_UTF8.csv'
FROM '/home/synthese/geonature/data/inpn/PROTECTION_ESPECES_TYPES_70.csv'
WITH CSV HEADER
DELIMITER ';';
DELIMITER ';' encoding 'LATIN1';


---import des statuts de protections associés au taxon
Expand All @@ -121,9 +122,9 @@ CREATE TABLE import_protection_especes (
);

COPY import_protection_especes
FROM '/home/synthese/geonature/data/inpn/taxref_PROTECTION_ESPECES_70_UTF8.csv'
FROM '/home/synthese/geonature/data/inpn/PROTECTION_ESPECES_70.csv'
WITH CSV HEADER
DELIMITER ';';
DELIMITER ';' encoding 'LATIN1';


TRUNCATE TABLE taxref_protection_especes;
Expand Down
20 changes: 15 additions & 5 deletions install_db.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -45,24 +45,31 @@ then
# Mise en place de la structure de la base et des données permettant son focntionnement avec l'application
echo "Grant..."
export PGPASSWORD=$admin_pg_pass;psql -h geonatdbhost -U $admin_pg -d $db_name -f data/grant.sql &> log/install_db.log

echo "Création de la structure de la base..."
export PGPASSWORD=$user_pg_pass;psql -h geonatdbhost -U $user_pg -d $db_name -f data/2154/synthese_2154.sql &>> log/install_db.log

echo "Décompression des fichiers du taxref..."
cd data/inpn
tar -xzvf data_inpn_v7.tar.gz
unzip TAXREF_INPN_v8.0.zip
unzip ESPECES_REGLEMENTEES.zip
cd ../..
echo "Insertion des données taxonomiques de l'inpn... (cette opération peut être longue)"
DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
sed -i "s#/home/synthese/geonature#${DIR}#g" data/inpn/data_inpn_v7_synthese.sql
export PGPASSWORD=$admin_pg_pass;psql -h geonatdbhost -U $admin_pg -d $db_name -f data/inpn/data_inpn_v7_synthese.sql &>> log/install_db.log
sed -i "s#/home/synthese/geonature#${DIR}#g" data/inpn/data_inpn_v8_synthese.sql
export PGPASSWORD=$admin_pg_pass;psql -h geonatdbhost -U $admin_pg -d $db_name -f data/inpn/data_inpn_v8_synthese.sql &>> log/install_db.log

echo "Décompression des fichiers des communes de France métropolitaine..."
cd data/layers
tar -xzvf layers.tar.gz
cd ../..

echo "Insertion du référentiel géographique : communes métropolitaines... (cette opération peut être longue)"
export PGPASSWORD=$user_pg_pass;psql -h geonatdbhost -U $user_pg -d $db_name -f data/layers/communes_metropole.sql &>> log/install_db.log

echo "Insertion des données des tables dictionnaires de la base..."
export PGPASSWORD=$user_pg_pass;psql -h geonatdbhost -U $user_pg -d $db_name -f data/2154/data_synthese_2154.sql &>> log/install_db.log

echo "Décompression des fichiers du référentiel géographique..."
cd data/layers
unzip apb.zip
Expand All @@ -88,6 +95,7 @@ then
unzip znieff2_mer.zip
mkdir sql
cd ../..

echo "Insertion du référentiel géographique : zones à statut de france métropolitaine..."
echo "...Aires de protection de biotope..."
sudo -n -u postgres -s shp2pgsql -s 2154 -a -g the_geom -W "LATIN1" data/layers/apb/apb.shp layers.l_zonesstatut > data/layers/sql/apb.sql
Expand Down Expand Up @@ -151,14 +159,16 @@ then
echo "...ZNIEFF 2 mer..."
sudo -n -u postgres -s shp2pgsql -s 2154 -a -g the_geom -W "LATIN1" data/layers/znieff2_mer/znieff2_mer.shp layers.l_zonesstatut > data/layers/sql/znieff2_mer.sql
export PGPASSWORD=$user_pg_pass;psql -h geonatdbhost -U $user_pg -d $db_name -f data/layers/sql/znieff2_mer.sql &>> log/install_db.log

#export PGPASSWORD=$user_pg_pass;psql -h geonatdbhost -U $user_pg -d $db_name -f data/layers/zonesstatut.sql &>> log/install_db.log

echo "Insertion d'un jeu de données test dans les schémas contactfaune et contactinv de la base"
export PGPASSWORD=$admin_pg_pass;psql -h geonatdbhost -U $admin_pg -d $db_name -f data/2154/data_set_synthese_2154.sql &>> log/install_db.log

# suppression des fichiers : on ne conserve que les fichiers compressés
echo "nettoyage..."
rm data/inpn/taxref*
rm data/inpn/*.txt
rm data/inpn/*.xls
rm data/inpn/*.csv
rm data/layers/communes_metropole.sql
# rm data/layers/zonesstatut.sql
rm -R data/layers/apb
Expand Down

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