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install_db.sh
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install_db.sh
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#!/bin/bash
SECONDS=0
# FR: S'assurer que le script n'est pas lancer en root (utilisation de whoami)
# EN: Make sure the script is not runn with root (use whoami)
if [ "$(id -u)" == "0" ];
then
echo -e "\e[91m\e[1mThis script should NOT be run as root\e[0m" >&2
exit 1
fi
# FR: sudo ls pour demander le mot de passe une fois
# EN: sudo ls to request the password once
sudo ls
if [ ! -d 'log' ]
then
mkdir log
fi
. atlas/configuration/settings.ini
sudo mkdir /tmp/atlas
sudo cp data/atlas/* /tmp/atlas/
function print_time () {
echo $(date +'%H:%M:%S')
}
function database_exists () {
# /!\ Will return false if psql can't list database. Edit your pg_hba.conf as appropriate.
if [ -z $1 ]
then
# Argument is null
return 0
else
# Grep db name in the list of database
sudo -u postgres -s -- psql -tAl | grep -q "^$1|"
return $?
fi
}
function test_settings() {
fields=('owner_atlas' 'user_pg' 'altitudes' 'time' 'attr_desc' 'attr_commentaire' 'attr_milieu' 'attr_chorologie')
echo "Checking the validity of settings.ini"
for i in "${!fields[@]}"
do
if [ -z ${!fields[$i]} ];
then
echo -e "\033\033[31m Error : \033[0m attribut ${fields[$i]} manquant dans settings.ini"
exit
fi
done
}
test_settings
# FR: Suppression du fichier de log d'installation s'il existe déjà puis création de ce fichier vide.
# EN: Delete the install log file if it already exists and create this empty file.
rm -f ./log/install_db.log
touch ./log/install_db.log
# FR: Si la BDD existe, je verifie le parametre qui indique si je dois la supprimer ou non
# EN: If the DB exists, I check the parameter that indicates whether I should delete it or not
if database_exists $db_name
then
if $drop_apps_db
then
echo "Deleting DB..."
sudo -u postgres -s dropdb $db_name &>> log/install_db.log
else
echo "The database exists and the settings file says not to delete it."
fi
fi
# FR: Sinon je créé la BDD
# EN: Else I create the DB
if ! database_exists $db_name
then
print_time
echo "Creating DB..."
sudo -u postgres psql -c "CREATE USER $owner_atlas WITH PASSWORD '$owner_atlas_pass' " &>> log/install_db.log
sudo -u postgres psql -c "CREATE USER $user_pg WITH PASSWORD '$user_pg_pass' " &>> log/install_db.log
sudo -u postgres -s createdb -O $owner_atlas $db_name
echo "Adding postGIS and pgSQL to DB"
sudo -u postgres -s psql -d $db_name -c "CREATE EXTENSION IF NOT EXISTS postgis;" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE EXTENSION IF NOT EXISTS plpgsql WITH SCHEMA pg_catalog; COMMENT ON EXTENSION plpgsql IS 'PL/pgSQL procedural language';" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE EXTENSION IF NOT EXISTS pg_trgm;" &>> log/install_db.log
# FR: Si j'utilise GeoNature ($geonature_source = True), alors je créé les connexions en FWD à la BDD GeoNature
# EN: If I use GeoNature ($geonature_source = True), then I create the connections in FWD to the GeoNature DB
if $geonature_source
then
echo "Adding FDW and connection to the GeoNature parent DB"
sudo -u postgres -s psql -d $db_name -c "CREATE EXTENSION IF NOT EXISTS postgres_fdw;" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE SERVER geonaturedbserver FOREIGN DATA WRAPPER postgres_fdw OPTIONS (host '$db_source_host', dbname '$db_source_name', port '$db_source_port');" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "ALTER SERVER geonaturedbserver OWNER TO $owner_atlas;" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE USER MAPPING FOR $owner_atlas SERVER geonaturedbserver OPTIONS (user '$atlas_source_user', password '$atlas_source_pass') ;" &>> log/install_db.log
fi
# FR: Création des schémas de la BDD
# EN: Creating DB schemes
sudo -u postgres -s psql -d $db_name -c "CREATE SCHEMA atlas AUTHORIZATION "$owner_atlas";" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE SCHEMA synthese AUTHORIZATION "$owner_atlas";" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE SCHEMA utilisateurs AUTHORIZATION "$owner_atlas";" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE SCHEMA gn_meta AUTHORIZATION "$owner_atlas";" &>> log/install_db.log
if [ $install_taxonomie = "false" ] # Pourquoi ce if ? TODO
then
sudo -u postgres -s psql -d $db_name -c "CREATE SCHEMA taxonomie AUTHORIZATION "$owner_atlas";" &>> log/install_db.log
fi
if $geonature_source
then
echo "Creating FDW from GN2"
echo "--------------------" &>> log/install_db.log #en double non? TODO
echo "Creating FDW from GN2" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f data/gn2/atlas_gn2.sql &>> log/install_db.log
fi
if $use_ref_geo_gn2
then
echo "Creation of geographic tables from the ref_geo schema of the geonature database"
echo "--------------------" &>> log/install_db.log
echo "Creation of layers table from ref_geo of geonaturedb" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass; psql -d $db_name -U $owner_atlas -h $db_host -p $db_port \
-v type_maille=$type_maille \
-v type_territoire=$type_territoire \
-f data/gn2/atlas_ref_geo.sql &>> log/install_db.log
else
# FR: Import du shape des limites du territoire ($limit_shp) dans la BDD / atlas.t_layer_territoire
# EN: Import of the shape of the territory limits ($limit_shp) in the BDD / atlas.t_layer_territory
ogr2ogr -f "ESRI Shapefile" -t_srs EPSG:4326 data/ref/emprise_territoire_4326.shp $limit_shp
sudo -u postgres -s shp2pgsql -W "LATIN1" -s 4326 -D -I ./data/ref/emprise_territoire_4326.shp atlas.t_layer_territoire | sudo -n -u postgres -s psql -d $db_name &>> log/install_db.log
rm data/ref/emprise_territoire_4326.*
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.t_layer_territoire OWNER TO "$owner_atlas";"
# FR: Creation de l'index GIST sur la couche territoire atlas.t_layer_territoire
# EN: Creation of the GIST index on the territory layer atlas.t_layer_territory
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.t_layer_territoire RENAME COLUMN geom TO the_geom; CREATE INDEX index_gist_t_layer_territoire ON atlas.t_layer_territoire USING gist(the_geom); " &>> log/install_db.log
# FR: Import du shape des communes ($communes_shp) dans la BDD (si parametre import_commune_shp = TRUE) / atlas.l_communes
# EN: Import of the shape of the communes ($communes_shp) in the DB (if parameter import_commune_shp = TRUE) / atlas.l_communes
if $import_commune_shp
then
ogr2ogr -f "ESRI Shapefile" -t_srs EPSG:4326 ./data/ref/communes_4326.shp $communes_shp
sudo -u postgres -s shp2pgsql -W "LATIN1" -s 4326 -D -I ./data/ref/communes_4326.shp atlas.l_communes | sudo -n -u postgres -s psql -d $db_name &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.l_communes RENAME COLUMN "$colonne_nom_commune" TO commune_maj;" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.l_communes RENAME COLUMN "$colonne_insee" TO insee;" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.l_communes RENAME COLUMN geom TO the_geom;" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE INDEX index_gist_t_layers_communes ON atlas.l_communes USING gist (the_geom);" &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.l_communes OWNER TO "$owner_atlas";"
rm ./data/ref/communes_4326.*
fi
# FR: Mise en place des mailles
# EN: Setting up the meshes
echo "Cutting of meshes and creation of the mesh table"
cd data/ref
rm -f L93*.dbf L93*.prj L93*.sbn L93*.sbx L93*.shp L93*.shx
# FR: Si je suis en métropole (metropole=true), alors j'utilise les mailles fournies par l'INPN
# EN: If I am in metropolitan France (metropole=true), then I use the grids provided by the INPN, comments are only in french here
if $metropole
then
# Je dézippe mailles fournies par l'INPN aux 3 échelles
unzip L93_1K.zip
unzip L93_5K.zip
unzip L93_10K.zip
# Je les reprojete les SHP en 4326 et les renomme
ogr2ogr -f "ESRI Shapefile" -t_srs EPSG:4326 ./mailles_1.shp L93_1x1.shp
ogr2ogr -f "ESRI Shapefile" -t_srs EPSG:4326 ./mailles_5.shp L93_5K.shp
ogr2ogr -f "ESRI Shapefile" -t_srs EPSG:4326 ./mailles_10.shp L93_10K.shp
# J'importe dans la BDD le SHP des mailles à l'échelle définie en parametre ($taillemaille)
sudo -n -u postgres -s shp2pgsql -W "LATIN1" -s 4326 -D -I mailles_$taillemaille.shp atlas.t_mailles_$taillemaille | sudo -n -u postgres -s psql -d $db_name &>> ../../log/install_db.log
sudo -n -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.t_mailles_"$taillemaille" OWNER TO "$owner_atlas";"
rm mailles_1.* mailles_5.* mailles_10.*
cd ../../
# Creation de la table atlas.t_mailles_territoire avec la taille de maille passée en parametre ($taillemaille). Pour cela j'intersecte toutes les mailles avec mon territoire
sudo -u postgres -s psql -d $db_name -c "CREATE TABLE atlas.t_mailles_territoire as
SELECT m.geom AS the_geom, ST_AsGeoJSON(st_transform(m.geom, 4326)) as geojson_maille
FROM atlas.t_mailles_"$taillemaille" m, atlas.t_layer_territoire t
WHERE ST_Intersects(m.geom, t.the_geom);
CREATE INDEX index_gist_t_mailles_territoire
ON atlas.t_mailles_territoire
USING gist (the_geom);
ALTER TABLE atlas.t_mailles_territoire
ADD COLUMN id_maille serial;
ALTER TABLE atlas.t_mailles_territoire
ADD PRIMARY KEY (id_maille);" &>> log/install_db.log
# FR: Sinon j'utilise un SHP des mailles fournies par l'utilisateur
# EN: Otherwise I use a SHP of user supplied meshes
else
ogr2ogr -f "ESRI Shapefile" -t_srs EPSG:4326 custom_mailles_4326.shp $chemin_custom_maille
sudo -u postgres -s shp2pgsql -W "LATIN1" -s 4326 -D -I custom_mailles_4326.shp atlas.t_mailles_custom | sudo -n -u postgres -s psql -d $db_name &>> log/install_db.log
sudo -u postgres -s psql -d $db_name -c "CREATE TABLE atlas.t_mailles_territoire as
SELECT m.geom AS the_geom, ST_AsGeoJSON(st_transform(m.geom, 4326)) as geojson_maille
FROM atlas.t_mailles_custom m, atlas.t_layer_territoire t
WHERE ST_Intersects(m.geom, t.the_geom);
CREATE INDEX index_gist_t_mailles_custom
ON atlas.t_mailles_territoire
USING gist (the_geom);
ALTER TABLE atlas.t_mailles_territoire
ADD COLUMN id_maille serial;
ALTER TABLE atlas.t_mailles_territoire
ADD PRIMARY KEY (id_maille);" &>> log/install_db.log
fi
sudo -n -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.t_mailles_territoire OWNER TO "$owner_atlas";"
fi
# FR: Conversion des limites du territoire en json
# EN: Conversion of territory boundaries to json
rm -f ./atlas/static/custom/territoire.json
ogr2ogr -f "GeoJSON" -t_srs "EPSG:4326" -s_srs "EPSG:4326" ./atlas/static/custom/territoire.json \
PG:"host=$db_host user=$owner_atlas dbname=$db_name port=$db_port password=$owner_atlas_pass" "atlas.t_layer_territoire"
# FR: Si j'installe le schéma taxonomie de TaxHub dans la BDD de GeoNature-atlas ($install_taxonomie = True),
# alors je récupère les fichiers dans le dépôt de TaxHub et les éxécute
# EN: If I install the TaxHub taxonomy schema in the GeoNature-atlas DB ($install_taxonomy = True),
# then I get the files from the TaxHub repository and run them
if $install_taxonomie
then
wget https://raw.githubusercontent.com/PnX-SI/TaxHub/$taxhub_release/data/inpn/data_inpn_taxhub.sql -P /tmp/taxhub
array=( TAXREF_INPN_v11.zip ESPECES_REGLEMENTEES_v11.zip LR_FRANCE_20160000.zip )
for i in "${array[@]}"
do
if [ ! -f '/tmp/taxhub/'$i ]
then
wget http:https://geonature.fr/data/inpn/taxonomie/$i -P /tmp/taxhub
else
echo $i exists
fi
unzip /tmp/taxhub/$i -d /tmp/taxhub
done
echo "Getting 'taxonomie' schema creation scripts..."
wget https://raw.githubusercontent.com/PnX-SI/TaxHub/$taxhub_release/data/taxhubdb.sql -P /tmp/taxhub
wget https://raw.githubusercontent.com/PnX-SI/TaxHub/$taxhub_release/data/taxhubdata.sql -P /tmp/taxhub
wget https://raw.githubusercontent.com/PnX-SI/TaxHub/$taxhub_release/data/taxhubdata_taxons_example.sql -P /tmp/taxhub
wget https://raw.githubusercontent.com/PnX-SI/TaxHub/$taxhub_release/data/taxhubdata_atlas.sql -P /tmp/taxhub
wget https://raw.githubusercontent.com/PnX-SI/TaxHub/$taxhub_release/data/materialized_views.sql -P /tmp/taxhub
echo "Creating 'taxonomie' schema..."
echo "" &>> log/install_db.log
echo "" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "Creating 'taxonomie' schema" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/taxhub/taxhubdb.sql &>> log/install_db.log
echo "Inserting INPN taxonomic data... (This may take a few minutes)"
echo "" &>> log/install_db.log
echo "" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "Inserting INPN taxonomic data" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "" &>> log/install_db.log
sudo -n -u postgres -s psql -d $db_name -f /tmp/taxhub/data_inpn_taxhub.sql &>> log/install_db.log
echo "Creating dictionaries data for taxonomic schema..."
echo "" &>> log/install_db.log
echo "" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "Creating dictionaries data for taxonomic schema" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/taxhub/taxhubdata.sql &>> log/install_db.log
echo "Inserting sample dataset of taxons for taxonomic schema..."
echo "" &>> log/install_db.log
echo "" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "Inserting sample dataset of taxons for taxonomic schema" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/taxhub/taxhubdata_taxons_example.sql &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "Inserting sample dataset - atlas attributes" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/taxhub/taxhubdata_atlas.sql &>> log/install_db.log
echo "Creating a view that represent the taxonomic hierarchy..."
echo "" &>> log/install_db.log
echo "" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "Creating a view that represent the taxonomic hierarchy" &>> log/install_db.log
echo "--------------------" &>> log/install_db.log
echo "" &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/taxhub/materialized_views.sql &>> log/install_db.log
elif $geonature_source
then
# FR: Creation des tables filles en FWD
# EN: Creation of daughter tables in FWD
echo "Creating the connection to GeoNature for the taxonomy"
sudo cp data/gn2/atlas_ref_taxonomie.sql /tmp/atlas/atlas_ref_taxonomie.sql &>> log/install_db.log
sudo sed -i "s/myuser;$/$owner_atlas;/" /tmp/atlas/atlas_ref_taxonomie.sql &>> log/install_db.log
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/atlas_ref_taxonomie.sql &>> log/install_db.log
fi
echo "Creating DB structure"
# FR: Si j'utilise GeoNature ($geonature_source = True), alors je créé les tables filles en FDW connectées à la BDD de GeoNature
# EN: If I use GeoNature ($geonature_source = True), then I create the child tables in FDW connected to the GeoNature DB
if $geonature_source
then
sudo cp data/gn2/atlas_synthese.sql /tmp/atlas/atlas_synthese_extended.sql
sudo sed -i "s/myuser;$/$owner_atlas;/" /tmp/atlas/atlas_synthese_extended.sql
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/atlas_synthese_extended.sql &>> log/install_db.log
# FR: Sinon je créé une table synthese.syntheseff avec 2 observations exemple
# EN: Otherwise I created a table synthese.syntheseff with 2 observations example
else
echo "Creating syntheseff example table"
sudo -n -u postgres -s psql -d $db_name -f /tmp/atlas/without_geonature.sql &>> log/install_db.log
sudo -n -u postgres -s psql -d $db_name -c "ALTER TABLE synthese.syntheseff OWNER TO "$owner_atlas";"
fi
# FR: Creation des Vues Matérialisées (et remplacement éventuel des valeurs en dur par les paramètres)
# EN: Creation of Materialized Views (and possible replacement of hard values by parameters)
echo "----- Creating materialized views ------"
sudo sed -i "s/date - 15$/date - $time/" /tmp/atlas/10.atlas.vm_taxons_plus_observes.sql
sudo sed -i "s/date + 15$/date - $time/" /tmp/atlas/10.atlas.vm_taxons_plus_observes.sql
# FR: customisation de l'altitude
# EN: customisation of altitude
insert=""
for i in "${!altitudes[@]}"
do
if [ $i -gt 0 ];
then
let max=${altitudes[$i]}-1
sql="INSERT INTO atlas.bib_altitudes VALUES ($i,${altitudes[$i-1]},$max);"
insert="${insert}\n${sql}"
fi
done
sudo sed -i "s/INSERT_ALTITUDE/${insert}/" /tmp/atlas/4.atlas.vm_altitudes.sql
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_taxref..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/1.atlas.vm_taxref.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_observations..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/2.atlas.vm_observations.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_taxons..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/3.atlas.vm_taxons.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_altitudes..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/4.atlas.vm_altitudes.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_search_taxon..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/5.atlas.vm_search_taxon.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_mois..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/6.atlas.vm_mois.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_communes..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/7.atlas.vm_communes.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_medias"
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/8.atlas.vm_medias.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_cor_taxon_attribut..."
time_temp=$SECONDS
sudo sed -i "s/WHERE id_attribut IN (100, 101, 102, 103);$/WHERE id_attribut IN ($attr_desc, $attr_commentaire, $attr_milieu, $attr_chorologie);/" /tmp/atlas/9.atlas.vm_cor_taxon_attribut.sql
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/9.atlas.vm_cor_taxon_attribut.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_taxons_plus_observes..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/10.atlas.vm_taxons_plus_observes.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_cor_taxon_organism..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/11.atlas.vm_cor_taxon_organism.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
echo "[$(date +'%H:%M:%S')] Creating function refresh vm..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/atlas.refresh_materialized_view_data.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
if $use_ref_geo_gn2
then
echo "[$(date +'%H:%M:%S')] Creating atlas.t_mailles_territoire..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port \
-f data/atlas/12.atlas.t_mailles_territoire.sql \
-v type_maille=$type_maille &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
fi
# FR: Création de la vue matérialisée vm_mailles_observations (nombre d'observations par maille et par taxon)
# EN: Creation of the materialized view vm_meshes_observations (number of observations per mesh and per taxon)
echo "[$(date +'%H:%M:%S')] Creating atlas.vm_observations_mailles..."
time_temp=$SECONDS
export PGPASSWORD=$owner_atlas_pass;psql -d $db_name -U $owner_atlas -h $db_host -p $db_port -f /tmp/atlas/13.atlas.vm_observations_mailles.sql &>> log/install_db.log
echo "[$(date +'%H:%M:%S')] Passed - Duration : $((($SECONDS-$time_temp)/60))m$((($SECONDS-$time_temp)%60))s"
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.bib_taxref_rangs OWNER TO "$owner_atlas";"
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.bib_taxref_rangs OWNER TO "$owner_atlas";"
sudo -u postgres -s psql -d $db_name -c "ALTER FUNCTION atlas.create_vm_altitudes() OWNER TO "$owner_atlas";"
sudo -u postgres -s psql -d $db_name -c "ALTER FUNCTION atlas.find_all_taxons_childs(integer) OWNER TO "$owner_atlas";"
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.t_mailles_territoire OWNER TO "$owner_atlas";"
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.vm_observations_mailles OWNER TO "$owner_atlas";"
sudo -u postgres -s psql -d $db_name -c "ALTER TABLE atlas.vm_cor_taxon_organism OWNER TO "$owner_atlas";"
# FR: Affectation de droits en lecture sur les VM à l'utilisateur de l'application ($user_pg)
# EN: Assign read rights on VMs to the application user ($user_pg)
echo "Grant..."
sudo sed -i "s/my_reader_user;$/$user_pg;/" /tmp/atlas/14.grant.sql
sudo -n -u postgres -s psql -d $db_name -f /tmp/atlas/14.grant.sql &>> log/install_db.log
# Clean file
echo "Cleaning files..."
cd data/ref
rm -f L*.shp L*.dbf L*.prj L*.sbn L*.sbx L*.shx output_clip.*
cd ../..
sudo -n rm -r /tmp/atlas
if [ -d '/tmp/taxhub' ]
then
rm -r /tmp/taxhub
fi
echo "Install finished - Duration :$(($SECONDS/60))m$(($SECONDS%60))s"
fi