diff --git a/insert_liste_alerte.py b/insert_liste_alerte.py new file mode 100644 index 0000000..b9201db --- /dev/null +++ b/insert_liste_alerte.py @@ -0,0 +1,289 @@ +#!/usr/bin/env python3 +# -*- coding: UTF-8 -*- + +def test_data(con,tab,col,status): + sql = ''' + SELECT count({col}) FROM {sch}.{tab} WHERE {col} = '{status}' + ;'''.format(sch='taxonomie',tab=tab,col=col,status=status) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def test_cor_values(con,vals): + sql = ''' + SELECT count(id_value_text) FROM {sch}.{tab} WHERE (id_value,id_text) = {vals} + ;'''.format(sch='taxonomie',tab='bdc_statut_cor_text_values',vals=vals) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def test_status_type(con,col,status): + sql = ''' + SELECT count({col}) FROM {sch}.{tab} WHERE {col} = '{status}' + ;'''.format(sch='taxonomie',tab='bdc_statut_type',col=col,status=status) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def insert_status_alerte(con): + """ + Insert type de statut pour les alertes + + Si la valeur AL n'existe pas dans la table bdc_statut_type, on l'insert + """ + if test_data(con,'bdc_statut_type','cd_type_statut','AL') > 0: + # if test_status_type(con,'cd_type_statut','AL') > 0: + print('ALERTE STATUS ALREADY EXISTS') + else: + sql = ''' + INSERT INTO {sch}.{tab} (cd_type_statut,lb_type_statut,regroupement_type,thematique,type_value) VALUES + ('AL','Liste d''alerte départementale','Alerte','STATUTS','VALUE') + ;'''.format(sch='taxonomie',tab='bdc_statut_type') + with con_gn.begin() as cnx: + cnx.execute(sql) + +def insert_status_values(con): + """ + Inserts predefined status values into the 'bdc_statut_values' table if they do not already exist. + + This function iterates over a list of status values, checking whether each value already exists in the + specified database table. If a value does not exist, it inserts the value into the table. Status values + include a code and a label, which describe the extinction risk or conservation status of a taxonomic + group at the departmental level. + + Args: + con: A SQLAlchemy connection object to the database. + + Note: + This function assumes the existence of a schema named 'taxonomie' and a table named + 'bdc_statut_values' in the database connected via 'con'. It also assumes the availability of a + 'con_gn' connection for executing the SQL commands. + """ + + vals = [ + ['RE','Disparue au niveau départemental'], + ['AS-1','Quasi menacée (localisées sans signe de déclin)'], + ['AS-2','Quasi menacée (répandues mais en déclin)'], + ['AS-3','Quasi menacée (répandues, déclin à confirmer)'] + ] + for val in vals: + if test_data(con,'bdc_statut_values','label_statut',val[1]) > 0: + print('ALERTE VALUE STATUS ALREADY EXISTS : ',val[1]) + else: + sql = ''' + INSERT INTO {sch}.{tab} (code_statut,label_statut) VALUES + ('{val0}','{val1}') + '''.format(sch='taxonomie',tab='bdc_statut_values',val0=val[0],val1=val[1]) + with con_gn.begin() as cnx: + cnx.execute(sql) + +def get_text_id(con,cd_doc): + sql = ''' + SELECT id_text FROM {sch}.{tab} WHERE cd_doc = '{cd_doc}' + ;'''.format(sch='taxonomie',tab='bdc_statut_text',cd_doc=cd_doc) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def get_area_id(con,area): + sql = ''' + SELECT id_area FROM {sch}.{tab} WHERE area_name = '{area}' + ;'''.format(sch='ref_geo',tab='l_areas',area=area) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def get_values_id(con,col,terme): + if isinstance(terme,int|str): + terme = [terme] + else: + terme = list(terme) + sql = ''' + SELECT id_value FROM {sch}.{tab} WHERE {col} IN {terme} AND label_statut <> 'Disparue au niveau régional' + ;'''.format(sch='taxonomie',tab='bdc_statut_values',col=col,terme=tuple(terme)).replace(',)',')') + with con.begin() as cnx: + return cnx.execute(sql).all() + +def insert_status_cor_text_area(con,id_doc): + id_text = get_text_id(con,id_doc) + id_area = get_area_id(con,'Isère') + + check_sql = ''' + SELECT count(id_text) FROM {sch}.{tab} WHERE (id_text,id_area) = ({id_text},{id_area}) + ;'''.format(sch='taxonomie',tab='bdc_statut_cor_text_area',id_text=id_text,id_area=id_area) + with con.begin() as cnx: + if cnx.execute(check_sql).one()[0] == 0: + sql = (''' + INSERT INTO {sch}.{tab} (id_text,id_area) VALUES ({id_text},{id_area}) + ;'''.format(sch='taxonomie',tab='bdc_statut_cor_text_area',id_text=id_text,id_area=id_area)) + cnx.execute(sql) + + +def insert_status_cor_text_values(con,id_doc,values): + insert_status_values(con) + id_text = get_text_id(con,id_doc) + id_vals = [x[0] for x in get_values_id(con,'code_statut',values)] + + zip_vals = tuple(zip(id_vals,[id_text]*len(id_vals))) + cor_vals = [x for x in zip_vals if test_cor_values(con,x)==0] + + sql = (''' + INSERT INTO {sch}.{tab} (id_value,id_text) VALUES {values} + ;''' + .format(sch='taxonomie',tab='bdc_statut_cor_text_values',values=cor_vals) + .replace(r'[','') + .replace(r']','')) + + with con_gn.begin() as cnx: + cnx.execute(sql) + +def get_id_status_cor_text_values(con,id_doc,values): + id_text = get_text_id(con,id_doc) + id_vals = [x[0] for x in get_values_id(con,'code_statut',values)] + + zip_vals = tuple(zip(id_vals,[id_text]*len(id_vals))) + cor_vals = tuple(x for x in zip_vals if test_cor_values(con,x)>0) + + sql = (''' + SELECT id_value_text FROM {sch}.{tab} WHERE (id_value,id_text) IN {cor_vals} + ;''' + .format(sch='taxonomie',tab='bdc_statut_cor_text_values',cor_vals=cor_vals) + .replace('),)','))')) + + with con.begin() as cnx: + return cnx.execute(sql).all() + +def test_status_text(con,col,cd_doc): + sql = ''' + SELECT count({col}) FROM {sch}.{tab} WHERE {col} = '{cd_doc}' + ;'''.format(sch='taxonomie',tab='bdc_statut_text',col=col,cd_doc=cd_doc) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def insert_statut_text(con,cd_doc,doc): + if test_data(con,'bdc_statut_text','cd_doc',cd_doc['id_doc']) > 0: + # if test_status_text(con,'cd_doc',cd_doc) > 0: + print('ALERTE TEXT STATUS ALREADY EXISTS : ',doc) + else: + sql = ''' + INSERT INTO {sch}.{tab} (cd_type_statut,cd_doc,cd_sig,niveau_admin,lb_adm_tr,doc_url,enable) VALUES + ('AL',{cd_doc},'INSEED38','Département','Isère','{doc}',TRUE) + ;'''.format(sch='taxonomie',tab='bdc_statut_text',cd_doc=cd_doc['id_doc'],doc=doc) + with con_gn.begin() as cnx: + cnx.execute(sql) + + insert_status_cor_text_area(con,cd_doc['id_doc']) + insert_status_cor_text_values(con,cd_doc['id_doc'],cd_doc['id_values']) + +def get_cd_ref(con,cd_nom): + sql = ''' + SELECT cd_ref FROM {sch}.{tab} WHERE cd_nom = '{cd_nom}' + ;'''.format(sch='taxonomie',tab='taxref',cd_nom=cd_nom) + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def get_max_idstatuttaxo(con): + sql = ''' + SELECT max(id) FROM {sch}.{tab} + ;'''.format(sch='taxonomie',tab='bdc_statut_taxons') + with con.begin() as cnx: + return cnx.execute(sql).one()[0] + +def insert_status_taxo(con,cd_nom,cd_doc,status): + id_statut_cor = get_id_status_cor_text_values(con,cd_doc,status)[0][0] + cd_ref = get_cd_ref(con,cd_nom) + id_statut_taxo = get_max_idstatuttaxo(con) + 1 + + sql_check = ''' + SELECT count(id) FROM {sch}.{tab} + WHERE id_value_text = '{id_statut_cor}' AND cd_nom = '{cd_nom}' AND cd_ref = '{cd_ref}' + ;'''.format(sch='taxonomie',tab='bdc_statut_taxons',cd_ref=cd_ref,cd_nom=cd_nom,id_statut_cor=id_statut_cor) + with con.begin() as cnx: + check = cnx.execute(sql_check).one()[0] + + if check == 0: + sql = ''' + INSERT INTO {sch}.{tab} (id,id_value_text,cd_nom,cd_ref) VALUES + ('{id_statut_taxo}','{id_statut_cor}','{cd_nom}','{cd_ref}') + ;'''.format(sch='taxonomie',tab='bdc_statut_taxons',id_statut_taxo=id_statut_taxo,cd_ref=cd_ref,cd_nom=cd_nom,id_statut_cor=id_statut_cor) + with con_gn.begin() as cnx: + cnx.execute(sql) + +def get_status_type(con,col,status): + sql = ''' + SELECT * FROM {sch}.{tab} WHERE {col} = '{status}' + ;'''.format(sch='taxonomie',tab='bdc_statut_type',col=col,status=status) + return pd.read_sql(sql,con) + +def get_taxonomie(con,cd_nom): + if isinstance(cd_nom,int): + cd_nom = [cd_nom] + else: + cd_nom = list(cd_nom) + sql = ''' + SELECT cd_nom,cd_ref,cd_sup,lb_nom,lb_auteur,nom_complet_html,nom_valide,regne,phylum,classe,ordre,famille,group1_inpn,group2_inpn FROM {sch}.{tab} WHERE cd_nom IN {cd_nom} + ;'''.format(sch='taxonomie',tab='taxref',cd_nom=tuple(cd_nom)).replace(",)",")") + return pd.read_sql(sql,con) + + +if __name__ == "__main__": + + import pandas as pd + # Définition de la connection à la bdd GéoNature + from pycen import con_gn + + # Le premier feuillet du fichier Excel lu. + # Composition minimale: [CD_NOM,Statut, Source, Source_url] + # ATTENTION: + # - le CD_NOM doit correspondre au CD_NOM de la table taxref + # - Les taxons dont la Source_url est None ou NA seront ignorés + file = '/home/colas/Documents/9_PROJETS/6_GEONATURE/listes_alertes_isère.xlsx' + # Echelle administratif des listes à implémenter + niveau_admin = 'Département' + # Nom du niveau adminsitratif + lb_adm_tr = 'Isère' + # Code SIG du niveau adminnistratif + cd_sig = 'INSEED38' + + insert_status_alerte(con_gn) + # Dictionnaire des listes d’alerte à intégrer, + # identifiant et codes status respectivement concernés + cd_doc = { + 'Statut_de_conservation_des_poissons_et_écrevisses_en_Isère_2015':{'id_doc':999990,'id_values':['RE','CR','EN','VU','NT','LC','DD','NA',]}, + 'Liste_d’alerte_sur_les_orthoptères_menacés_en_Isère_2014':{'id_doc':999991,'id_values':['RE','CR','EN','VU','AS-1','AS-2','AS-3','LC','DD','NA']}, + 'Statuts_de_conservation_de_la_faune_sauvage_en_isere_2016':{'id_doc':999992,'id_values':['RE','CR','EN','VU','NT','LC','DD','NA','NE',]}, + 'Liste_rouge_des_Odonates_de_l’Isère_2013':{'id_doc':999993,'id_values':['RE','CR','EN','VU','NT','LC','DD','NA',]}, + 'Liste_rouge_des_lépidoprere_rhopaloceres_et_zygenes_de_l’Isère_2015':{'id_doc':999994,'id_values':['RE','CR','EN','VU','NT','LC','DD','NA','NE','EX']}, + } + + df = (pd.read_excel(file,keep_default_na=False) + .rename(columns={ + 'Statut':'code_statut', + 'CD_NOM':'cd_nom', + 'Source':'source', + 'Source_url':'doc_url', + })) + df = df.loc[df.doc_url!=''] + for d in df.source.unique(): + doc_url = df.loc[df.source==d,'doc_url'].unique()[0] + insert_statut_text(con_gn,cd_doc[d],doc_url) + + # INSERTION dans la table bdc_statut_taxons + # Boucle sur chaque taxon. Peu prendre quelques minutes. + [ + insert_status_taxo( + con = con_gn, + cd_nom = row.cd_nom, + cd_doc = cd_doc[row.source]['id_doc'], + status = row.code_statut) + for row in df.itertuples() + ] + + st = get_status_type(con_gn,'cd_type_statut','AL') + for c in st: + df[c] = st[c][0] + tax = get_taxonomie(con_gn,df['cd_nom']) + del tax['nom_valide'] + del df['source'] + del df['nom_français'] + del df['nom_latin'] + df = df.merge(tax,how='inner',on='cd_nom') + df['cd_sig'] = cd_sig + df['lb_adm_tr'] = lb_adm_tr + df['niveau_admin'] = niveau_admin + df.to_sql('bdc_statut',con_gn,schema='taxonomie',if_exists='append',index=False)