Add region parameters for taxref import migrate

apptax/taxonomie/commands/migrate_taxref/commands_v17.py

@@ -73,11 +73,12 @@ def test_changes_detection(keep_cdnom):
 @click.option("--keep-oldtaxref", is_flag=True)
 @click.option("--keep-oldbdc", is_flag=True)
 @click.option("--keep-cdnom", is_flag=True)
+@click.option("--region", type=str)
 @click.option("--script_predetection", type=click.Path(exists=True))
 @click.option("--script_postdetection", type=click.Path(exists=True))
 @with_appcontext
 def apply_changes(
-    keep_oldtaxref, keep_oldbdc, keep_cdnom, script_predetection, script_postdetection
+    keep_oldtaxref, keep_oldbdc, keep_cdnom, region, script_predetection, script_postdetection
 ):
     """Procédure de migration de taxref vers la version 17
          Application des changements import des données dans les tables taxref et bdc_status
@@ -114,7 +115,7 @@ def apply_changes(
                 "3.2_alter_taxref_data.sql",
             )
         )
-        db.session.execute(query, {"keep_cd_nom": keep_cdnom})
+        db.session.execute(query, {"keep_cd_nom": keep_cdnom, "region": region})
         db.session.commit()
         logger.info("it's done")
     except Exception as e:

apptax/taxonomie/commands/migrate_taxref/data/specific_taxref_v15_v16/3.2_alter_taxref_data.sql

@@ -20,12 +20,9 @@ ALTER TABLE taxonomie.cor_nom_liste DROP CONSTRAINT cor_nom_listes_taxref_fkey;
 ------------------------------------------------
 ------------------------------------------------
 
--- CORRECTION
-UPDATE taxonomie.import_taxref SET fr = NULL WHERE fr='';
-
 -- UPDATE EXISTING CD_NOM
 UPDATE taxonomie.taxref t
-   SET id_statut = fr, id_habitat = it.habitat::int, id_rang = it.rang, regne = it.regne, phylum = it.phylum,
+   SET id_habitat = it.habitat::int, id_rang = it.rang, regne = it.regne, phylum = it.phylum,
        classe = it.classe, ordre = it.ordre, famille = it.famille, cd_taxsup = it.cd_taxsup,
        cd_sup = it.cd_sup, cd_ref = it.cd_ref,
        lb_nom = it.lb_nom, lb_auteur = it.lb_auteur, nom_complet = it.nom_complet,
@@ -38,11 +35,11 @@ WHERE it.cd_nom  = t.cd_nom;
 
 -- ADD NEW CD_NOM
 INSERT INTO taxonomie.taxref(
-            cd_nom, id_statut, id_habitat, id_rang, regne, phylum, classe,
+            cd_nom, id_habitat, id_rang, regne, phylum, classe,
             ordre, famille, cd_taxsup, cd_sup, cd_ref, lb_nom, lb_auteur,
             nom_complet, nom_complet_html, nom_valide, nom_vern, nom_vern_eng,
             group1_inpn, group2_inpn, sous_famille, tribu, url, group3_inpn)
-SELECT it.cd_nom, it.fr, it.habitat::int, it.rang, it.regne, it.phylum, it.classe,
+SELECT it.cd_nom,it.habitat::int, it.rang, it.regne, it.phylum, it.classe,
     it.ordre, it.famille, it.cd_taxsup, it.cd_sup, it.cd_ref, it.lb_nom, it.lb_auteur,
     it.nom_complet, it.nom_complet_html, it.nom_valide, it.nom_vern, it.nom_vern_eng,
     it.group1_inpn, it.group2_inpn, it.sous_famille, it.tribu, it.url, it.group3_inpn
@@ -51,6 +48,29 @@ LEFT OUTER JOIN taxonomie.taxref t
 ON it.cd_nom = t.cd_nom
 WHERE t.cd_nom IS NULL;
 
+-- Regional Status
+
+DO $$ BEGIN   
+   IF :region = 'gf' THEN UPDATE taxonomie.import_taxref SET gf = NULL Where gf=''; UPDATE taxonomie.taxref t SET id_statut = it.gf  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'mar' THEN UPDATE taxonomie.import_taxref SET mar = NULL Where mar=''; UPDATE taxonomie.taxref t SET id_statut = it.mar  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'gua' THEN UPDATE taxonomie.import_taxref SET gua = NULL Where gua=''; UPDATE taxonomie.taxref t SET id_statut = it.gua  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'sm' THEN UPDATE taxonomie.import_taxref SET sm = NULL Where sm=''; UPDATE taxonomie.taxref t SET id_statut = it.sm  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'sb' THEN UPDATE taxonomie.import_taxref SET sb = NULL Where sb=''; UPDATE taxonomie.taxref t SET id_statut = it.sb  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'spm' THEN UPDATE taxonomie.import_taxref SET spm = NULL Where spm=''; UPDATE taxonomie.taxref t SET id_statut = it.spm  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'may' THEN UPDATE taxonomie.import_taxref SET may = NULL Where may=''; UPDATE taxonomie.taxref t SET id_statut = it.may  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'epa' THEN UPDATE taxonomie.import_taxref SET epa = NULL Where epa=''; UPDATE taxonomie.taxref t SET id_statut = it.epa  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'reu' THEN UPDATE taxonomie.import_taxref SET reu = NULL Where reu=''; UPDATE taxonomie.taxref t SET id_statut = it.reu  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'sa' THEN UPDATE taxonomie.import_taxref SET sa = NULL Where sa=''; UPDATE taxonomie.taxref t SET id_statut = it.sa  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'ta' THEN UPDATE taxonomie.import_taxref SET ta = NULL Where ta=''; UPDATE taxonomie.taxref t SET id_statut = it.ta  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'taaf' THEN UPDATE taxonomie.import_taxref SET taaf = NULL Where taaf=''; UPDATE taxonomie.taxref t SET id_statut = it.taaf  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'pf' THEN UPDATE taxonomie.import_taxref SET pf = NULL Where pf=''; UPDATE taxonomie.taxref t SET id_statut = it.pf  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'nc' THEN UPDATE taxonomie.import_taxref SET nc = NULL Where nc=''; UPDATE taxonomie.taxref t SET id_statut = it.nc  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'wf' THEN UPDATE taxonomie.import_taxref SET wf = NULL Where wf=''; UPDATE taxonomie.taxref t SET id_statut = it.wf  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSIF :region = 'cli' THEN UPDATE taxonomie.import_taxref SET cli = NULL Where cli=''; UPDATE taxonomie.taxref t SET id_statut = it.cli  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+   ELSE UPDATE taxonomie.import_taxref SET fr = NULL WHERE fr=''; UPDATE taxonomie.taxref t SET id_statut = it.fr  FROM taxonomie.import_taxref it WHERE it.cd_nom  = t.cd_nom;
+END IF;
+END $$;
+
 -- DELETE MISSING CD_NOM if not keep_cdnom is specify
 DO $$ BEGIN
     IF  :keep_cd_nom = FALSE THEN

apptax/taxonomie/commands/taxref_v15_v16.py

@@ -55,7 +55,7 @@ def import_bdc_statuts_v17(logger):
     )
 
 
-def import_taxref(logger, num_version, taxref_archive_name, taxref_file_name):
+def import_taxref(logger, num_version, taxref_archive_name, taxref_file_name, region="fr"):
     with open_remote_file(base_url, taxref_archive_name, open_fct=ZipFile) as archive:
         with archive.open("habitats_note.csv") as f:
             logger.info(f"Insert TAXREF v{num_version} habitats…")
@@ -114,7 +114,7 @@ def import_taxref(logger, num_version, taxref_archive_name, taxref_file_name):
                 ),
                 source_cols=(
                     "cd_nom::int",
-                    "NULLIF(fr, '') as id_statut",
+                    f"NULLIF({region}, '') as id_statut",
                     "habitat::int as id_habitat",
                     "rang as id_rang",
                     "regne",
@@ -146,15 +146,17 @@ def import_taxref(logger, num_version, taxref_archive_name, taxref_file_name):
 
 @click.command()
 @click.option("--skip-bdc-statuts", is_flag=True, help="Skip import of BDC Statuts")
+@click.option("--region", type=str, default="fr", help="Region : column status")
 @with_appcontext
-def import_v15(skip_bdc_statuts):
+def import_v15(skip_bdc_statuts, region):
     logger = logging.getLogger()
 
     import_taxref(
         logger,
         num_version="15",
         taxref_archive_name="TAXREF_v15_2021.zip",
         taxref_file_name="TAXREFv15.txt",
+        region=region,
     )
 
     if not skip_bdc_statuts:
@@ -171,15 +173,17 @@ def import_v15(skip_bdc_statuts):
 
 @click.command()
 @click.option("--skip-bdc-statuts", is_flag=True, help="Skip import of BDC Statuts")
+@click.option("--region", type=str, default="fr", help="Region : column status")
 @with_appcontext
-def import_v16(skip_bdc_statuts):
+def import_v16(skip_bdc_statuts, region):
     logger = logging.getLogger()
 
     import_taxref(
         logger,
         num_version="16",
         taxref_archive_name="TAXREF_v16_2022.zip",
         taxref_file_name="TAXREFv16.txt",
+        region=region,
     )
 
     if not skip_bdc_statuts:
@@ -196,15 +200,17 @@ def import_v16(skip_bdc_statuts):
 
 @click.command()
 @click.option("--skip-bdc-statuts", is_flag=True, help="Skip import of BDC Statuts")
+@click.option("--region", type=str, default="fr", help="Region : column status")
 @with_appcontext
-def import_v17(skip_bdc_statuts):
+def import_v17(skip_bdc_statuts, region):
     logger = logging.getLogger()
 
     import_taxref(
         logger,
         num_version="17",
         taxref_archive_name="TAXREF_v17_2024.zip",
         taxref_file_name="TAXREFv17.txt",
+        region=region,
     )
 
     if not skip_bdc_statuts: