Merge branch 'main' into biometrie_hack

Author: davidsean

.github/workflows/documentation.yml

@@ -8,6 +8,8 @@ jobs:
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3
+        with:
+          python-version: '3.10' 
       - name: Install dependencies
         run: |
           pip install -r requirements.txt

andes_migrate/biodiversity.py

@@ -0,0 +1,194 @@
+
+
+from andes_migrate.andes_helper import AndesHelper
+from andes_migrate.projet_mollusque import ProjetMollusque
+from andes_migrate.table_peche_sentinelle import TablePecheSentinelle
+
+
+Catch_ID
+Date
+secteur
+fieldNumber #DarwinCore
+trait
+station
+verbatimIdentification #DarwinCore
+scientificName #DarwinCore
+lifeStage #DarwinCore
+identificationRemarks #DarwinCore
+taxonRemarks #DarwinCore
+organismRemarks	#DarwinCore
+associatedTaxa #DarwinCore
+cote_abond
+Abond
+Poids_g
+Abond_ech
+Poids_ech
+multiplier
+Abon_tot
+Poids_tot_g
+notes
+
+
+
+https://iml-science-1.ent.dfo-mpo.ca:8181/turbot/
+https://dmapps/fr/dfodots/collections/33/view/
+http://iml-science-1.ent.dfo-mpo.ca:8180/turbot/
+recordedBy
+class Biodiversity():
+
+    def __init__(self, andes_db: AndesHelper):
+
+        self.andes_db = andes_db
+
+        # call this form outside
+        self._init_rows()
+
+    def populate_data(self):
+        """Populate data: run all getters"""
+        # secteur	trait	no	taille	poids_vif	poids_muscle	poids_gonade	poids_visceres	sexe	espece	comment
+        if self.collection_name == 'Conserver le spécimen (Biométrie Centre)':
+            secteur = "Centre"
+        if self.collection_name == 'Conserver le spécimen (Biométrie Ouest)':
+            secteur = "Ouest"
+        sexe_dict={'0':"I",
+                   '1':'M',
+                   '2':'F',
+                   }
+        self.data["id_specimen"] = self._get_current_row_pk()
+        self.data["secteur"] = secteur
+        self.data["trait"] = self.get_ident_no_trait()
+        self.data["no"] = int(self.get_observation("Code Collection coquille").strip().split("-")[-1])
+        self.data["taille"] = self.get_observation("Longueur (non officiel)").replace(".",",")
+        self.data["poids_vif"] = self.get_observation("Poids vif").replace(".",",")
+        self.data["poids_muscle"] = self.get_observation("Poids du muscle").replace(".",",")
+        self.data["poids_gonade"] = self.get_observation("Poids des gonades").replace(".",",")
+        self.data["poids_visceres"] = self.get_observation("Poids des viscères").replace(".",",")
+        self.data["poids_gonade"] = self.get_observation("Poids des gonades").replace(".",",")
+        self.data["sexe"] = self.get_observation("Sexe")
+        self.data["comment"] = self.get_comment()
+
+    def __next__(self):
+        """
+        Increment to focus on next row
+        """
+        # print(self.table_name)
+        # print(f"{self._row_idx} of {len(self._row_list)}")
+        # print()
+        if self._row_idx is not None and self._row_list is not None:
+            if self._row_idx < len(self._row_list):
+                # increment first,  it'l be adjusted in _get_current_row_pk()
+                self._row_idx += 1
+                self.populate_data()
+
+                # self.write_row()
+                return self.data
+            else:
+                raise StopIteration
+        else:
+            self.logger.error("Row data not initialise, did you run _init_rows()?")
+            raise ValueError
+
+
+    def _init_rows(self):
+        """Initialisation method
+        This queries the Andes DB and creates a list of row entries to be added to the current table
+
+        After running this methods initialises the following attribute:
+        self._row_list
+        self._row_idx (hopefully to self._row_idx=0)
+
+        self._row_list will be populated with the specimen ids belonging in the collection
+        self._row_idx will start at 0
+
+        """
+        query = (
+                 "SELECT specimen_id "
+                 "FROM ecosystem_survey_observation "
+                 "LEFT JOIN ecosystem_survey_specimen "
+                 "ON ecosystem_survey_observation.specimen_id = ecosystem_survey_specimen.id "
+                 "LEFT JOIN ecosystem_survey_basket "
+                 "ON ecosystem_survey_specimen.basket_id = ecosystem_survey_basket.id "
+                 "LEFT JOIN ecosystem_survey_catch "
+                 "ON ecosystem_survey_basket.catch_id=ecosystem_survey_catch.id  "
+                 "LEFT JOIN shared_models_set "
+                 "ON shared_models_set.id=ecosystem_survey_catch.set_id "
+                 "LEFT JOIN shared_models_observationtype "
+                 "ON shared_models_observationtype.id=observation_type_id "
+                 f"WHERE shared_models_set.cruise_id = {self.proj._get_current_row_pk()} "
+                 f"AND (shared_models_observationtype.nom ='{self.collection_name}' AND observation_value=1) "
+        )
+        result = self.andes_db.execute_query(query)
+        self._assert_not_empty(result)
+        self._row_list = [specimen[0] for specimen in result]
+        self._row_idx = 0
+
+    # @validate_int()
+    # @log_results
+    def get_ident_no_trait(self) -> int:
+        """IDENT_NO_TRAIT INTEGER / NUMBER(5,0)
+        Numéro séquentiel d'identification du trait
+
+        Andes
+        -----
+        shared_models.set.set_number
+        """
+        specimen_pk = self._get_current_row_pk()
+        query = (
+            "SELECT shared_models_set.set_number "
+            "FROM ecosystem_survey_specimen "
+            "LEFT JOIN ecosystem_survey_basket "
+            "ON ecosystem_survey_specimen.basket_id=ecosystem_survey_basket.id "
+            "LEFT JOIN ecosystem_survey_catch "
+            "ON ecosystem_survey_basket.catch_id=ecosystem_survey_catch.id "
+            "LEFT JOIN shared_models_set "
+            "ON shared_models_set.id=ecosystem_survey_catch.set_id "
+            f"WHERE ecosystem_survey_specimen.id={specimen_pk} "
+        )
+        result = self.andes_db.execute_query(query)
+        self._assert_one(result)
+        to_return = result[0][0]
+        return to_return
+
+
+    def get_observation(self, name_fr):
+        specimen_pk = self._get_current_row_pk()
+        query = (
+            "SELECT observation_value "
+            "FROM ecosystem_survey_observation "
+            "LEFT JOIN shared_models_observationtype "
+            "ON ecosystem_survey_observation.observation_type_id=shared_models_observationtype.id "
+            f"WHERE ecosystem_survey_observation.specimen_id={specimen_pk} "
+            f"AND shared_models_observationtype.nom='{name_fr}' "
+        )
+        result = self.andes_db.execute_query(query)
+        try:
+            self._assert_one(result)
+            to_return = result[0][0]
+        except ValueError:
+            print(specimen_pk, name_fr,result)
+            to_return = None
+        if to_return is None:
+            to_return=""
+        return to_return
+    
+    def get_comment(self):
+        specimen_pk = self._get_current_row_pk()
+        query = (
+             "SELECT ecosystem_survey_specimen.comment "
+             "FROM ecosystem_survey_specimen "
+            f"WHERE ecosystem_survey_specimen.id={specimen_pk} "
+        )
+        result = self.andes_db.execute_query(query)
+        self._assert_one(result)
+        to_return = result[0][0]
+        if to_return is None:
+            to_return=""
+        to_return.replace("\n", " ")
+        to_return.replace("\r", " ")
+        return to_return
+
+
+
+
+
+