refactor: consolidate transferer classes to use ChemistryTransferer a…

core/initializers.py

@@ -16,13 +16,18 @@
 from pathlib import Path
 
 from fastapi_pagination import add_pagination
-from sqlalchemy import text
+from sqlalchemy import text, select
+from sqlalchemy.dialects.postgresql import insert
 from sqlalchemy.exc import DatabaseError
 
 from db import Base
 from db.engine import session_ctx
+from db.lexicon import (
+    LexiconCategory,
+    LexiconTerm,
+    LexiconTermCategoryAssociation,
+)
 from db.parameter import Parameter
-from services.lexicon_helper import add_lexicon_term, add_lexicon_category
 
 
 def init_parameter(path: str = None) -> None:
@@ -77,33 +82,112 @@ def init_lexicon(path: str = None) -> None:
 
         default_lexicon = json.load(f)
 
-    # populate lexicon
-
     with session_ctx() as session:
         terms = default_lexicon["terms"]
         categories = default_lexicon["categories"]
-        for category in categories:
-            try:
-                add_lexicon_category(session, category["name"], category["description"])
-            except DatabaseError as e:
-                print(f"Failed to add category {category['name']}: error: {e}")
-                session.rollback()
-                continue
-
-        for term_dict in terms:
-            try:
-                add_lexicon_term(
-                    session,
-                    term_dict["term"],
-                    term_dict["definition"],
-                    term_dict["categories"],
+        category_names = [category["name"] for category in categories]
+        existing_categories = dict(
+            session.execute(
+                select(LexiconCategory.name, LexiconCategory.id).where(
+                    LexiconCategory.name.in_(category_names)
                 )
-            except DatabaseError as e:
-                print(
-                    f"Failed to add term {term_dict['term']}: {term_dict['definition']} error: {e}"
+            ).all()
+        )
+        category_rows = [
+            {"name": category["name"], "description": category["description"]}
+            for category in categories
+            if category["name"] not in existing_categories
+        ]
+        if category_rows:
+            session.execute(
+                insert(LexiconCategory)
+                .values(category_rows)
+                .on_conflict_do_nothing(index_elements=["name"])
+            )
+            session.commit()
+            existing_categories = dict(
+                session.execute(
+                    select(LexiconCategory.name, LexiconCategory.id).where(
+                        LexiconCategory.name.in_(category_names)
+                    )
+                ).all()
+            )
+
+        term_names = [term_dict["term"] for term_dict in terms]
+        existing_terms = dict(
+            session.execute(
+                select(LexiconTerm.term, LexiconTerm.id).where(
+                    LexiconTerm.term.in_(term_names)
+                )
+            ).all()
+        )
+        term_rows = [
+            {"term": term_dict["term"], "definition": term_dict["definition"]}
+            for term_dict in terms
+            if term_dict["term"] not in existing_terms
+        ]
+        if term_rows:
+            session.execute(
+                insert(LexiconTerm)
+                .values(term_rows)
+                .on_conflict_do_nothing(index_elements=["term"])
+            )
+            session.commit()
+            existing_terms = dict(
+                session.execute(
+                    select(LexiconTerm.term, LexiconTerm.id).where(
+                        LexiconTerm.term.in_(term_names)
+                    )
+                ).all()
+            )
+
+        term_ids = [existing_terms.get(term_name) for term_name in term_names]
+        category_ids = [
+            existing_categories.get(category_name) for category_name in category_names
+        ]
+        existing_links = set()
+        if term_ids and category_ids:
+            existing_links = set(
+                session.execute(
+                    select(
+                        LexiconTermCategoryAssociation.term_id,
+                        LexiconTermCategoryAssociation.category_id,
+                    ).where(
+                        LexiconTermCategoryAssociation.term_id.in_(
+                            [term_id for term_id in term_ids if term_id is not None]
+                        ),
+                        LexiconTermCategoryAssociation.category_id.in_(
+                            [
+                                category_id
+                                for category_id in category_ids
+                                if category_id is not None
+                            ]
+                        ),
+                    )
+                ).all()
+            )
+
+        association_rows = []
+        for term_dict in terms:
+            term_id = existing_terms.get(term_dict["term"])
+            if term_id is None:
+                continue
+            for category in term_dict["categories"]:
+                category_id = existing_categories.get(category)
+                if category_id is None:
+                    continue
+                key = (term_id, category_id)
+                if key in existing_links:
+                    continue
+                association_rows.append(
+                    {"term_id": term_id, "category_id": category_id}
                 )
 
-                session.rollback()
+        if association_rows:
+            session.execute(
+                insert(LexiconTermCategoryAssociation).values(association_rows)
+            )
+            session.commit()
 
 
 def register_routes(app):

transfers/associated_data.py

@@ -169,18 +169,6 @@ def _normalize_point_id(value: str) -> str:
     def _normalize_location_id(value: str) -> str:
         return value.strip().lower()
 
-    def _dedupe_rows(
-        self, rows: list[dict[str, Any]], key: str
-    ) -> list[dict[str, Any]]:
-        """Dedupe rows by unique key to avoid ON CONFLICT loops. Later rows win."""
-        deduped = {}
-        for row in rows:
-            assoc_id = row.get(key)
-            if assoc_id is None:
-                continue
-            deduped[assoc_id] = row
-        return list(deduped.values())
-
     def _uuid_val(self, value: Any) -> Optional[UUID]:
         if value is None or pd.isna(value):
             return None

transfers/chemistry_sampleinfo.py

@@ -361,21 +361,6 @@ def bool_val(key: str) -> Optional[bool]:
             "SampleNotes": str_val("SampleNotes"),
         }
 
-    def _dedupe_rows(
-        self, rows: list[dict[str, Any]], key: str
-    ) -> list[dict[str, Any]]:
-        """
-        Deduplicate rows within a batch by the given key to avoid ON CONFLICT loops.
-        Later rows win.
-        """
-        deduped = {}
-        for row in rows:
-            oid = row.get(key)
-            if oid is None:
-                continue
-            deduped[oid] = row
-        return list(deduped.values())
-
 
 def run(batch_size: int = 1000) -> None:
     """Entrypoint to execute the transfer."""

transfers/field_parameters_transfer.py

@@ -31,20 +31,17 @@
 from __future__ import annotations
 
 from typing import Any, Optional
-from uuid import UUID
 
 import pandas as pd
 from sqlalchemy.dialects.postgresql import insert
 from sqlalchemy.orm import Session
 
-from db import NMA_Chemistry_SampleInfo, NMA_FieldParameters
-from db.engine import session_ctx
+from db import NMA_FieldParameters
 from transfers.logger import logger
-from transfers.transferer import Transferer
-from transfers.util import read_csv
+from transfers.transferer import ChemistryTransferer
 
 
-class FieldParametersTransferer(Transferer):
+class FieldParametersTransferer(ChemistryTransferer):
     """
     Transfer FieldParameters records to NMA_FieldParameters.
 
@@ -54,59 +51,6 @@ class FieldParametersTransferer(Transferer):
 
     source_table = "FieldParameters"
 
-    def __init__(self, *args, batch_size: int = 1000, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.batch_size = batch_size
-        # Cache: legacy UUID -> Integer id
-        self._sample_info_cache: dict[UUID, int] = {}
-        self._build_sample_info_cache()
-
-    def _build_sample_info_cache(self) -> None:
-        """Build cache of nma_sample_pt_id -> id for FK lookups."""
-        with session_ctx() as session:
-            sample_infos = (
-                session.query(
-                    NMA_Chemistry_SampleInfo.nma_sample_pt_id,
-                    NMA_Chemistry_SampleInfo.id,
-                )
-                .filter(NMA_Chemistry_SampleInfo.nma_sample_pt_id.isnot(None))
-                .all()
-            )
-            self._sample_info_cache = {
-                nma_sample_pt_id: csi_id for nma_sample_pt_id, csi_id in sample_infos
-            }
-        logger.info(
-            f"Built ChemistrySampleInfo cache with {len(self._sample_info_cache)} entries"
-        )
-
-    def _get_dfs(self) -> tuple[pd.DataFrame, pd.DataFrame]:
-        input_df = read_csv(self.source_table)
-        cleaned_df = self._filter_to_valid_sample_infos(input_df)
-        return input_df, cleaned_df
-
-    def _filter_to_valid_sample_infos(self, df: pd.DataFrame) -> pd.DataFrame:
-        """
-        Filter to only include rows where SamplePtID matches a ChemistrySampleInfo.
-
-        This prevents orphan records and ensures the FK constraint will be satisfied.
-        """
-        valid_sample_pt_ids = set(self._sample_info_cache.keys())
-        before_count = len(df)
-        mask = df["SamplePtID"].apply(
-            lambda value: self._uuid_val(value) in valid_sample_pt_ids
-        )
-        filtered_df = df[mask].copy()
-        after_count = len(filtered_df)
-
-        if before_count > after_count:
-            skipped = before_count - after_count
-            logger.warning(
-                f"Filtered out {skipped} FieldParameters records without matching "
-                f"ChemistrySampleInfo ({after_count} valid, {skipped} orphan records prevented)"
-            )
-
-        return filtered_df
-
     def _transfer_hook(self, session: Session) -> None:
         """
         Override transfer hook to use batch upsert for idempotent transfers.
@@ -206,55 +150,6 @@ def _row_to_dict(self, row) -> Optional[dict[str, Any]]:
             "AnalysesAgency": self._safe_str(row, "AnalysesAgency"),
         }
 
-    def _dedupe_rows(self, rows: list[dict[str, Any]]) -> list[dict[str, Any]]:
-        """Dedupe rows by unique key to avoid ON CONFLICT loops. Later rows win."""
-        deduped = {}
-        for row in rows:
-            key = row.get("nma_GlobalID")
-            if key is None:
-                continue
-            deduped[key] = row
-        return list(deduped.values())
-
-    def _safe_str(self, row, attr: str) -> Optional[str]:
-        """Safely get a string value, returning None for NaN."""
-        val = getattr(row, attr, None)
-        if val is None or pd.isna(val):
-            return None
-        return str(val)
-
-    def _safe_float(self, row, attr: str) -> Optional[float]:
-        """Safely get a float value, returning None for NaN."""
-        val = getattr(row, attr, None)
-        if val is None or pd.isna(val):
-            return None
-        try:
-            return float(val)
-        except (TypeError, ValueError):
-            return None
-
-    def _safe_int(self, row, attr: str) -> Optional[int]:
-        """Safely get an int value, returning None for NaN."""
-        val = getattr(row, attr, None)
-        if val is None or pd.isna(val):
-            return None
-        try:
-            return int(val)
-        except (TypeError, ValueError):
-            return None
-
-    def _uuid_val(self, value: Any) -> Optional[UUID]:
-        if value is None or pd.isna(value):
-            return None
-        if isinstance(value, UUID):
-            return value
-        if isinstance(value, str):
-            try:
-                return UUID(value)
-            except ValueError:
-                return None
-        return None
-
 
 def run(flags: dict = None) -> tuple[pd.DataFrame, pd.DataFrame, list]:
     """Entrypoint to execute the transfer."""

transfers/hydraulicsdata.py

@@ -100,7 +100,7 @@ def _transfer_hook(self, session: Session) -> None:
                 f"(orphan prevention)"
             )
 
-        rows = self._dedupe_rows(row_dicts, key="nma_GlobalID")
+        rows = self._dedupe_rows(row_dicts)
 
         insert_stmt = insert(NMA_HydraulicsData)
         excluded = insert_stmt.excluded
@@ -198,21 +198,6 @@ def as_int(key: str) -> Optional[int]:
             "Data Source": val("Data Source"),
         }
 
-    def _dedupe_rows(
-        self, rows: list[dict[str, Any]], key: str
-    ) -> list[dict[str, Any]]:
-        """
-        Deduplicate rows within a batch by the given key to avoid ON CONFLICT loops.
-        Later rows win.
-        """
-        deduped = {}
-        for row in rows:
-            gid = row.get(key)
-            if gid is None:
-                continue
-            deduped[gid] = row
-        return list(deduped.values())
-
 
 def run(batch_size: int = 1000) -> None:
     """Entrypoint to execute the transfer."""