bunch of changes
This commit is contained in:
@ -1,16 +1,25 @@
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# plugins/importer/routes.py
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import csv
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import io
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import difflib
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from flask import Blueprint, request, render_template, redirect, flash, session, url_for
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from flask_login import login_required, current_user
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from app.neo4j_utils import get_neo4j_handler
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from plugins.plant.models import db, Plant, PlantCommon, PlantScientific
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from flask_wtf.csrf import generate_csrf
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bp = Blueprint("importer", __name__, template_folder="templates")
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from app.neo4j_utils import get_neo4j_handler
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from plugins.plant.models import (
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db,
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Plant, PlantCommonName, PlantScientificName, PlantOwnershipLog
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)
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bp = Blueprint("importer", __name__, template_folder="templates", url_prefix="/import")
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REQUIRED_HEADERS = {"uuid", "plant_type", "name"}
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@bp.route("/import/", methods=["GET", "POST"])
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@bp.route("/", methods=["GET", "POST"])
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@login_required
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def upload():
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if request.method == "POST":
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@ -24,48 +33,58 @@ def upload():
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stream = io.StringIO(decoded)
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reader = csv.DictReader(stream)
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headers = set(reader.fieldnames)
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if not REQUIRED_HEADERS.issubset(headers):
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flash(f"Missing required CSV headers: {REQUIRED_HEADERS - headers}", "error")
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headers = set(reader.fieldnames or [])
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missing = REQUIRED_HEADERS - headers
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if missing:
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flash(f"Missing required CSV headers: {missing}", "error")
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return redirect(request.url)
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session["pending_rows"] = []
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review_list = []
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all_common = {c.name.lower(): c for c in PlantCommon.query.all()}
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all_scientific = {s.name.lower(): s for s in PlantScientific.query.all()}
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# Preload existing common/scientific names
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all_common = {c.name.lower(): c for c in PlantCommonName.query.all()}
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all_scientific = {s.name.lower(): s for s in PlantScientificName.query.all()}
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for row in reader:
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uuid = row.get("uuid")
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name = row.get("name", "").strip()
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sci_name = row.get("scientific_name", "").strip()
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plant_type = row.get("plant_type", "plant")
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mother_uuid = row.get("mother_uuid", "").strip()
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uuid_raw = row.get("uuid", "")
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uuid = uuid_raw.strip().strip('"')
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if not all([uuid, name, plant_type]):
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name_raw = row.get("name", "")
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name = name_raw.strip()
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sci_raw = row.get("scientific_name", "")
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sci_name = sci_raw.strip()
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plant_type = row.get("plant_type", "").strip() or "plant"
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mother_raw = row.get("mother_uuid", "")
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mother_uuid = mother_raw.strip().strip('"')
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# If any required field is missing, skip
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if not (uuid and name and plant_type):
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continue
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name_lc = name.lower()
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sci_lc = sci_name.lower()
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# Try fuzzy‐matching scientific names if needed
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suggested_match = None
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original_input = sci_name
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original_sci = sci_name
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name_lc = name.lower()
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sci_lc = sci_name.lower()
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# Fuzzy match scientific name
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if sci_lc and sci_lc not in all_scientific:
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close = difflib.get_close_matches(sci_lc, all_scientific.keys(), n=1, cutoff=0.85)
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if close:
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suggested_match = all_scientific[close[0]].name
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# Infer from common name
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if not sci_lc and name_lc in all_common:
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sci_obj = PlantScientific.query.filter_by(common_id=all_common[name_lc].id).first()
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sci_obj = PlantScientificName.query.filter_by(common_id=all_common[name_lc].id).first()
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if sci_obj:
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sci_name = sci_obj.name
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elif not sci_lc:
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close_common = difflib.get_close_matches(name_lc, all_common.keys(), n=1, cutoff=0.85)
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if close_common:
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match_name = close_common[0]
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sci_obj = PlantScientific.query.filter_by(common_id=all_common[match_name].id).first()
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sci_obj = PlantScientificName.query.filter_by(common_id=all_common[match_name].id).first()
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if sci_obj:
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suggested_match = sci_obj.name
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sci_name = sci_obj.name
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@ -74,17 +93,17 @@ def upload():
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"uuid": uuid,
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"name": name,
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"sci_name": sci_name,
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"original_sci_name": original_input,
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"original_sci_name": original_sci,
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"plant_type": plant_type,
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"mother_uuid": mother_uuid,
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"suggested_scientific_name": suggested_match,
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})
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if suggested_match and suggested_match != original_input:
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if suggested_match and suggested_match != original_sci:
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review_list.append({
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"uuid": uuid,
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"common_name": name,
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"user_input": original_input or "(blank)",
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"user_input": original_sci or "(blank)",
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"suggested_name": suggested_match
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})
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@ -92,44 +111,60 @@ def upload():
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return redirect(url_for("importer.review"))
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except Exception as e:
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flash(f"Import failed: {str(e)}", "error")
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flash(f"Import failed: {e}", "error")
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return redirect(request.url)
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return render_template("importer/upload.html")
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return render_template("importer/upload.html", csrf_token=generate_csrf())
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@bp.route("/import/review", methods=["GET", "POST"])
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@bp.route("/review", methods=["GET", "POST"])
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@login_required
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def review():
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rows = session.get("pending_rows", [])
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rows = session.get("pending_rows", [])
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review_list = session.get("review_list", [])
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if request.method == "POST":
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neo = get_neo4j_handler()
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neo = get_neo4j_handler()
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added = 0
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# —————————————————————————————————————————————
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# (1) CREATE MySQL records & MERGE every Neo4j node
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# —————————————————————————————————————————————
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for row in rows:
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uuid = row["uuid"]
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name = row["name"]
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sci_name = row["sci_name"]
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user_input = row["original_sci_name"]
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plant_type = row["plant_type"]
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mother_uuid = row["mother_uuid"]
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suggested = row.get("suggested_scientific_name")
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uuid_raw = row["uuid"]
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uuid = uuid_raw.strip().strip('"')
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common = PlantCommon.query.filter_by(name=name).first()
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name_raw = row["name"]
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name = name_raw.strip()
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sci_raw = row["sci_name"]
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sci_name = sci_raw.strip()
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plant_type = row["plant_type"].strip()
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mother_raw = row["mother_uuid"]
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mother_uuid = mother_raw.strip().strip('"')
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suggested = row.get("suggested_scientific_name")
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# ——— MySQL: PlantCommonName ———
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common = PlantCommonName.query.filter_by(name=name).first()
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if not common:
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common = PlantCommon(name=name)
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common = PlantCommonName(name=name)
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db.session.add(common)
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db.session.flush()
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accepted = request.form.get(f"confirm_{uuid}")
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sci_name_to_use = suggested if (suggested and accepted) else sci_name
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# ——— MySQL: PlantScientificName ———
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accepted = request.form.get(f"confirm_{uuid}")
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sci_to_use = suggested if (suggested and accepted) else sci_name
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scientific = PlantScientific.query.filter_by(name=sci_name_to_use).first()
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scientific = PlantScientificName.query.filter_by(name=sci_to_use).first()
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if not scientific:
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scientific = PlantScientific(name=sci_name_to_use, common_id=common.id)
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scientific = PlantScientificName(name=sci_to_use, common_id=common.id)
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db.session.add(scientific)
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db.session.flush()
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# ——— MySQL: Plant row ———
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plant = Plant.query.filter_by(uuid=uuid).first()
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if not plant:
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plant = Plant(
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@ -141,18 +176,60 @@ def review():
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is_verified=bool(accepted)
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)
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db.session.add(plant)
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db.session.flush() # so plant.id is available immediately
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added += 1
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neo.create_plant_node(uuid, name)
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if mother_uuid:
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neo.create_plant_node(mother_uuid, "Parent")
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neo.create_lineage(uuid, mother_uuid)
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# ——— MySQL: Create initial ownership log entry ———
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log = PlantOwnershipLog(
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plant_id = plant.id,
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user_id = current_user.id,
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date_acquired = datetime.utcnow(),
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transferred = False,
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is_verified = bool(accepted)
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)
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db.session.add(log)
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# ——— Neo4j: ensure a node exists for this plant UUID ———
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neo.create_plant_node(uuid, name)
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# Commit MySQL so that all Plant/OwnershipLog rows exist
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db.session.commit()
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# —————————————————————————————————————————————
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# (2) CREATE Neo4j LINEAGE relationships (child → parent). (Unchanged)
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# —————————————————————————————————————————————
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for row in rows:
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child_raw = row.get("uuid", "")
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child_uuid = child_raw.strip().strip('"')
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mother_raw = row.get("mother_uuid", "")
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mother_uuid = mother_raw.strip().strip('"')
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print(
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f"[DEBUG] row → child_raw={child_raw!r}, child_uuid={child_uuid!r}; "
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f"mother_raw={mother_raw!r}, mother_uuid={mother_uuid!r}"
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)
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if mother_uuid:
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neo.create_plant_node(mother_uuid, name="Unknown")
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neo.create_lineage(child_uuid, mother_uuid)
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else:
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print(f"[DEBUG] Skipping LINEAGE creation for child {child_uuid!r} (no mother_uuid)")
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# (Optional) Check two known UUIDs
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neo.debug_check_node("8b1059c8-8dd3-487a-af19-1eb548788e87")
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neo.debug_check_node("2ee2e0e7-69de-4d8f-abfe-4ed973c3d760")
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neo.close()
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flash(f"{added} plants added.", "success")
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flash(f"{added} plants added (MySQL) + Neo4j nodes/relations created.", "success")
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session.pop("pending_rows", None)
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session.pop("review_list", None)
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return redirect(url_for("importer.upload"))
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return render_template("importer/review.html", review_list=review_list)
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return render_template(
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"importer/review.html",
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review_list=review_list,
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csrf_token=generate_csrf()
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)
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@ -1,43 +1,38 @@
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{% extends "core_ui/base.html" %}
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{% block title %}Review Scientific Names{% endblock %}
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{% block title %}Review Matches{% endblock %}
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{% block content %}
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<div class="container py-4">
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<h2 class="mb-4">🔍 Review Suggested Matches</h2>
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<form method="POST">
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<input type="hidden" name="csrf_token" value="{{ csrf_token() }}">
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<input type="hidden" name="csrf_token" value="{{ csrf_token }}">
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{% if review_list %}
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<div class="table-responsive">
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<table class="table table-bordered align-middle">
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<thead>
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<p class="text-muted mb-3">Confirm the suggested scientific name replacements below. Only confirmed matches will override user input.</p>
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<table class="table table-bordered table-sm align-middle">
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<thead>
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<tr>
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<th>Common Name</th>
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<th>User Input</th>
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<th>Suggested Match</th>
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<th>Confirm</th>
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</tr>
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</thead>
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<tbody>
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{% for row in review_list %}
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<tr>
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<th>Common Name</th>
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<th>Suggested Scientific Name</th>
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<th>Confirm?</th>
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<td>{{ row.common_name }}</td>
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<td><code>{{ row.user_input }}</code></td>
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<td><code>{{ row.suggested_name }}</code></td>
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<td>
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<input type="checkbox" name="confirm_{{ row.uuid }}" value="1">
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</td>
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</tr>
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</thead>
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<tbody>
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{% for row in review_list %}
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<tr>
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<td>{{ row.common_name }}</td>
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<td>{{ row.suggested_name }}</td>
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<td>
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<input class="form-check-input" type="checkbox" name="confirm_{{ row.uuid }}" value="1" checked>
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</td>
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</tr>
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{% endfor %}
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</tbody>
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</table>
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</div>
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{% endfor %}
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</tbody>
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</table>
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{% else %}
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<p>No suggestions were made. You can safely continue.</p>
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<p>No matches found that need confirmation.</p>
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{% endif %}
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<div class="mt-3">
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<button type="submit" class="btn btn-primary">Confirm and Import</button>
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</div>
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<button type="submit" class="btn btn-primary mt-3">Finalize Import</button>
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</form>
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</div>
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{% endblock %}
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@ -1,10 +1,8 @@
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{% extends "core_ui/base.html" %}
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{% block title %}CSV Import{% endblock %}
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{% block content %}
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<div class="container py-4">
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<h2 class="mb-4">📤 Import Plant Data</h2>
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{% with messages = get_flashed_messages(with_categories=true) %}
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{% if messages %}
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{% for category, message in messages %}
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@ -15,14 +13,13 @@
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{% endfor %}
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{% endif %}
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{% endwith %}
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<form method="POST" enctype="multipart/form-data">
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<input type="hidden" name="csrf_token" value="{{ csrf_token() }}">
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<input type="hidden" name="csrf_token" value="{{ csrf_token }}">
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<div class="mb-3">
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<label for="file" class="form-label">Choose CSV File</label>
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<input type="file" class="form-control" id="file" name="file" required>
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<div class="form-text">
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Must include: <code>uuid</code>, <code>plant_type</code>, <code>name</code><br>
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Required: <code>uuid</code>, <code>plant_type</code>, <code>name</code><br>
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Optional: <code>scientific_name</code>, <code>mother_uuid</code>
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</div>
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</div>
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Reference in New Issue
Block a user