fixed: taibol

app/blueprints/admin.py

@@ -416,8 +416,8 @@ def index():
         #return current_app.login_manager.unauthorized()
         return redirect(url_for('base.login'))
 
-    site = current_user.organization
-    collection_ids = site.collection_ids
+    site = current_user.site
+    collection_ids = [x.id for x in site.collections]
 
     record_query = session.query(
         Collection.label, func.count(Record.collection_id)
@@ -428,7 +428,7 @@ def index():
     ).group_by(
         Collection
     ).filter(
-        Collection.organization_id==site.id
+        Collection.site_id==site.id
     ).order_by(
         Collection.sort, Collection.id
     )
@@ -442,7 +442,7 @@ def index():
     ).group_by(
         Collection
     ).filter(
-        Collection.organization_id==site.id
+        Collection.site_id==site.id
     ).order_by(
         Collection.sort, Collection.id
     )
@@ -459,7 +459,7 @@ def index():
     ).group_by(
         Collection
     ).filter(
-        Collection.organization_id==site.id
+        Collection.site_id==site.id
     ).order_by(
         Collection.sort, Collection.id
     )
@@ -517,7 +517,7 @@ def index():
     ).group_by(
         text('1')
     ).filter(
-        Collection.organization_id==site.id,
+        Collection.site_id==site.id,
         Record.created >= '2023-04-01'
     )
 
@@ -558,8 +558,8 @@ def index():
 @admin.route('/records/', methods=['GET'])
 @login_required
 def record_list():
-    site = current_user.organization
-
+    site = current_user.site
+    collection_ids = [x.id for x in site.collections]
     current_page = int(request.args.get('page', 1))
     q = request.args.get('q', '')
     collectors = request.args.get('collectors', '')
@@ -572,7 +572,7 @@ def record_list():
     stmt = make_admin_record_query(dict(request.args))
 
     # apply collection filter by site
-    stmt = stmt.filter(Record.collection_id.in_(site.collection_ids))
+    stmt = stmt.filter(Record.collection_id.in_(collection_ids))
 
     # print(stmt, flush=True)
     base_stmt = stmt
@@ -684,8 +684,9 @@ def record_list():
 @admin.route('/<collection_name>/records/create', methods=['GET', 'POST'])
 @login_required
 def record_create(collection_name):
-    site = current_user.organization
-    if collection := Collection.query.filter(Collection.id.in_(site.collection_ids), Collection.name==collection_name).one():
+    site = current_user.site
+    collection_ids = [x.id for x in site.collections]
+    if collection := Collection.query.filter(Collection.id.in_(collection_ids), Collection.name==collection_name).one():
         if request.method == 'GET':
             x =  get_record_all_options(collection.id)
             return render_template(
@@ -964,9 +965,10 @@ def dispatch_request(self):
 
         if filter_by := self.register.get('filter_by'):
             if filter_by == 'organization':
-                query = query.filter(self.register['model'].organization_id==current_user.organization_id)
+                query = query.filter(self.register['model'].site_id==current_user.site_id)
             elif filter_by == 'collection':
-                query = query.filter(self.register['model'].collection_id.in_(current_user.organization.collection_ids))
+                collection_ids = [x.id for x in site.collections]
+                query = query.filter(self.register['model'].collection_id.in_(collection_ids))
 
         #print(query, flush=True)
         if list_filter := self.register.get('list_filter'):
@@ -1036,8 +1038,8 @@ def dispatch_request(self, item_id):
             # create new instance
             if self.is_create is True:
                 if 'filter_by' in self.register:
-                    if self.register['filter_by'] == 'organization':
-                        self.item = self.register['model'](organization_id=current_user.organization_id)
+                    if self.register['filter_by'] == 'site':
+                        self.item = self.register['model'](site_id=current_user.site_id)
                     else:
                         self.item = self.register['model']()
                 else:

app/blueprints/admin_register.py

@@ -37,7 +37,7 @@
         'display': 'title',
         'resource_name': 'related_links',
         'model': RelatedLink,
-        'filter_by': 'organization',
+        'filter_by': 'site',
         'fields': {
             'title': { 'label': '標題' },
             'category': { 'label': '類別', 'type': 'select', 'foreign': RelatedLinkCategory, 'display': 'label'},
@@ -52,7 +52,7 @@
         'display': 'label',
         'resource_name': 'related_link_categories',
         'model': RelatedLinkCategory,
-        'filter_by': 'organization',
+        'filter_by': 'site',
         'fields': {
             'label': { 'label': '標題' },
             'name': { 'label': 'key' },
@@ -66,7 +66,7 @@
         'display': 'subject',
         'resource_name': 'articles',
         'model': Article,
-        'filter_by': 'organization',
+        'filter_by': 'site',
         'list_query': Article.query.order_by(desc(Article.publish_date)),
         'fields': {
             'subject': { 'label': '標題' },
@@ -82,7 +82,7 @@
         'display': 'label',
         'resource_name': 'article_categories',
         'model': ArticleCategory,
-        'filter_by': 'organization',
+        'filter_by': 'site',
         'fields': {
             'label': { 'label': '標題' },
             'name': { 'label': 'key' },
@@ -162,7 +162,7 @@
         'display': 'label',
         'resource_name': 'collections',
         'model': Collection,
-        'filter_by': 'organization',
+        'filter_by': 'site',
         'fields': {
             'label': { 'label': '標題' },
             'name': { 'label': 'key',},

app/blueprints/base.py

@@ -82,8 +82,8 @@
 
 @base.route('/portals')
 def portal_list():
-    site_list = Organization.query.filter(Organization.is_site==True).all()
-    return render_template('portal-list.html', site_list=site_list)
+    #site_list = Organization.query.filter(Organization.is_site==True).all()
+    return render_template('portal-list.html', site_list=[])
 
 @base.route('/search')
 def portal_search():
@@ -185,7 +185,7 @@ def login():
         username = request.form.get('username', '')
         passwd = request.form.get('passwd', '')
 
-        if u := User.query.filter(User.username==username, User.organization_id==site.id).first():
+        if u := User.query.filter(User.username==username, User.site_id==site.id).first():
             if check_password_hash(u.passwd, passwd):
                 login_user(u)
 

app/blueprints/frontpage.py

@@ -143,7 +143,7 @@ def specimen_detail_legacy(lang_code):
 #@frontpage.route('/specimens/<record_key>')
 def specimen_detail(record_key, lang_code):
     entity = None
-
+    # TODO: 判斷domain
     if 'ark:/' in record_key:
         #ark:<naan>/<key>
         naan, identifier = record_key.replace('ark:/', '').split('/')
@@ -167,6 +167,27 @@ def specimen_detail(record_key, lang_code):
 
     return abort(404)
 
+
+@frontpage.route('/records/<int:record_id>', defaults={'lang_code': DEFAULT_LANG_CODE})
+@frontpage.route('/<lang_code>/records/<int:record_id>')
+def record_detail(record_id, lang_code):
+    entity = None
+    # TODO: 判斷domain
+    try:
+        id_ = int(record_id)
+        entity = session.get(Record, id_)
+    except ValueError:
+        pass
+
+    if entity:
+        try:
+            return render_template(f'sites/{g.site.name}/specimen-detail.html', entity=entity)
+        except TemplateNotFound:
+            return render_template('specimen-detail.html', entity=entity)
+
+    return abort(404)
+
+
 @frontpage.route('/species/<int:taxon_id>', defaults={'lang_code': DEFAULT_LANG_CODE})
 @frontpage.route('/<lang_code>/species/<int:taxon_id>')
 def species_detail(taxon_id, lang_code):

app/helpers_data.py

@@ -1,6 +1,8 @@
 import csv
 import math
 import time
+import sqlite3
+import re
 
 from sqlalchemy import (
     select,
@@ -16,6 +18,70 @@
      make_specimen_query,
 )
 
+class MiniMatch(object):
+
+    cur = None
+    values = []
+    hand_match_data = None
+
+    def __init__(self, db_path):
+        self.db_path = db_path
+        con = sqlite3.connect("names.sqlite3")
+        self.cur = con.cursor()
+
+
+    def exec_query(self, sql):
+        rows = []
+        res = self.cur.execute(sql)
+        for row in res.fetchall():
+            data = {}
+            if fields := self.values:
+                for i,field in enumerate(fields):
+                    data[field] = row[i]
+                rows.append(data)
+            #rows.append(row)
+
+        return rows
+
+    def select(self, *args):
+        self.values = args
+
+    def match(self, name, limit):
+        '''
+        sql = """SELECT bm25(taicol_fts, 0, 10), t.name_id, t.simple_name\
+        FROM taicol t INNER JOIN taicol_fts s ON s.name_id = t.name_id\
+        WHERE taicol_fts match '{{simple_name}}: {name}' LIMIT {limit}""".format(name=name, limit=limit);
+        '''
+        fields = ', '.join([f'"{x}"'for x in self.values])
+        sql = f'SELECT {fields} from taicol where simple_name like \'%{name}%\''
+        results = self.exec_query(sql)
+
+        if len(results) > 0:
+            return results[0] # first one
+        elif self.hand_match_data:
+            self.hand_match(name)
+
+    def set_hand_match_data(self, data):
+        self.hand_match_data = data
+
+    def hand_match(self, name):
+        # global names resolver copy and paste rank
+        if ranks := self.hand_match_data.get(name):
+            taxon = {}
+            for i in ranks.split('>>'):
+                for k in ['kingdom', 'phylum', 'class', 'order', 'family', 'genus']:
+                    if f'({k})' in i:
+                        taxon[f'{k}_name'] = i.replace(f'({k})', '').strip()
+
+            taxon_zh = {}
+            for k, v in taxon.items():
+                taxon_zh[k] = v
+                if res := self.match(v, 1):
+                    if cname := res.get('common_name_c'):
+                        taxon_zh[f'{k}_zh'] = cname
+
+            print(name)
+            print(taxon_zh)
 
 def export_specimen_dwc_csv():
 
@@ -135,6 +201,6 @@ def import_phase0(data, collection_id):
     session.add(r)
     session.commit()
 
-    u = Unit(collection_id=collection_id, record_id=r.id)
-    session.add(u)
-    session.commit()
+    #u = Unit(collection_id=collection_id, record_id=r.id)
+    #session.add(u)
+    #session.commit()

app/helpers_query.py

@@ -71,7 +71,14 @@ def make_specimen_query(filtr):
 
         if ft := sd.get('filters'):
             for k, v in ft.items():
-                stmt = stmt.where(Record.source_data[k].astext == v)
+                if v == '__NOT_NULL__':
+                    stmt = stmt.where(
+                        Record.source_data[k].astext != ''
+                    )
+                else:
+                    stmt = stmt.where(
+                        Record.source_data[k].astext == v
+                    )
 
         return stmt
 

app/models/site.py

@@ -121,13 +121,6 @@ def find_by_host(host='foo'):
 
         return None
 
-    @staticmethod
-    def find_collection_ids(host):
-        if site := Site.find_by_host(host):
-            print(site.organizations,'aaa',site.id, flush=True)
-            return [x.collections for x in site.organizations]
-            #return site.get_collection_ids()
-
     def get_units(self, num):
         from app.models.collection import Unit, Collection, Record
         #units = Unit.query.filter(Unit.accession_number!='').order_by(func.random()).limit(4).all()

app/templates/admin/base.html

@@ -15,7 +15,7 @@
 	<nav class="uk-navbar uk-light" data-uk-navbar="mode:click; duration: 250">
 	  <div class="uk-navbar-left">
 	    <div class="uk-navbar-item uk-visible@m">
-	      <a href="{{ url_for('admin.index' ) }}">{{ current_user.organization.name }}</a>{#<a class="uk-logo" href="#"><img class="custom-logo" src="img/dashboard-logo-white.svg" alt=""></a>#}
+	      <a href="{{ url_for('admin.index' ) }}">{{ current_user.site.name|upper }}</a>{#<a class="uk-logo" href="#"><img class="custom-logo" src="img/dashboard-logo-white.svg" alt=""></a>#}
 	    </div>
             <ul class="uk-navbar-nav uk-visible@m">
               <li>
@@ -49,7 +49,7 @@
     </header>
     <aside id="left-col" class="uk-light uk-visible@m">
       <div class="left-logo uk-flex uk-flex-middle">
-	{#<img class="custom-logo" src="img/dashboard-logo.svg" alt="">#}{{ current_user.organization.code }}
+	{#<img class="custom-logo" src="img/dashboard-logo.svg" alt="">#}{{ current_user.site.title }}
       </div>
       {#
       <div class="left-content-box  content-box-dark">
@@ -60,7 +60,7 @@ <h4 class="uk-text-center uk-margin-remove-vertical text-light">John Doe</h4>
 	  <!-- user dropdown -->
 	  <div class="uk-dropdown user-drop" data-uk-dropdown="mode: click; pos: bottom-center; animation: uk-animation-slide-bottom-small; duration: 150">
 	    <ul class="uk-nav uk-dropdown-nav uk-text-left">
-              {% for collection in current_user.organization.collections %}
+              {% for collection in current_user.site.collections %}
               <li><a href="{{ url_for('admin.dashboard', collection=collection.name )}}">{{ collection.label }}</a></li>
               {% endfor %}
 	      <li><a href="#"><span data-uk-icon="icon: info"></span> Summary</a></li>

app/templates/admin/record-list-view.html

@@ -56,7 +56,7 @@
 <div>
   新增
   <div class="uk-button-group">
-    {% for collection in current_user.organization.collections %}
+    {% for collection in current_user.site.collections %}
     {# url_for('admin.record_create', collection_name=collection.name) #}
     <a href="{{ url_for('admin.create_frontend_collection_record', collection_id=collection.id) }}?uid={{ current_user.id }}&uname={{ current_user.username }}" class="uk-button uk-button-default">{{ collection.label }}</a>
     {% endfor %}
@@ -171,7 +171,7 @@
 <div>
   <p uk-margin>
     新增:
-    {% for collection in current_user.organization.collections %}
+    {% for collection in current_user.site.collections %}
     <a href="{{ url_for('admin.record_create', collection_name=collection.name) }}" class="uk-button uk-button-default">{{ collection.label }}</a>
     {% endfor %}
   </p>