def get_all_nodes():
"""Get and return all type and place nodes"""
sql = """
SELECT
e.id,
e.name,
e.class_code,
e.description,
e.system_type,
e.created,
e.modified,
es.id AS super_id,
COUNT(e2.id) AS count,
COUNT(lp.id) AS count_property
FROM model.entity e
-- get super
LEFT JOIN model.link l ON e.id = l.domain_id AND l.property_code = %(property_code)s
LEFT JOIN model.entity es ON l.range_id = es.id
-- get count
LEFT JOIN model.link l2 ON e.id = l2.range_id
LEFT JOIN model.entity e2 ON l2.domain_id = e2.id AND
(l2.property_code = 'P2' OR
(l2.property_code = 'P89' AND e2.system_type = 'place location'))
LEFT JOIN model.link_property lp ON e.id = lp.range_id AND lp.property_code = 'P2'
WHERE e.class_code = %(class_code)s
AND (e.system_type IS NULL OR e.system_type != 'place location')
GROUP BY e.id, es.id
ORDER BY e.name;"""
g.cursor.execute(sql, {'class_code': 'E55', 'property_code': 'P127'})
debug_model['div sql'] += 1
types = g.cursor.fetchall()
g.cursor.execute(sql, {'class_code': 'E53', 'property_code': 'P89'})
debug_model['div sql'] += 1
places = g.cursor.fetchall()
nodes = OrderedDict()
for row in types + places:
node = Entity(row)
nodes[node.id] = node
node.count = row.count + row.count_property
node.count_subs = 0
node.subs = []
node.root = [row.super_id] if row.super_id else []
NodeMapper.populate_subs(nodes)
return nodes
def file_add(id_: int, view: str) -> Union[str, Response]:
entity = Entity.get_by_id(id_)
if request.method == 'POST':
if request.form['checkbox_values']:
entity.link_string('P67', request.form['checkbox_values'])
return redirect(f"{url_for('entity_view', id_=entity.id)}#tab-{view}")
return render_template(
'form.html',
form=build_table_form(view, entity.get_linked_entities('P67')),
title=entity.name,
crumbs=[
[_(entity.class_.view), url_for('index', view=entity.class_.view)],
entity,
f"{_('link')} {_(view)}"])
def insert_system(form: FlaskForm) -> Entity:
entity = Entity.insert('reference_system', form.name.data,
form.description.data)
Db.insert_system({
'entity_id':
entity.id,
'name':
entity.name,
'website_url':
form.website_url.data if form.website_url.data else None,
'resolver_url':
form.resolver_url.data if form.resolver_url.data else None
})
return ReferenceSystem.get_all()[entity.id]
def insert_system(data: dict[str, str]) -> Entity:
entity = Entity.insert('reference_system', data['name'],
data['description'])
Db.insert_system({
'entity_id':
entity.id,
'name':
entity.name,
'website_url':
data['website_url'] if data['website_url'] else None,
'resolver_url':
data['resolver_url'] if data['resolver_url'] else None
})
return ReferenceSystem.get_all()[entity.id]
def display_file_api(filename: str) -> Any: # pragma: no cover
parser = image_parser.parse_args()
from pathlib import Path as Pathlib_path
entity = Entity.get_by_id(int(Pathlib_path(filename).stem), nodes=True)
license_ = None
for node in entity.nodes:
if node.root and node.root[-1] == Node.get_hierarchy('License').id:
license_ = node.name
if not license_:
raise AccessDeniedError
if parser['download']:
return send_file(str(app.config['UPLOAD_DIR']) + '/' + filename,
as_attachment=True)
return send_from_directory(app.config['UPLOAD_DIR'], filename)
def translation_update(id_: int) -> Union[str, Response]:
translation = Entity.get_by_id(id_, nodes=True)
form = build_form('source_translation', translation)
if form.validate_on_submit():
save(form, translation)
flash(_('info update'), 'info')
return redirect(url_for('entity_view', id_=translation.id))
return render_template(
'display_form.html',
form=form,
title=translation.name,
crumbs=[[_('source'), url_for('index', view='source')],
translation.get_linked_entity('P73', True), translation,
_('edit')])
def get_by_class_code_api(code: Union[str, List[str]],
parser: Dict[str, Any]) -> List[Entity]:
parameters = {
'codes': tuple(code if isinstance(code, list) else [code])
}
sql = Db.build_sql(nodes=True) + """
WHERE class_code IN %(codes)s {clause}
GROUP BY e.id
ORDER BY {order} {sort};""".format(
clause=Filter.get_filter(parameters=parameters, parser=parser),
order=', '.join(parser['column']),
sort=parser['sort'])
g.cursor.execute(sql, parameters)
return [Entity(row) for row in g.cursor.fetchall()]
def translation_insert(source_id: int) -> Union[str, Response]:
source = Entity.get_by_id(source_id)
form = build_form('source_translation')
if form.validate_on_submit():
translation = save(form, source=source)
flash(_('entity created'), 'info')
if hasattr(form, 'continue_') and form.continue_.data == 'yes':
return redirect(url_for('translation_insert', source_id=source.id))
return redirect(url_for('entity_view', id_=translation.id))
return render_template(
'display_form.html',
form=form,
crumbs=[[_('source'), url_for('index', view='source')], source,
f"+ {uc_first(_('text'))}"])
def note_insert(entity_id: int) -> Union[str, Response]:
entity = Entity.get_by_id(entity_id)
form = build_form('note')
if form.validate_on_submit():
User.insert_note(entity_id, form.description.data, form.public.data)
flash(_('note added'), 'info')
return redirect(f"{url_for('view', id_=entity.id)}#tab-note")
return render_template('display_form.html',
form=form,
entity=entity,
crumbs=[[
_(entity.class_.view),
url_for('index', view=entity.class_.view)
], entity, f"+ {uc_first(_('note'))}"])
def get_by_system_class(classes: str, parser: Dict[str,
Any]) -> List[Entity]:
parameters = {
'class': tuple(classes if isinstance(classes, list) else [classes])
}
sql = Db.build_sql(nodes=True, aliases=True) + """
WHERE e.system_class
IN %(class)s {clause}
GROUP BY e.id ORDER BY {order} {sort};""".format(
clause=Filter.get_filter(parameters=parameters, parser=parser),
order=', '.join(parser['column']),
sort=parser['sort'])
g.cursor.execute(sql, parameters)
return [Entity(row) for row in g.cursor.fetchall()]
def member_insert(origin_id: int,
code: str = 'member') -> Union[str, Response]:
origin = Entity.get_by_id(origin_id)
form = build_form('actor_function', code=code)
form.member_origin_id.data = origin.id
if form.validate_on_submit():
Transaction.begin()
try:
member_field = getattr(form, 'actor') \
if code == 'member' else getattr(form, 'group')
for actor in Entity.get_by_ids(ast.literal_eval(
member_field.data)):
if code == 'membership':
link_ = Link.get_by_id(
actor.link('P107', origin, form.description.data)[0])
else:
link_ = Link.get_by_id(
origin.link('P107', actor, form.description.data)[0])
link_.set_dates(process_form_dates(form))
link_.type = get_link_type(form)
link_.update()
Transaction.commit()
flash(_('entity created'), 'info')
except Exception as e: # pragma: no cover
Transaction.rollback()
logger.log('error', 'database', 'transaction failed', e)
flash(_('error transaction'), 'error')
if hasattr(form, 'continue_') and form.continue_.data == 'yes':
return redirect(
url_for('member_insert', origin_id=origin_id, code=code))
return redirect(f"{url_for('view', id_=origin.id)}"
f"#tab-member{'' if code == 'member' else '-of'}")
return render_template(
'display_form.html',
form=form,
crumbs=[[_('actor'), url_for('index', view='actor')], origin,
_('member')])
def admin_check_link_duplicates(
delete: Optional[str] = None) -> Union[str, Response]:
if delete:
delete_count = str(Link.delete_link_duplicates())
logger.log('info', 'admin', 'Deleted duplicate links: ' + delete_count)
flash(_('deleted links') + ': ' + delete_count, 'info')
return redirect(url_for('admin_check_link_duplicates'))
table = Table([
'domain', 'range', 'property_code', 'description', 'type_id',
'begin_from', 'begin_to', 'begin_comment', 'end_from', 'end_to',
'end_comment', 'count'
])
for row in Link.check_link_duplicates():
table.rows.append([
link(Entity.get_by_id(row['domain_id'])),
link(Entity.get_by_id(row['range_id'])),
link(g.properties[row['property_code']]), row['description'],
link(g.nodes[row['type_id']]) if row['type_id'] else '',
format_date(row['begin_from']),
format_date(row['begin_to']), row['begin_comment'],
format_date(row['end_from']),
format_date(row['end_to']), row['end_comment'], row['count']
])
duplicates = False
if table.rows:
duplicates = True
else: # If no exact duplicates where found check if single types are used multiple times
table = Table(
['entity', 'class', 'base type', 'incorrect multiple types'],
rows=Link.check_single_type_duplicates())
return render_template(
'admin/check_link_duplicates.html',
table=table,
duplicates=duplicates,
title=_('admin'),
crumbs=[[_('admin'), url_for('admin_index') + '#tab-data'],
_('check link duplicates')])
def relation_update(id_: int, origin_id: int) -> Union[str, Response]:
link_ = Link.get_by_id(id_)
domain = Entity.get_by_id(link_.domain.id)
range_ = Entity.get_by_id(link_.range.id)
origin = range_ if origin_id == range_.id else domain
related = range_ if origin_id == domain.id else domain
form = build_form('actor_actor_relation', link_)
if form.validate_on_submit():
Transaction.begin()
try:
link_.delete()
if form.inverse.data:
link_ = Link.get_by_id(
related.link('OA7', origin, form.description.data)[0])
else:
link_ = Link.get_by_id(
origin.link('OA7', related, form.description.data)[0])
link_.set_dates(form)
link_.type = get_link_type(form)
link_.update()
Transaction.commit()
flash(_('info update'), 'info')
except Exception as e: # pragma: no cover
Transaction.rollback()
logger.log('error', 'database', 'transaction failed', e)
flash(_('error transaction'), 'error')
return redirect(
url_for('entity_view', id_=origin.id) + '#tab-relation')
if origin.id == range_.id:
form.inverse.data = True
return render_template(
'display_form.html',
form=form,
title=_('relation'),
crumbs=[[_('actor'), url_for('index', view='actor')], origin, related,
_('edit')])
def test_duplicates(self) -> None:
with app.app_context():
with app.test_request_context():
app.preprocess_request() # type: ignore
event = Entity.insert('acquisition', 'Event Horizon')
source = Entity.insert('source', 'Tha source')
source.link('P67', event)
source.link('P67', event)
source_type = Type.get_hierarchy('Source')
source.link('P2', g.types[source_type.subs[0]])
source.link('P2', g.types[source_type.subs[1]])
rv = self.app.get(url_for('admin_check_link_duplicates'))
assert b'Event Horizon' in rv.data
rv = self.app.get(
url_for('admin_check_link_duplicates', delete='delete'),
follow_redirects=True)
assert b'Remove' in rv.data
rv = self.app.get(
url_for(
'admin_delete_single_type_duplicate',
entity_id=source.id,
type_id=source_type.subs[0]),
follow_redirects=True)
assert b'Congratulations, everything looks fine!' in rv.data
def get_by_object(object_: Entity) -> Dict[int, Overlay]:
ids = [object_.id]
# Get overlays of parents
if object_.system_type == 'find':
stratigraphic_unit = object_.get_linked_entity_safe('P46', True)
ids.append(stratigraphic_unit.id)
feature = stratigraphic_unit.get_linked_entity_safe('P46', True)
ids.append(feature.id)
ids.append(feature.get_linked_entity_safe('P46', True).id)
elif object_.system_type == 'stratigraphic unit':
feature = object_.get_linked_entity_safe('P46', True)
ids.append(feature.id)
ids.append(feature.get_linked_entity_safe('P46', True).id)
elif object_.system_type == 'feature':
ids.append(object_.get_linked_entity_safe('P46', True).id)
sql = """
SELECT o.id, o.place_id, o.image_id, o.bounding_box, i.name
FROM web.map_overlay o
JOIN model.entity i ON o.image_id = i.id
WHERE o.place_id IN %(place_ids)s;"""
g.execute(sql, {'place_ids': tuple(ids)})
return {row.image_id: Overlay(row) for row in g.cursor.fetchall()}
def delete_entity(id_: int) -> Optional[str]:
url = None
entity = Entity.get_by_id(id_)
if not is_authorized(entity.class_.write_access):
abort(403) # pragma: no cover
if isinstance(entity, ReferenceSystem):
if entity.system:
abort(403)
if entity.forms:
flash(_('Deletion not possible if forms are attached'), 'error')
return url_for('entity_view', id_=id_)
if entity.class_.view in ['artifact', 'place']:
if entity.get_linked_entities('P46'):
flash(_('Deletion not possible if subunits exists'), 'error')
return url_for('entity_view', id_=id_)
parent = None if entity.class_.name == 'place' else entity.get_linked_entity(
'P46', True)
entity.delete()
logger.log_user(id_, 'delete')
flash(_('entity deleted'), 'info')
if parent:
tab = '#tab-' + entity.class_.name.replace('_', '-')
url = url_for('entity_view', id_=parent.id) + tab
else:
Entity.delete_(id_)
logger.log_user(id_, 'delete')
flash(_('entity deleted'), 'info')
if entity.class_.name == 'file':
try:
path = get_file_path(id_)
if path: # Only delete file on disk if it exists to prevent a missing file error
path.unlink()
except Exception as e: # pragma: no cover
logger.log('error', 'file', 'file deletion failed', e)
flash(_('error file delete'), 'error')
return url
def populate_reference_systems(form: FlaskForm, item: Entity) -> None:
system_links = {
# Can't use isinstance for class_ check here
link_.domain.id: link_
for link_ in item.get_links('P67', True)
if link_.domain.class_.name == 'reference_system'
}
for field in form:
if field.id.startswith('reference_system_id_'):
system_id = int(field.id.replace('reference_system_id_', ''))
if system_id in system_links:
field.data = system_links[system_id].description
precision_field = getattr(
form, f'reference_system_precision_{system_id}')
precision_field.data = str(system_links[system_id].type.id)
def add_tabs_for_file(entity: Entity) -> dict[str, Tab]:
tabs = {}
for name in [
'source', 'event', 'actor', 'place', 'feature',
'stratigraphic_unit', 'artifact', 'human_remains', 'reference',
'type'
]:
tabs[name] = Tab(name, entity=entity)
entity.image_id = entity.id if get_file_path(entity.id) else None
for link_ in entity.get_links('P67'):
range_ = link_.range
data = get_base_table_data(range_)
data.append(remove_link(range_.name, link_, entity,
range_.class_.name))
tabs[range_.class_.view].table.rows.append(data)
for link_ in entity.get_links('P67', True):
data = get_base_table_data(link_.domain)
data.append(link_.description)
data.append(
edit_link(url_for('link_update', id_=link_.id,
origin_id=entity.id)))
data.append(remove_link(link_.domain.name, link_, entity, 'reference'))
tabs['reference'].table.rows.append(data)
return tabs
def overlay_update(id_: int) -> Union[str, Response]:
overlay = Overlay.get_by_id(id_)
form = OverlayForm()
if form.validate_on_submit():
Overlay.update(form=form,
image_id=overlay.image_id,
place_id=overlay.place_id)
flash(_('info update'), 'info')
return redirect(
url_for('entity_view', id_=overlay.place_id) + '#tab-file')
bounding = ast.literal_eval(overlay.bounding_box)
form.top_left_easting.data = bounding[0][1]
form.top_left_northing.data = bounding[0][0]
form.bottom_right_easting.data = bounding[1][1]
form.bottom_right_northing.data = bounding[1][0]
entity = Entity.get_by_id(overlay.place_id)
return render_template(
'overlay/update.html',
form=form,
overlay=overlay,
entity=entity,
crumbs=[[_('place'), url_for('index', view='place')], entity,
Entity.get_by_id(overlay.image_id),
_('update overlay')])
def get_invalid_cidoc_links() -> List[Dict[str, str]]:
from openatlas.models.entity import Entity
from openatlas.util.util import link
invalid_linking = []
for row in Db.get_cidoc_links():
property_ = g.properties[row['property_code']]
domain_is_valid = property_.find_object(
'domain_class_code',
row['domain_code'])
range_is_valid = property_.find_object(
'range_class_code',
row['range_code'])
if not domain_is_valid or not range_is_valid:
invalid_linking.append(row)
invalid_links = []
for item in invalid_linking:
for row in Db.get_invalid_links(item):
domain = Entity.get_by_id(row['domain_id'])
range_ = Entity.get_by_id(row['range_id'])
invalid_links.append({
'domain': f"{link(domain)} ({domain.cidoc_class.code})",
'property': link(g.properties[row['property_code']]),
'range': f"{link(range_)} ({range_.cidoc_class.code})"})
return invalid_links
def update_links(form: FlaskForm, entity: Entity) -> None:
for field in form:
if field.id.startswith('reference_system_id_'): # Recreate link
system = Entity.get_by_id(
int(field.id.replace('reference_system_id_', '')))
precision_field = getattr(
form,
field.id.replace('id_', 'precision_'))
Db.remove_link(system.id, entity.id)
if field.data:
system.link(
'P67',
entity,
field.data,
type_id=precision_field.data)
def get_place_info_for_update(entity: Entity) -> dict[str, Any]:
if entity.class_.view not in ['artifact', 'place']:
return {
'structure': None,
'gis_data': None,
'overlays': None,
'location': None
}
structure = get_structure(entity)
return {
'structure': structure,
'gis_data': Gis.get_all([entity], structure),
'overlays': Overlay.get_by_object(entity),
'location': entity.get_linked_entity_safe('P53', types=True)
}
def get(filename: str) -> Response: # pragma: no cover
entity = Entity.get_by_id(int(Pathlib_path(filename).stem), types=True)
license_ = get_license(entity)
if not license_:
raise AccessDeniedError
parser = image.parse_args()
if parser['download']:
return send_file(
f"{app.config['UPLOAD_DIR']}/{filename}",
as_attachment=True)
if parser['image_size'] and check_processed_image(filename):
size = app.config['IMAGE_SIZE'][parser['image_size']]
return send_from_directory(
f"{app.config['RESIZED_IMAGES']}/{size}",
filename)
return send_from_directory(app.config['UPLOAD_DIR'], filename)
def entity_add_reference(id_: int) -> Union[str, Response]:
entity = Entity.get_by_id(id_)
form = AddReferenceForm()
if form.validate_on_submit():
entity.link_string('P67',
form.reference.data,
description=form.page.data,
inverse=True)
return redirect(f"{url_for('entity_view', id_=id_)}#tab-reference")
form.page.label.text = uc_first(_('page / link text'))
return render_template('display_form.html',
entity=entity,
form=form,
crumbs=[[
_(entity.class_.view),
url_for('index', view=entity.class_.view)
], entity, f"{_('link')} {_('reference')}"])
def entity_add_source(id_: int) -> Union[str, Response]:
entity = Entity.get_by_id(id_)
if request.method == 'POST':
if request.form['checkbox_values']:
entity.link_string('P67',
request.form['checkbox_values'],
inverse=True)
return redirect(f"{url_for('entity_view', id_=id_)}#tab-source")
form = build_table_form('source',
entity.get_linked_entities('P67', inverse=True))
return render_template('form.html',
form=form,
title=entity.name,
crumbs=[[
_(entity.class_.view),
url_for('index', view=entity.class_.view)
], entity, f"{_('link')} {_('source')}"])
def get_subunits(id_: int) -> List[Dict[str, Any]]:
# Get first level of subunits
try:
entity = Entity.get_by_id(id_, nodes=True, aliases=True)
except Exception: # pragma: no cover
raise EntityDoesNotExistError
structure = get_structure(entity)
data = []
if not structure or not structure['subunits']:
raise InvalidSubunitError # pragma: no cover
for n in structure['subunits']:
data.append({
'id': n.id,
'label': n.name,
'url': url_for('entity', id_=n.id, _external=True)
})
return data
def save(form: FlaskForm,
node: Optional[Node] = None,
param: Optional[str] = None) -> Optional[Node]:
Transaction.begin()
try:
if node:
Node.update_hierarchy(node, form)
else:
node = Entity.insert('type', sanitize(form.name.data))
Node.insert_hierarchy(node, form, value_type=(param == 'value'))
node.update(form)
Transaction.commit()
except Exception as e: # pragma: no cover
Transaction.rollback()
logger.log('error', 'database', 'transaction failed', e)
flash(_('error transaction'), 'error')
abort(418)
return node
def get(filename: str) -> Response:
from pathlib import Path as Pathlib_path
entity = Entity.get_by_id(int(Pathlib_path(filename).stem), nodes=True)
license_ = None
for node in entity.nodes:
if node.root and node.root[-1] == Node.get_hierarchy('License').id:
license_ = node.name
if not license_:
raise AccessDeniedError
parser = image.parse_args()
if parser['download']:
return send_file(f"{app.config['UPLOAD_DIR']}/{filename}",
as_attachment=True)
if parser['image_size']:
size = app.config['IMAGE_SIZE'][parser['image_size']]
return send_from_directory(
f"{app.config['RESIZED_IMAGES']}/{size}", filename)
return send_from_directory(app.config['UPLOAD_DIR'], filename)
def get_untyped(hierarchy_id: int) -> list[Entity]:
hierarchy = g.types[hierarchy_id]
classes = hierarchy.classes
if hierarchy.name in ('Administrative unit', 'Historical place'):
classes = 'object_location' # pragma: no cover
untyped = []
for entity in Entity.get_by_class(classes, types=True):
linked = False
for type_ in entity.types:
if type_.root[0] == hierarchy_id:
linked = True
break
if not linked:
if classes == 'object_location': # pragma: no cover
if entity.get_linked_entity('P53', True):
untyped.append(entity)
else:
untyped.append(entity)
return untyped
def admin_check_similar() -> str:
form = SimilarForm()
form.classes.choices = [(x.name, x.label) for name, x in g.classes.items()
if x.label]
table = None
if form.validate_on_submit():
table = Table(['name', _('count')])
for sample in Entity.get_similar_named(form).values():
html = link(sample['entity'])
for entity in sample['entities']: # Table linebreaks workaround
html += f'<br><br><br><br><br>{link(entity)}'
table.rows.append([html, len(sample['entities']) + 1])
return render_template(
'admin/check_similar.html',
table=table,
form=form,
title=_('admin'),
crumbs=[[_('admin'), f"{url_for('admin_index')}#tab-data"],
_('check similar names')])
def search(data: dict[str, Any]) -> list[Entity]:
if not data['term']:
return []
if 'person' in data['classes'] \
or 'place' in data['classes'] \
or 'group' in data['classes']:
data['classes'].append('appellation')
entities = []
for row in Db.search(data['term'], data['classes'], data['desc'],
data['own'], current_user.id):
if row['openatlas_class_name'] == 'appellation':
entity = Link.get_linked_entity_safe(row['id'], 'P1', True)
if entity.class_.name not in data['classes']:
continue
else:
entity = Entity(row)
if entity and check_dates(entity, data):
entities.append(entity)
return list({d.id: d for d in entities}.values()) # Remove duplicates