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Merge pull request #400 from mboudet/fix_220
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Fix 387,313
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@mboudet
mboudet committed Jun 12, 2023
2 parents 92c3422 + c143f38 commit 0fe36d1
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Showing 15 changed files with 4,159 additions and 2,896 deletions.
3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,8 @@ This changelog was started for release 4.2.0.
- These enable 'anonymous query' mode, allowing anonymous users to send 'full queries'. See documentation
- Added 'overview' button in the query page. This button will show all 'selected' attributes, and allow users to quickly select the related entity.
- Added 'Abstraction' tab on the navbar. This will print the whole abstraction as a 2d/3d graph.
- Added 'distance' notion, using attribute link. This allows user to filter a value based on another value, with an optional modifier.
- Added 'custom distance' option for faldo relation (instead of just 'included_in' and 'overlap_with')

### Fixed

Expand All @@ -23,6 +25,7 @@ This changelog was started for release 4.2.0.
- Fixed profile update & password reset tab in user profile page
- Fixed Gff Faldo integration (was only integrating the last selected entity)
- Fixed an issue when using filters and an 'UNION' node
- Fixed an issue when launching a query with a 'linked' attribute toggled but unselected

### Changed

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74 changes: 60 additions & 14 deletions askomics/libaskomics/SparqlQuery.py
View file
Expand Up @@ -1116,7 +1116,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
pblock_ids = link["source"]["specialPreviousIds"]

# Position
if link["uri"] in ('included_in', 'overlap_with'):
if link["uri"] in ('included_in', 'overlap_with', 'distance_from'):

# If source of target is a special node, replace the id with the id of the concerned node
source_id = link["source"]["id"]
Expand Down Expand Up @@ -1192,6 +1192,16 @@ def build_query_from_json(self, preview=False, for_editor=False):
end2=end_2,
equalsign=equal_sign
), block_id, sblock_id, pblock_ids)
else:
for filter in link.get('faldoFilters', []):
modifier_string = ""
if filter['filterValue']:
modifier_string = " {} {}".format(filter['filterModifier'], filter['filterValue'])

start = start_1 if filter['filterStart'] == "start" else end_1
end = start_2 if filter['filterEnd'] == "start" else end_2
filter_string = "FILTER ( {} {} {} {} ) .".format(start, filter['filterSign'], end, modifier_string)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)

# Classic relation
else:
Expand Down Expand Up @@ -1225,7 +1235,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
"entity_label": attribute["entityLabel"],
"entity_id": attribute["nodeId"]
}
if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
linked_attributes.extend((attribute["id"], attribute["linkedWith"]))

# Browse attributes
Expand Down Expand Up @@ -1269,7 +1279,7 @@ def build_query_from_json(self, preview=False, for_editor=False):
else:
self.store_value("VALUES {} {{ {} }} .".format(subject, filter_value), block_id, sblock_id, pblock_ids)

if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
var_2 = self.format_sparql_variable("{}{}_uri".format(
attributes[attribute["linkedWith"]]["entity_label"],
attributes[attribute["linkedWith"]]["entity_id"]
Expand Down Expand Up @@ -1305,13 +1315,17 @@ def build_query_from_json(self, preview=False, for_editor=False):

if uri_val_list:
self.store_value("VALUES {} {{ {} }}".format(value_var, ' '.join(uri_val_list)), block_id, sblock_id, pblock_ids)
if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
var_2 = self.format_sparql_variable("{}{}_{}".format(
attributes[attribute["linkedWith"]]["entity_label"],
attributes[attribute["linkedWith"]]["entity_id"],
attributes[attribute["linkedWith"]]["label"]
))
var_to_replace.append((obj, var_2))
if not attribute.get('linkedNegative', False):
var_to_replace.append((obj, var_2))
else:
filter_string = "FILTER ( {} {} {} ) .".format(obj, "!=", var_2)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)

# Text
if attribute["type"] == "text":
Expand Down Expand Up @@ -1346,13 +1360,21 @@ def build_query_from_json(self, preview=False, for_editor=False):
self.store_filter("FILTER (str({}) != '{}') .".format(obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
else:
self.store_value("VALUES {} {{ '{}' }} .".format(obj, attribute["filterValue"]), block_id, sblock_id, pblock_ids)
if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
var_2 = self.format_sparql_variable("{}{}_{}".format(
attributes[attribute["linkedWith"]]["entity_label"],
attributes[attribute["linkedWith"]]["entity_id"],
attributes[attribute["linkedWith"]]["label"]
))
var_to_replace.append((obj, var_2))
if not (attribute.get('linkedNegative', False) or attribute.get('linkedFilterValue')):
var_to_replace.append((obj, var_2))
else:
filter = "!" if attribute.get('linkedNegative', False) else ""
regex_clause = "{} = {}".format(obj, var_2)
if attribute.get('linkedFilterValue'):
regex_clause = r"REGEX({}, REPLACE('{}', '\\$1', {}), 'i')".format(obj, attribute.get('linkedFilterValue', "$1"), var_2)
filter_string = "FILTER ( {} {} ) .".format(filter, regex_clause)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)

# Numeric
if attribute["type"] == "decimal":
Expand All @@ -1379,13 +1401,21 @@ def build_query_from_json(self, preview=False, for_editor=False):
else:
filter_string = "FILTER ( {} {} {} ) .".format(obj, filtr["filterSign"], filtr["filterValue"])
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)
if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
var_2 = self.format_sparql_variable("{}{}_{}".format(
attributes[attribute["linkedWith"]]["entity_label"],
attributes[attribute["linkedWith"]]["entity_id"],
attributes[attribute["linkedWith"]]["label"]
))
var_to_replace.append((obj, var_2))
if any([filter['filterSign'] == "=" and not filter['filterValue'] for filter in attribute.get('linkedFilters', [])]):
var_to_replace.append((obj, var_2))
else:
for filter in attribute.get('linkedFilters', []):
modifier_string = ""
if filter['filterValue']:
modifier_string = " {} {}".format(filter['filterModifier'], filter['filterValue'])
filter_string = "FILTER ( {} {} {} {} ) .".format(obj, filter['filterSign'], var_2, modifier_string)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)

if attribute["type"] == "date":
if attribute["visible"] or Utils.check_key_in_list_of_dict(attribute["filters"], "filterValue") or attribute["id"] in linked_attributes:
Expand All @@ -1410,14 +1440,25 @@ def build_query_from_json(self, preview=False, for_editor=False):
else:
filter_string = "FILTER ( {} {} '{}'^^xsd:date ) .".format(obj, filtr["filterSign"], val)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)
if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
var_2 = self.format_sparql_variable("{}{}_{}".format(
attributes[attribute["linkedWith"]]["entity_label"],
attributes[attribute["linkedWith"]]["entity_id"],
attributes[attribute["linkedWith"]]["label"]
))
var_to_replace.append((obj, var_2))

if any([filter['filterSign'] == "=" and not filter['filterValue'] for filter in attribute.get('linkedFilters', [])]):
var_to_replace.append((obj, var_2))
else:
for filter in attribute.get('linkedFilters', []):
modifier_string = ""
if filter['filterValue']:
# Issue with virtuoso: engine-specific syntax for now (convert days to seconds)
if self.settings.get('triplestore', 'triplestore') == "virtuoso":
modifier_string = " {} {}".format(filter['filterModifier'], 24 * 3600 * int(filter['filterValue']))
else:
modifier_string = ' {} "P{}D"xsd:duration'.format(filter['filterModifier'], filter['filterValue'])
filter_string = "FILTER ( {} {} {} {} ) .".format(obj, filter['filterSign'], var_2, modifier_string)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)
# Category
if attribute["type"] == "category":
if attribute["visible"] or attribute["filterSelectedValues"] != [] or attribute["id"] in strands or attribute["id"] in linked_attributes:
Expand Down Expand Up @@ -1499,13 +1540,18 @@ def build_query_from_json(self, preview=False, for_editor=False):
else:
self.store_value("VALUES {} {{ {} }}".format(value_var, ' '.join(uri_val_list)), block_id, sblock_id, pblock_ids)

if attribute["linked"]:
if attribute["linked"] and attribute["linkedWith"]:
var_2 = self.format_sparql_variable("{}{}_{}Category".format(
attributes[attribute["linkedWith"]]["entity_label"],
attributes[attribute["linkedWith"]]["entity_id"],
attributes[attribute["linkedWith"]]["label"]
))
var_to_replace.append((category_value_uri, var_2))

if not attribute.get('linkedNegative', False):
var_to_replace.append((category_value_uri, var_2))
else:
filter_string = "FILTER ( {} {} {} ) .".format(category_value_uri, "!=", var_2)
self.store_filter(filter_string, block_id, sblock_id, pblock_ids)

from_string = "" if self.settings.getboolean("askomics", "single_tenant", fallback=False) else self.get_froms_from_graphs(self.graphs)
federated_from_string = self.get_federated_froms_from_graphs(self.graphs)
Expand Down
4 changes: 3 additions & 1 deletion askomics/react/src/navbar.jsx
View file
Expand Up @@ -44,6 +44,7 @@ export default class AskoNavbar extends Component {

links = (
<>
{overviewLink}
{contactLink}
<NavItem><Link className="nav-link" to="/about"><i className="fas fa-info"></i> About</Link></NavItem>
<NavItem><Link className="nav-link" to="/login"><i className="fas fa-sign-in-alt"></i> Login</Link></NavItem>
Expand Down Expand Up @@ -75,6 +76,7 @@ export default class AskoNavbar extends Component {
<>
<NavItem><Link className="nav-link" to="/results"><i className="fas fa-tasks"></i> Results</Link></NavItem>
{integrationLinks}
{overviewLink}
{contactLink}
<NavItem><Link className="nav-link" to="/about"><i className="fas fa-info"></i> About</Link></NavItem>
<NavItem>
Expand All @@ -100,6 +102,7 @@ export default class AskoNavbar extends Component {
links = (
<>
<NavItem><Link className="nav-link" to="/results"><i className="fas fa-tasks"></i> Results</Link></NavItem>
{overviewLink}
{contactLink}
<NavItem><Link className="nav-link" to="/about"><i className="fas fa-info"></i> About</Link></NavItem>
<NavItem><Link className="nav-link" to="/login"><i className="fas fa-sign-in-alt"></i> Login</Link></NavItem>
Expand All @@ -116,7 +119,6 @@ export default class AskoNavbar extends Component {
<Collapse navbar>
<Nav className="ml-auto" navbar>
{askLink}
{overviewLink}
{links}
</Nav>
</Collapse>
Expand Down

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