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updated taxonomy query #30

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89 changes: 75 additions & 14 deletions query_service/core/routers/query.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,22 +68,51 @@ async def get_taxonomy():
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bican: <https://identifiers.org/brain-bican/vocab/>
PREFIX DHBA: <https://purl.brain-bican.org/ontology/dmbao/DMBA_>
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medium

The DHBA prefix is defined but not used in the SPARQL query. It should be removed to avoid confusion and keep the code clean.


SELECT ?id ?parent ?name ?hex
SELECT ?id ?name ?accession_id ?parentNode ?abbrNode ?abbrMeaning ?abbrTerm ?parcellationTerm ?geneAnnotation ?cellType ?hex ?setAccessionId
WHERE {
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high

The GRAPH clause has been removed from this query. The previous version specified GRAPH <http://hmbataxonomy20250927.com/>. If the taxonomy data resides exclusively within that named graph, this query will no longer find it because it now targets the default graph. This could lead to empty results. If the data is in that named graph, the GRAPH clause should be restored around the WHERE clause body.

GRAPH <http://hmbataxonomy20250927.com/> {
?id a bican:CellTypeTaxon .
OPTIONAL { ?id bican:has_parent ?parent . }
OPTIONAL { ?id rdfs:label ?name . }

# Find a DisplayColor node linked to this taxon
OPTIONAL {
?colorNode a bican:DisplayColor ;
bican:is_color_for_taxon ?cid ;
bican:color_hex_triplet ?hex .
FILTER(STR(?id) = STR(?cid))
}
}
# 1. Find all CellTypeTaxon nodes
?id a bican:CellTypeTaxon .

# 2. Get CellTypeTaxon name
OPTIONAL { ?id rdfs:label ?name . }

# 3. Get CellTypeTaxon accession_id
OPTIONAL { ?id bican:accession_id ?accession_id . }

# 4. Get CellTypeTaxon Parent Node
OPTIONAL {
?id bican:has_parent ?parentNode .
}

# 5. Get CellTypeTaxon Abbreviation Nodes
OPTIONAL {
?id bican:has_abbreviation ?abbrNode .
?abbrNode a bican:Abbreviation ;
bican:meaning ?abbrMeaning ;
bican:term ?abbrTerm .
OPTIONAL { ?abbrNode bican:denotes_parcellation_term ?parcellationTerm . }
OPTIONAL { ?abbrNode bican:denotes_gene_annotation ?geneAnnotation . }
OPTIONAL { ?abbrNode bican:denotes_cell_type ?cellType . }
}

# 6. Get CellTypeTaxon Color Hex Triplet
OPTIONAL {
?colorNode a bican:DisplayColor ;
bican:is_color_for_taxon ?cid ;
bican:color_hex_triplet ?hex .
FILTER(STR(?id) = STR(?cid))
}

# 7. Get CellTypeSet Node
OPTIONAL {
?cellTypeSetNode a bican:CellTypeSet ;
bican:contains_taxon ?id ;
bican:accession_id ?setAccessionId .
}


}
"""
response = fetch_data_gdb(query_taxonomy)
Expand All @@ -98,4 +127,36 @@ async def get_taxonomy():
processed_taxonomy = taxonomy_postprocessing(response_taxonomy)
return processed_taxonomy

#! TODO: Update lines 119-126 with this:
# data = {}
# for row in response:
# id_, name, accession_id, parentNode, abbrNode, abbrMeaning, abbrTerm, parcellationTerm, geneAnnotation, cellType, hex_, setAccessionId = row
# id_ = str(id_)
# name = str(name) if name else None
# accession_id = str(accession_id) if accession_id else None
# parentNode = str(parentNode) if parentNode else None
# abbrNode = str(abbrNode) if abbrNode else None
# abbrMeaning = str(abbrMeaning) if abbrMeaning else None
# abbrTerm = str(abbrTerm) if abbrTerm else None
# denotes = str(parcellationTerm) if parcellationTerm else None
# denotes = str(geneAnnotation) if geneAnnotation else denotes
# denotes = str(cellType) if cellType else denotes
# hex_ = str(hex_) if hex_ else None

# if str(id_) in data:
# if abbrNode in data[id_]["abbreviations"]:
# if denotes:
# data[id_]["abbreviations"][abbrNode]["denotes"].append(denotes)
# else:
# data[id_]["abbreviations"][abbrNode] = {"term": abbrTerm, "meaning": abbrMeaning, "denotes": [denotes]}
# else:
# data[id_] = {
# "name": name,
# "accession_id": accession_id,
# "parent": parentNode,
# "abbreviations": dict({abbrNode: {"term": abbrTerm, "meaning": abbrMeaning, "denotes": [denotes]}}) if abbrNode else {},
# "hex": hex_,
# "belongs_to_set": setAccessionId
# }

Comment on lines +130 to +161
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critical

This TODO correctly identifies that the data processing logic (lines 119-126) needs to be updated to match the new query. The current, old logic is still in place and will cause runtime errors because it references fields that are no longer returned by the query.

Additionally, the proposed logic in this commented-out block has some issues:

  • It iterates over response directly, but it should iterate over response["message"]["results"]["bindings"].
  • It attempts to unpack each row as a tuple, but the rows are dictionaries.
  • The logic for handling denotes is flawed and will overwrite values.

Since I cannot comment on the unchanged lines (119-128), I'm providing a corrected implementation here. Please replace lines 119-128 with the following code:

    response_taxonomy = {}
    for taxon_info in response["message"]["results"]["bindings"]:
        tax_id = taxon_info.get("id", {}).get("value")
        if not tax_id:
            continue

        if tax_id not in response_taxonomy:
            response_taxonomy[tax_id] = {
                "id": tax_id,
                "parent": taxon_info.get("parentNode", {}).get("value"),
                "name": taxon_info.get("name", {}).get("value"),
                "hex": taxon_info.get("hex", {}).get("value"),
                "accession_id": taxon_info.get("accession_id", {}).get("value"),
                "belongs_to_set": taxon_info.get("setAccessionId", {}).get("value"),
                "abbreviations": {}
            }

        abbr_node = taxon_info.get("abbrNode", {}).get("value")
        if abbr_node and abbr_node not in response_taxonomy[tax_id]["abbreviations"]:
            denotes = []
            if "parcellationTerm" in taxon_info:
                denotes.append(taxon_info["parcellationTerm"]["value"])
            if "geneAnnotation" in taxon_info:
                denotes.append(taxon_info["geneAnnotation"]["value"])
            if "cellType" in taxon_info:
                denotes.append(taxon_info["cellType"]["value"])

            response_taxonomy[tax_id]["abbreviations"][abbr_node] = {
                "term": taxon_info.get("abbrTerm", {}).get("value"),
                "meaning": taxon_info.get("abbrMeaning", {}).get("value"),
                "denotes": denotes
            }
    
    processed_taxonomy = taxonomy_postprocessing(response_taxonomy)
    return processed_taxonomy


37 changes: 6 additions & 31 deletions query_service/core/shared.py
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Original file line number Diff line number Diff line change
Expand Up @@ -443,49 +443,26 @@ def named_graph_metadata(named_graph_url, description):
)
return named_graph_metadata

# def taxonomy_postprocessing(items):
# # going through the query output and create dictionary with parents_id and lists of childs ids
# taxon_dict = {}
# for tax_id, el in items.items():
# if el['parent'] is None:
# par_id = "root"
# par_nm = "root"
# else:
# par_id = el['parent']
# par_nm = items[par_id]["name"]

# if par_id not in taxon_dict:
# taxon_dict[par_id] = {"meta": {"name": par_nm}, "childrens_id": [tax_id]}
# else:
# taxon_dict[par_id]["childrens_id"].append(tax_id)


# # creating a simple function for one level of children for testing the figure:
# fig_dict = {"name": "root", "nodeColor": "#ffffff", "children": []}
# for child_id in taxon_dict["root"]['childrens_id']:
# fig_dict["children"].append({"name": taxon_dict[child_id]["meta"]["name"], "nodeColor": "#ebb3a7", "children": []})

# return fig_dict
def getting_childrens(items):
# going through the query output and create dictionary with parents_id and lists of childs ids
taxon_dict = {}
for tax_id, el in items.items():
if el['parent'] is None:
par_id = "root"
par_nm, par_col = "root", '#ffffff'
par_name, par_color, par_accession_id, par_abbreviations, par_belongs_to_set = "root", '#ffffff', None, [], None
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medium

This line is quite long and assigns multiple variables at once, which can harm readability. To improve clarity and adhere to common style guidelines (like PEP 8's line length recommendations), consider breaking this into multiple assignment statements.

Suggested change
par_name, par_color, par_accession_id, par_abbreviations, par_belongs_to_set = "root", '#ffffff', None, [], None
par_name = "root"
par_color = '#ffffff'
par_accession_id = None
par_abbreviations = []
par_belongs_to_set = None

else:
par_id = el['parent']
par_nm, par_col = items[par_id]["name"], items[par_id]["hex"]
par_name, par_color, par_accession_id, par_abbreviations, par_belongs_to_set = items[par_id]["name"], items[par_id]["hex"], items[par_id]["accession_id"], items[par_id]["abbreviations"].values(), items[par_id]["belongs_to_set"]
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medium

Similar to the line above, this line is very long and assigns many variables from a dictionary lookup. This can be hard to read and debug. Breaking it down into individual assignments would improve maintainability.

Suggested change
par_name, par_color, par_accession_id, par_abbreviations, par_belongs_to_set = items[par_id]["name"], items[par_id]["hex"], items[par_id]["accession_id"], items[par_id]["abbreviations"].values(), items[par_id]["belongs_to_set"]
par_name = items[par_id]["name"]
par_color = items[par_id]["hex"]
par_accession_id = items[par_id]["accession_id"]
par_abbreviations = items[par_id]["abbreviations"].values()
par_belongs_to_set = items[par_id]["belongs_to_set"]


if par_id not in taxon_dict:
taxon_dict[par_id] = {"meta": {"name": par_nm, "color": par_col}, "childrens_id": [tax_id]}
taxon_dict[par_id] = {"meta": {"name": par_name, "color": par_color, "accession_id": par_accession_id, "abbreviations": list(par_abbreviations), "belongs_to_set": par_belongs_to_set}, "childrens_id": [tax_id]}
else:
taxon_dict[par_id]["childrens_id"].append(tax_id)

# adding elements without children
for tax_id, el in items.items():
if tax_id not in taxon_dict:
taxon_dict[tax_id] = {"meta": {"name": items[tax_id]["name"], "color": items[tax_id]["hex"]}, "childrens_id": []}
taxon_dict[tax_id] = {"meta": {"name": items[tax_id]["name"], "color": items[tax_id]["hex"], "accession_id": items[tax_id]["accession_id"], "abbreviations": list(items[tax_id]["abbreviations"].values()), "belongs_to_set": items[tax_id]["belongs_to_set"]}, "childrens_id": []}

return taxon_dict

Expand All @@ -505,12 +482,10 @@ def update_childrens(children_list, parent_id, taxon_children_dict):
#print("child id", child_id)
children_list_current = []
update_childrens(children_list_current, child_id, taxon_children_dict)
children_list.append({"name": taxon_children_dict[child_id]["meta"]["name"], "nodeColor": taxon_children_dict[child_id]["meta"]["color"], "children": children_list_current})
children_list.append({"name": taxon_children_dict[child_id]["meta"]["name"], "nodeColor": taxon_children_dict[child_id]["meta"]["color"], "accession_id": taxon_children_dict[child_id]["meta"]["accession_id"], "abbreviations": taxon_children_dict[child_id]["meta"]["abbreviations"], "belongs_to_set": taxon_children_dict[child_id]["meta"]["belongs_to_set"], "children": children_list_current})
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medium

This line has become very long with the addition of new keys. To improve readability, consider creating the dictionary first and then appending it to the list. This also allows you to reduce repetition by getting the meta dictionary once.

Suggested change
children_list.append({"name": taxon_children_dict[child_id]["meta"]["name"], "nodeColor": taxon_children_dict[child_id]["meta"]["color"], "accession_id": taxon_children_dict[child_id]["meta"]["accession_id"], "abbreviations": taxon_children_dict[child_id]["meta"]["abbreviations"], "belongs_to_set": taxon_children_dict[child_id]["meta"]["belongs_to_set"], "children": children_list_current})
child_meta = taxon_children_dict[child_id]["meta"]
child_node = {
"name": child_meta["name"],
"nodeColor": child_meta["color"],
"accession_id": child_meta["accession_id"],
"abbreviations": child_meta["abbreviations"],
"belongs_to_set": child_meta["belongs_to_set"],
"children": children_list_current
}
children_list.append(child_node)

return
else:
return


def taxonomy_postprocessing(items):
taxon_children = getting_childrens(items)

Expand Down