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Improve the function for finding shared nodes easier.
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@yjcyxky
yjcyxky committed Mar 6, 2024
1 parent 81f6f9c commit e92c1f0
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Showing 3 changed files with 179 additions and 77 deletions.
246 changes: 174 additions & 72 deletions src/query_builder/cypher_builder.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ pub async fn query_nhops(
}

// Parse the shared nodes and edges from the result.
// NOTE: the name of the results should be 'common', 'relatedStartNodes', and 'relations'.
// NOTE: the name of the results should be 'common', 'relatedNodes', and 'relations'.
//
// # Arguments
// * `result` - The result of the query.
Expand All @@ -186,18 +186,27 @@ async fn parse_shared_results(
let node = NodeData::from_neo_node(node);
node_map.insert(id, node);
}
None => continue,
None => (),
};

match row.get::<Vec<NeoNode>>("relatedStartNodes") {
match row.get::<Vec<NeoNode>>("relatedNodes") {
Some(related_start_nodes) => {
for node in related_start_nodes {
let id = node.id();
let node = NodeData::from_neo_node(node);
node_map.insert(id, node);
}
}
None => continue,
None => (),
};

match row.get::<NeoNode>("startNode") {
Some(node) => {
let id = node.id();
let node = NodeData::from_neo_node(node);
node_map.insert(id, node);
}
None => (),
};

// If you want to know the format of the relations, you can run the related cypher query in the Neo4j Browser.
Expand All @@ -209,9 +218,29 @@ async fn parse_shared_results(
}
}
}
None => continue,
None => (),
};

match row.get::<Vec<Relation>>("relations1") {
Some(relation) => {
for r in relation {
relations.push(r);
}
}
None => (),
};

match row.get::<Vec<Relation>>("relations2") {
Some(relation) => {
for r in relation {
relations.push(r);
}
}
None => (),
};
}
info!("Number of entities: {}", &node_map.len());
info!("Number of relations: {}", &relations.len());

for relation in relations.iter() {
let start_node_id = relation.start_node_id();
Expand Down Expand Up @@ -251,27 +280,14 @@ pub async fn query_shared_nodes(
nums_shared_by: usize,
start_node_id: Option<&str>,
) -> Result<(Vec<NodeData>, Vec<EdgeData>), anyhow::Error> {
let nums_shared_by = if nums_shared_by == 0 || nums_shared_by > node_ids.len() {
node_ids.len()
} else {
nums_shared_by
};

let where_clauses = match target_node_types {
Some(target_node_types) => {
format!(
"sharedBy = {} AND ANY(label IN labels(common) WHERE label IN ['{}'])",
nums_shared_by,
target_node_types.join("', '")
)
}
None => format!("sharedBy = {}", nums_shared_by),
if nums_shared_by > node_ids.len() {
return Err(anyhow::anyhow!(
"The number of shared nodes should be less than the number of start nodes."
));
};

let hop_str = match nhops {
1 => "*1",
2 => "*1..2",
_ => "",
if nhops > 2 {
return Err(anyhow::anyhow!("The number of hops should be less than 3."));
};

let query_str = if start_node_id.is_none() {
Expand All @@ -283,9 +299,9 @@ pub async fn query_shared_nodes(
// UNWIND startNodes AS startNode
// MATCH p=(startNode)-[r*1]-(common:Disease)
// WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN startNodes OR x = common)
// WITH common, COLLECT(DISTINCT startNode) AS relatedStartNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy
// WITH common, COLLECT(DISTINCT startNode) AS relatedNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy
// WHERE sharedBy = 2
// RETURN common, relatedStartNodes, relations
// RETURN common, relatedNodes, relations
// ORDER BY sharedBy DESC
// LIMIT 100

Expand All @@ -297,28 +313,65 @@ pub async fn query_shared_nodes(
if i < node_ids.len() - 1 {
start_nodes_details.push_str(", ");
}
}
let nums_shared_by = if nums_shared_by == 0 || nums_shared_by > node_ids.len() {
node_ids.len()
} else {
nums_shared_by
};

format!("
WITH [{start_nodes_details}] AS startNodesDetails
UNWIND startNodesDetails AS nodeDetails
MATCH (start)
WHERE start.id = nodeDetails.id AND ANY(label IN labels(start) WHERE label = nodeDetails.label)
WITH COLLECT(DISTINCT start) AS startNodes
UNWIND startNodes AS startNode
MATCH p=(startNode)-[r{hop_str}]-(common)
WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN startNodes OR x = common) AND startNode IN startNodes
WITH common, COLLECT(DISTINCT startNode) AS relatedStartNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy
WHERE {where_clauses}
WITH common, relatedStartNodes, relations, sharedBy
ORDER BY sharedBy DESC
LIMIT {topk}
RETURN common, relatedStartNodes, relations",
topk = topk,
start_nodes_details = start_nodes_details,
hop_str = hop_str,
where_clauses = where_clauses
)
let where_clauses = match target_node_types {
Some(target_node_types) => {
format!(
"sharedBy = {} AND ANY(label IN labels(common) WHERE label IN ['{}'])",
nums_shared_by,
target_node_types.join("', '")
)
}
None => format!("sharedBy = {}", nums_shared_by),
};

if nhops == 1 {
format!("
WITH [{start_nodes_details}] AS startNodesDetails
UNWIND startNodesDetails AS nodeDetails
MATCH (start)
WHERE start.id = nodeDetails.id AND ANY(label IN labels(start) WHERE label = nodeDetails.label)
WITH COLLECT(DISTINCT start) AS startNodes
UNWIND startNodes AS startNode
MATCH p=(startNode)-[r]-(common)
WHERE (NOT startNode = common) AND ALL(x IN nodes(p) WHERE x IN startNodes) AND startNode IN startNodes
WITH common, COLLECT(DISTINCT startNode) AS relatedNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy
WHERE {where_clauses}
WITH common, relatedNodes, relations, sharedBy
ORDER BY sharedBy DESC
LIMIT {topk}
RETURN common, relatedNodes, relations",
topk = topk,
start_nodes_details = start_nodes_details,
where_clauses = where_clauses
)
} else {
format!("
WITH [{start_nodes_details}] AS startNodesDetails
UNWIND startNodesDetails AS nodeDetails
MATCH (start)
WHERE start.id = nodeDetails.id AND ANY(label IN labels(start) WHERE label = nodeDetails.label)
WITH COLLECT(DISTINCT start) AS startNodes
UNWIND startNodes AS startNode
MATCH p=(startNode)-[r*1..2]-(common)
WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN startNodes OR x = common) AND startNode IN startNodes
WITH common, COLLECT(DISTINCT startNode) AS relatedNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT startNode) AS sharedBy
WHERE {where_clauses}
WITH common, relatedNodes, relations, sharedBy
ORDER BY sharedBy DESC
LIMIT {topk}
RETURN common, relatedNodes, relations",
topk = topk,
start_nodes_details = start_nodes_details,
where_clauses = where_clauses
)
}
} else {
let start_node_id = start_node_id.unwrap();
let (start_node_label, start_node_id) = split_id(start_node_id)?;
Expand All @@ -332,32 +385,81 @@ pub async fn query_shared_nodes(
.collect::<Vec<String>>()
.join(", ");

format!("
// 假设 start_node_id 和 start_node_label 代表我们感兴趣的起始节点的ID和标签
MATCH (start)
WHERE start.id = '{start_node_id}' AND ANY(label IN labels(start) WHERE label = '{start_node_label}')
WITH start AS startNode
// 这里不再需要收集起始节点，因为我们只有一个起始节点
UNWIND [{other_nodes_details}] AS otherNodeDetails
MATCH (other)
WHERE other.id = otherNodeDetails.id AND ANY(label IN labels(other) WHERE label = otherNodeDetails.label)
WITH COLLECT(DISTINCT other) AS otherNodes, startNode
UNWIND otherNodes AS otherNode
MATCH p=(startNode)-[r{hop_str}]-(common)
WHERE NOT startNode = common AND ALL(x IN nodes(p) WHERE x IN otherNodes OR x = common) AND startNode = startNode
WITH common, COLLECT(DISTINCT otherNode) AS relatedOtherNodes, COLLECT(DISTINCT r) AS relations, COUNT(DISTINCT otherNode) AS sharedBy
WHERE {where_clauses}
WITH common, relatedOtherNodes, relations, sharedBy
ORDER BY sharedBy DESC
LIMIT {topk}
RETURN common, relatedOtherNodes, relations",
topk = topk,
other_nodes_details = other_nodes_details, // 该变量需要提供其他节点的详情，例如ID和标签
hop_str = hop_str,
where_clauses = where_clauses,
start_node_id = start_node_id, // 指定的起始节点ID
start_node_label = start_node_label // 指定的起始节点标签
)
if nhops == 1 {
format!("
MATCH (start)
WHERE start.id = '{start_node_id}' AND ANY(label IN labels(start) WHERE label = '{start_node_label}')
WITH start AS startNode
UNWIND [{other_nodes_details}] AS otherNodeDetails
MATCH (other)
WHERE other.id = otherNodeDetails.id AND ANY(label IN labels(other) WHERE label = otherNodeDetails.label)
WITH COLLECT(DISTINCT other) AS otherNodes, startNode
UNWIND otherNodes AS otherNode
MATCH (startNode)-[r]-(sharedNode)
WHERE sharedNode = otherNode
WITH sharedNode, COLLECT(r) AS relations1, startNode, COLLECT(DISTINCT otherNode) AS relatedNodes
RETURN sharedNode AS common, relations1, relatedNodes, startNode",
other_nodes_details = other_nodes_details,
start_node_id = start_node_id,
start_node_label = start_node_label
)
} else {
let where_clauses = match target_node_types {
Some(target_node_types) => {
format!(
"sharedBy = {} AND ANY(label IN labels(common) WHERE label IN ['{}'])",
nums_shared_by,
target_node_types.join("', '")
)
}
None => format!("sharedBy = {}", nums_shared_by),
};

// Example query string:
// MATCH (startNode)
// WHERE startNode.id = 'ENTREZ:3569' AND ANY(label IN labels(startNode) WHERE label = 'Gene')
// WITH startNode
// UNWIND [{label: 'Gene', id: 'ENTREZ:3107'}, {label: 'Gene', id: 'ENTREZ:3119'}, {label: 'Gene', id: 'ENTREZ:3569'}] AS otherNodeDetail
// MATCH (otherNode)
// WHERE otherNode.id = otherNodeDetail.id AND ANY(label IN labels(otherNode) WHERE label = otherNodeDetail.label)
// WITH COLLECT(DISTINCT otherNode) AS otherNodes, startNode
// MATCH (startNode)-[r1]-(sharedNode)
// WHERE NOT (sharedNode IN otherNodes)
// WITH sharedNode, COLLECT(DISTINCT r1) AS relations, startNode, otherNodes
// MATCH (sharedNode)-[r2]-(otherNode)
// WHERE otherNode IN otherNodes AND otherNode <> startNode
// WITH sharedNode, relations, startNode, COLLECT(DISTINCT otherNode) AS relatedNodes, COLLECT(DISTINCT r2) AS relations2, COUNT(DISTINCT otherNode) AS sharedBy
// WHERE sharedBy = 2 AND ANY(label IN labels(sharedNode) WHERE label IN ['Gene'])
// WITH sharedNode AS common, relations AS relations1, relatedNodes, startNode, relations2, sharedBy
// ORDER BY sharedBy DESC
// LIMIT 3
// RETURN common, relations1, relatedNodes, startNode, relations2
format!("
MATCH (startNode)
WHERE startNode.id = '{start_node_id}' AND ANY(label IN labels(startNode) WHERE label = '{start_node_label}')
WITH startNode
UNWIND [{other_nodes_details}] AS otherNodeDetail
MATCH (otherNode)
WHERE otherNode.id = otherNodeDetail.id AND ANY(label IN labels(otherNode) WHERE label = otherNodeDetail.label)
WITH COLLECT(DISTINCT otherNode) AS otherNodes, startNode
MATCH (startNode)-[r1]-(sharedNode)
WHERE NOT (sharedNode IN otherNodes)
WITH sharedNode, COLLECT(DISTINCT r1) AS relations, startNode, otherNodes
MATCH (sharedNode)-[r2]-(otherNode)
WHERE otherNode IN otherNodes AND otherNode <> startNode
WITH sharedNode AS common, relations, startNode, COLLECT(DISTINCT otherNode) AS relatedNodes, COLLECT(DISTINCT r2) AS relations2, COUNT(DISTINCT otherNode) AS sharedBy
WHERE {where_clauses}
WITH common, relations AS relations1, relatedNodes, startNode, relations2, sharedBy
ORDER BY sharedBy DESC
LIMIT {topk}
RETURN common, relations1, relatedNodes, startNode, relations2",
other_nodes_details = other_nodes_details,
where_clauses = where_clauses,
start_node_id = start_node_id,
start_node_label = start_node_label,
topk = topk
)
}
};

info!("query_shared_nodes's query_str: {}", query_str);
Expand Down
2 changes: 1 addition & 1 deletion studio/package.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@
"antd": "5.7.0",
"antd-schema-form": "^4.5.1",
"axios": "^1.1.2",
"biominer-components": "0.2.77",
"biominer-components": "0.2.78",
"classnames": "^2.3.0",
"handlebars": "^4.7.7",
"handsontable": "^12.1.3",
Expand Down
8 changes: 4 additions & 4 deletions studio/yarn.lock
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5772,10 +5772,10 @@ bindings@^1.5.0:
dependencies:
file-uri-to-path "1.0.0"

[email protected].77:
version "0.2.77"
resolved "https://registry.yarnpkg.com/biominer-components/-/biominer-components-0.2.77.tgz#ec89d0463140993509a7eb20f876d1bc8428bba4"
integrity sha512-RqE19JGB9J12dXm6l6Q16nVxU1pLeFI+9FC70hXRFYSYSaYkJnGlRWy/qjn7KWRsWiJXGA4hZjmfAdVzM1mI5g==
[email protected].78:
version "0.2.78"
resolved "https://registry.yarnpkg.com/biominer-components/-/biominer-components-0.2.78.tgz#d74e8c4bbe29e48d349242fb5d7f3875593deef4"
integrity sha512-xOyatggnwtzLDbMxM8kzksFvhM5VzU195RuLG8ixXjdYT1HKZRpphv2wA1PVjju3at6FlLhon4JYOkz3eF7e3Q==
dependencies:
"@fingerprintjs/fingerprintjs" "^3.4.2"
"@types/openseadragon" "^3.0.3"
Expand Down

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