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Changes to WIP_query_update
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kataikko committed Sep 12, 2023
1 parent e6b6fdf commit 7579f45
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Showing 9 changed files with 7 additions and 933 deletions.
596 changes: 0 additions & 596 deletions backend/src/cypher_queries.py

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4 changes: 1 addition & 3 deletions backend/src/enrichment.py
Original file line number Diff line number Diff line change
Expand Up @@ -78,9 +78,7 @@ def functional_enrichment(driver: neo4j.Driver, in_proteins, species_id: Any):
# Get number of all proteins in the organism (from Cypher)
bg_proteins = queries.get_number_of_proteins(driver, species_id)
num_in_prot = len(in_proteins)

# TODO: Improve runtime?

prots = set(in_proteins)
# pandas DataFrames for nodes and edges
csv.field_size_limit(sys.maxsize)

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11 changes: 5 additions & 6 deletions backend/src/enrichment_graph.py
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Expand Up @@ -14,18 +14,14 @@
_BACKEND_JAR_PATH = "../gephi/target/gephi.backend-1.0-SNAPSHOT.jar"




def get_functional_graph(list_enrichment, species_id):
stopwatch = Stopwatch()

list_term = []
if list_enrichment is not None:
list_term = [i["id"] for i in list_enrichment]

# Create a query to find all associations between protein_ids and create a file with all properties
def create_query_assoc():
# Query for terms based on protein input
driver = database.get_driver()

# Execute the query and retrieve the CSV data
terms, source, target, score = queries.get_terms_connected_by_overlap(driver, list_term, species_id)
Expand Down Expand Up @@ -117,7 +113,10 @@ def create_query_assoc():
sub_proteins.append(node["attributes"]["Ensembl ID"])
else:
node["color"] = "rgb(255,255,153)"
node["hidden"] = True

for edge in sigmajs_data["edges"]:
if edge["source"] not in ensembl_sub and edge["target"] not in ensembl_sub:
edge["color"] = "rgba(255,255,153,0.2)"

sigmajs_data["subgraph"] = sub_proteins

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14 changes: 1 addition & 13 deletions frontend/src/components/enrichment/EnrichmentTool.vue
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Expand Up @@ -367,18 +367,6 @@
font-weight: 900;
font-family: 'Roboto Mono', monospace;
}
#result_select{
appearance: none;
border-style: none;
width: 100%;
padding: 10px;
background: none;
color: white;
height: 100%;
font-weight: 900;
font-family: 'Roboto Mono', monospace;
}
.tabsystem-enrichment {
position: relative;
Expand Down Expand Up @@ -415,7 +403,7 @@
.selected {
background-color: rgba(255,0,0,0.7); /* Customize the selected style as desired */
}
#visualize-favourites {
margin-left:5px;
background-color: rgba(0, 0, 0, 0.5);
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107 changes: 0 additions & 107 deletions frontend/src/components/toolbar/select_options/HubsSelection.vue

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63 changes: 0 additions & 63 deletions frontend/src/components/toolbar/select_options/PageRank.vue

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