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Suggested update for TRAPI 1.4 #2

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Suggested update for TRAPI 1.4 #2

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38 changes: 34 additions & 4 deletions BigGIM_Parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -400,7 +400,9 @@ def parse_edge_attributes(row, column_names):
return edge_attributes


def load_tsv_data(file_path):
def load_tsv_data(file_path, attribute_data_source):
attribute_source = "infores:biothings-multiomics-biggim-drugresponse"

file_formated = pd.read_csv(file_path)
file_formated = file_formated.dropna()
if not header_check(file_formated):
Expand All @@ -425,13 +427,25 @@ def load_tsv_data(file_path):
"edge_label": predicates,
"edge_attributes": edge_attributes
}

edge_sources = [
{
"resource_id": attribute_source,
"resource_role": "primary_knowledge_source"
},
{
"resource_id": attribute_data_source,
"resource_role": "supporting_data_source"
}
]

json = {
# "_id":'-'.join(unique_id_list),
"_id": subject_json["type"] + "_" + predicates + "_" + object_json["type"] + "_" + file_path.split("/")[-1] + "_" + str(index),
"subject": subject_json,
"association": association_json,
"object": object_json
"object": object_json,
"sources": edge_sources
}
yield json

Expand All @@ -452,7 +466,23 @@ def load_data(data_folder):
"GTEX_liver_negative_correlated_formated.csv",
"GTEX_liver_positively_correlated_formated.csv"
]
data_sources = [
"infores:gdsc",
"infores:gdsc",
"infores:tcga",
"???",
"infores:gdsc",
"???",
"???",
"???",
"???",
"???",
"???",
"infores:gtex",
"infores:gtex"
]

file_paths = [os.path.join(data_folder, fn) for fn in file_names]
for file_path in file_paths:
for json in load_tsv_data(file_path):
for (file_path, source) in zip(file_paths, data_sources):
for json in load_tsv_data(file_path, source):
yield json