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split object.name, subject.name & object.chembl #1

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May 30, 2024
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split object.name, subject.name & object.chembl #1

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14 changes: 9 additions & 5 deletions parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,7 @@
COLUMN_DATA stores where each column should go in the actual document. Each key corresponds to a column name in the csv. For each of these, four fields must be defined:

- "location": defines the location of the column in the document, nested layers should be separated with a "."
- "type": The type of data in the column. Supported types include "int", "string", "split_comma" (ie. "a,b,c"), and "split_semicolon" (ie "a;b;c")
- "type": The type of data in the column. Supported types include "int", "string", "split_comma" (ie. "a,b,c"), "split_semicolon" (ie "a;b;c"), "split_chembl" (ie "CHEMBL1CHEMBL2CHEMBL3"), "split_colon" (ie "a::b::c")
- "uniprot_type": This indicates whether the data is specifically applicable for "swissprot" or "trembl" documents, if it is applicable for both use "all"
- "relation": This simply should store a boolean of whether this field is in the relation of the document, as the relation is treated a bit differently in terms of merging
"""
Expand Down Expand Up @@ -105,13 +105,13 @@
},
"BindingDB Ligand Name": {
"location": "object.name",
"type": "string",
"type": "split_colon",
"uniprot_type": "all",
"relation": False
},
"Target Name Assigned by Curator or DataSource": {
"location": "subject.name",
"type": "string",
"type": "split_colon",
"uniprot_type": "all",
"relation": False
},
Expand Down Expand Up @@ -261,7 +261,7 @@
},
"ChEMBL ID of Ligand": {
"location": "object.chembl",
"type": "string",
"type": "split_chembl",
"uniprot_type": "all",
"relation": False
},
Expand Down Expand Up @@ -377,7 +377,7 @@ def append_field(doc: dict, key: str, value: any):
for i in keys[:len(keys)-1]:
key_ref = key_ref[i]

if COLUMN_DATA[key]['type'] == "split_comma" or COLUMN_DATA[key]['type'] == "split_semicolon":
if COLUMN_DATA[key]['type'] == "split_comma" or COLUMN_DATA[key]['type'] == "split_semicolon" or COLUMN_DATA[key]['type'] == "split_chembl" or COLUMN_DATA[key]['type'] == "split_colon":
if isinstance(key_ref[keys[-1]][0], list) and value not in key_ref[keys[-1]]:
key_ref[keys[-1]].append(value)
if not isinstance(key_ref[keys[-1]][0], list) and value != key_ref[keys[-1]]:
Expand Down Expand Up @@ -427,6 +427,10 @@ def process_field(field_name: str, value: str):
return value.split(',')
if field_type == "split_semicolon":
return value.split('; ')
if field_type == "split_colon":
return value.split('::')
if field_type == "split_chembl":
return ['CHEMBL' + x for x in value.split('CHEMBL') if x != '']
return value


Expand Down