Upload meshutils.py

meshutils.py

@@ -0,0 +1,52 @@
+import pandas as pd
+
+
+from collections import defaultdict
+
+
+
+# load file
+def df_mem(df):
+	return '%.1f Mb' % (df.memory_usage(index=True, deep=True).values.sum() / 1024 / 1024)
+
+
+def load_df(file_name, nrows=1000, header='infer', names=None):
+	df = pd.read_csv(file_name, sep='|', nrows=nrows, low_memory=False, header=header, names=names)
+	# print("loaded '%s', %d rows (%s)" % (file_name, len(df), df_mem(df)))
+	return df
+
+
+# Map Studies to Mesh
+df_mesh_ct = load_df('asset/data/browse_conditions.txt', nrows=None)
+df_mesh_ct = df_mesh_ct[['nct_id', 'downcase_mesh_term']]
+
+## search mesh_term
+nct_to_mesh_term = defaultdict(set)
+
+for row in df_mesh_ct[['nct_id', 'downcase_mesh_term']].itertuples():
+	nct_to_mesh_term[row[1]].add(row[2])
+
+###==========================================================================================================
+
+# # Map Mesh to Keywords
+# df_mesh_kw = load_df('data/keywords.txt', nrows=None)
+# df_mesh_kw = df_mesh_kw[['nct_id', 'downcase_name']]
+
+# ## get mesh keywords
+# nct_to_mesh_kywd = defaultdict(set)
+
+# for row in df_mesh_kw[['nct_id','downcase_name']].itertuples():
+#     nct_to_mesh_kywd[row[1]].add(row[2])
+
+###==========================================================================================================
+# original mesh fuction in creator py
+###==========================================================================================================
+# load mesh dataframe
+
+df_mesh = pd.read_csv('asset/data/df_mesh.csv', encoding='unicode_escape')
+
+# Map Mesh Term to ID
+mesh_term_to_id = {}
+
+for row in df_mesh[['name', 'ui']].itertuples():
+	mesh_term_to_id[row[1]] = row[2]