Update untar->unpack for fetch_file

Author: jmohdyusof

Pilot1/P1B3/p1b3.py

@@ -477,15 +477,15 @@ def load_dose_response(path, seed, dtype, min_logconc=-5., max_logconc=-5., subs
 def stage_data():
     server = 'http://ftp.mcs.anl.gov/pub/candle/public/benchmarks/P1B3/'
 
-    cell_expr_path = candle.fetch_file(server + 'P1B3_cellline_expressions.tsv', 'Pilot1', untar=False)
-    cell_mrna_path = candle.fetch_file(server + 'P1B3_cellline_mirna.tsv', 'Pilot1', untar=False)
-    cell_prot_path = candle.fetch_file(server + 'P1B3_cellline_proteome.tsv', 'Pilot1', untar=False)
-    cell_kino_path = candle.fetch_file(server + 'P1B3_cellline_kinome.tsv', 'Pilot1', untar=False)
-    drug_desc_path = candle.fetch_file(server + 'P1B3_drug_descriptors.tsv', 'Pilot1', untar=False)
-    drug_auen_path = candle.fetch_file(server + 'P1B3_drug_latent.csv', 'Pilot1', untar=False)
-    dose_resp_path = candle.fetch_file(server + 'P1B3_dose_response.csv', 'Pilot1', untar=False)
-    test_cell_path = candle.fetch_file(server + 'P1B3_test_celllines.txt', 'Pilot1', untar=False)
-    test_drug_path = candle.fetch_file(server + 'P1B3_test_drugs.txt', 'Pilot1', untar=False)
+    cell_expr_path = candle.fetch_file(server + 'P1B3_cellline_expressions.tsv', 'Pilot1', unpack=False)
+    cell_mrna_path = candle.fetch_file(server + 'P1B3_cellline_mirna.tsv', 'Pilot1', unpack=False)
+    cell_prot_path = candle.fetch_file(server + 'P1B3_cellline_proteome.tsv', 'Pilot1', unpack=False)
+    cell_kino_path = candle.fetch_file(server + 'P1B3_cellline_kinome.tsv', 'Pilot1', unpack=False)
+    drug_desc_path = candle.fetch_file(server + 'P1B3_drug_descriptors.tsv', 'Pilot1', unpack=False)
+    drug_auen_path = candle.fetch_file(server + 'P1B3_drug_latent.csv', 'Pilot1', unpack=False)
+    dose_resp_path = candle.fetch_file(server + 'P1B3_dose_response.csv', 'Pilot1', unpack=False)
+    test_cell_path = candle.fetch_file(server + 'P1B3_test_celllines.txt', 'Pilot1', unpack=False)
+    test_drug_path = candle.fetch_file(server + 'P1B3_test_drugs.txt', 'Pilot1', unpack=False)
 
     return(cell_expr_path, cell_mrna_path, cell_prot_path, cell_kino_path,
            drug_desc_path, drug_auen_path, dose_resp_path, test_cell_path,

Pilot2/P2B1/p2b1.py

@@ -103,7 +103,7 @@ def get_list_of_data_files(GP):
     # data_hash = p2.data_sets[GP['set_sel']][1]
     print('Reading Data Files... %s->%s' % (GP['set_sel'], data_set))
     # Check if the data files are in the data director, otherwise fetch from FTP
-    data_file = candle.fetch_file('http://ftp.mcs.anl.gov/pub/candle/public/benchmarks/Pilot2/' + data_set + '.tar.gz', untar=True, subdir='Pilot2')
+    data_file = candle.fetch_file('http://ftp.mcs.anl.gov/pub/candle/public/benchmarks/Pilot2/' + data_set + '.tar.gz', unpack=True, subdir='Pilot2')
     data_dir = os.path.join(os.path.dirname(data_file), data_set)
     # Make a list of all of the data files in the data set
     data_files = glob.glob('%s/*.npz' % data_dir)

Pilot3/P3B1/p3b1_baseline_keras2.py

@@ -35,7 +35,7 @@ def fetch_data(gParameters):
     """
 
     path = gParameters['data_url']
-    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', untar=True)
+    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', unpack=True)
 
     return fpath
 

Pilot3/P3B2/p3b2_baseline_keras2.py

@@ -50,7 +50,7 @@ def run(gParameters):
 
     origin = gParameters['data_url']
     train_data = gParameters['train_data']
-    data_loc = candle.fetch_file(origin + train_data, untar=True, md5_hash=None, subdir='Pilot3')
+    data_loc = candle.fetch_file(origin + train_data, unpack=True, md5_hash=None, subdir='Pilot3')
 
     print('Data downloaded and stored at: ' + data_loc)
     data_path = os.path.dirname(data_loc)

Pilot3/P3B3/p3b3_baseline_keras2.py

@@ -40,7 +40,7 @@ def fetch_data(gParameters):
     """
 
     path = gParameters['data_url']
-    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', untar=True)
+    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', unpack=True)
 
     return fpath
 

Pilot3/P3B4/p3b4_baseline_keras2.py

@@ -35,7 +35,7 @@ def fetch_data(gParameters):
     """
 
     path = gParameters['data_url']
-    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', untar=True)
+    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', unpack=True)
 
     return fpath
 

Pilot3/P3B4/p3b4_baseline_tf2.py

@@ -26,7 +26,7 @@ def fetch_data(gParameters):
 
     path = gParameters['data_url']
     fpath = candle.fetch_file(
-        path + gParameters['train_data'], 'Pilot3', untar=True)
+        path + gParameters['train_data'], 'Pilot3', unpack=True)
 
     return fpath
 

Pilot3/P3B5/p3b5_baseline_pytorch.py

@@ -29,7 +29,7 @@ def initialize_parameters():
 
 
 def fetch_data(gParameters):
-    """ Download and untar data
+    """ Download and unpack data
 
     Args:
         gParameters: parameters from candle
@@ -38,7 +38,7 @@ def fetch_data(gParameters):
         path to where the data is located
     """
     path = gParameters['data_url']
-    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', untar=True)
+    fpath = candle.fetch_file(path + gParameters['train_data'], 'Pilot3', unpack=True)
     return fpath
 
 

Pilot3/P3B7/p3b7_baseline.py

@@ -48,7 +48,7 @@ def initialize_parameters():
 
 
 def fetch_data(gParameters):
-    """Download and untar data
+    """Download and unpack data
 
     Args:
         gParameters: parameters from candle
@@ -58,7 +58,7 @@ def fetch_data(gParameters):
     """
     path = gParameters.data_url
     fpath = candle.fetch_file(
-        path + gParameters.train_data, 'Pilot3', untar=True
+        path + gParameters.train_data, 'Pilot3', unpack=True
     )
     return fpath