diff options
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 8 | ||||
| -rw-r--r-- | wqflask/wqflask/correlation/show_corr_results.py | 8 |
2 files changed, 10 insertions, 6 deletions
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index d0016b33..f6140ac3 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -8,7 +8,7 @@ # ######################################### -from utility.tools import mk_dir, assert_dir, flat_files, TEMPDIR +from utility.tools import valid_path, mk_dir, assert_dir, flat_files, TEMPDIR #Debug Level #1 for debug, mod python will reload import each time @@ -69,7 +69,11 @@ GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/') # Flat file directories GENODIR = flat_files('genotype')+'/' -JSON_GENODIR = flat_files('json')+'/' +JSON_GENODIR = flat_files('genotype/json')+'/' +if not valid_path(JSON_GENODIR): + # fall back on old location (move the dir, FIXME) + JSON_GENODIR = flat_files('json') +assert_dir(GENODIR) PORTADDR = "http://50.16.251.170" diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 6d8dd76a..c1ad1c84 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -161,7 +161,7 @@ class CorrelationResults(object): self.correlation_data = {} db_filename = self.getFileName(target_db_name = self.target_dataset.name) - cache_available = db_filename in os.listdir(webqtlConfig.TEXTDIR) + cache_available = db_filename in os.listdir(webqtlConfig.GENERATED_TEXT_DIR) if self.corr_type == "tissue": self.trait_symbol_dict = self.dataset.retrieve_genes("Symbol") @@ -179,7 +179,7 @@ class CorrelationResults(object): elif self.corr_type == "sample": if self.dataset.type == "ProbeSet" and cache_available: - dataset_file = open(webqtlConfig.TEXTDIR+db_filename,'r') + dataset_file = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') #XZ, 01/08/2009: read the first line line = dataset_file.readline() @@ -571,7 +571,7 @@ class CorrelationResults(object): #db_filename = self.getFileName(target_db_name=self.target_db_name) # - #cache_available = db_filename in os.listdir(webqtlConfig.TEXTDIR) + #cache_available = db_filename in os.listdir(webqtlConfig.GENERATED_TEXT_DIR) # If the cache file exists, do a cached correlation for probeset data if self.dataset.type == "ProbeSet": @@ -1308,7 +1308,7 @@ class CorrelationResults(object): # return allcorrelations - datasetFile = open(webqtlConfig.TEXTDIR+db_filename,'r') + datasetFile = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') print("Invoking parallel computing") input_line_list = datasetFile.readlines() |