diff options
Diffstat (limited to 'wqflask/base')
| -rw-r--r-- | wqflask/base/data_set/datasetgroup.py | 2 | ||||
| -rw-r--r-- | wqflask/base/data_set/utils.py | 4 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 35 |
3 files changed, 20 insertions, 21 deletions
diff --git a/wqflask/base/data_set/datasetgroup.py b/wqflask/base/data_set/datasetgroup.py index a44cf18d..7c3301fe 100644 --- a/wqflask/base/data_set/datasetgroup.py +++ b/wqflask/base/data_set/datasetgroup.py @@ -129,7 +129,7 @@ class DatasetGroup: return study_samples def get_genofiles(self): - jsonfile = "%s/%s.json" % (get_setting(app, "WEBQTL_GENODIR"), self.name) + jsonfile = "%s/%s.json" % (get_setting(app, "GENODIR"), self.name) try: f = open(jsonfile) except: diff --git a/wqflask/base/data_set/utils.py b/wqflask/base/data_set/utils.py index 11391d69..7f55989f 100644 --- a/wqflask/base/data_set/utils.py +++ b/wqflask/base/data_set/utils.py @@ -57,7 +57,7 @@ def cache_dataset_results(dataset_name: str, dataset_type: str, samplelist: List samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) - file_path = os.path.join(app.config["WEBQTL_TMPDIR"], f"{file_name}.json") + file_path = os.path.join(app.config["TMPDIR"], f"{file_name}.json") with open(file_path, "w") as file_handler: json.dump(query_results, file_handler) @@ -70,7 +70,7 @@ def fetch_cached_results(dataset_name: str, dataset_type: str, samplelist: List) samplelist_as_str = ",".join(samplelist) file_name = generate_hash_file(dataset_name, dataset_type, table_timestamp, samplelist_as_str) - file_path = os.path.join(app.config["WEBQTL_TMPDIR"], f"{file_name}.json") + file_path = os.path.join(app.config["TMPDIR"], f"{file_name}.json") try: with open(file_path, "r") as file_handler: diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 600c6800..a5797f60 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -91,34 +91,33 @@ def init_app(app): TEMPDIR = app.config["TEMPDIR"] mkdir_with_temp_dir = lambda child: mkdir_with_assert_writable( TEMPDIR, child) - WEBQTL_TMPDIR = mkdir_with_temp_dir("/gn2/") - app.config["WEBQTL_TMPDIR"] = WEBQTL_TMPDIR - app.config["TMPDIR"] = WEBQTL_TMPDIR - app.config["WEBQTL_CACHEDIR"] = mkdir_with_temp_dir( - f"{WEBQTL_TMPDIR}cache/") + TMPDIR = mkdir_with_temp_dir("/gn2/") + app.config["TMPDIR"] = TMPDIR + app.config["CACHEDIR"] = mkdir_with_temp_dir( + f"{TMPDIR}cache/") # We can no longer write into the git tree: - app.config["WEBQTL_GENERATED_IMAGE_DIR"] = mkdir_with_temp_dir( - f"{WEBQTL_TMPDIR}generated/") - app.config["WEBQTL_GENERATED_TEXT_DIR"] = mkdir_with_temp_dir( - f"{WEBQTL_TMPDIR}generated_text/") + app.config["GENERATED_IMAGE_DIR"] = mkdir_with_temp_dir( + f"{TMPDIR}generated/") + app.config["GENERATED_TEXT_DIR"] = mkdir_with_temp_dir( + f"{TMPDIR}generated_text/") # Flat file directories - app.config["WEBQTL_GENODIR"] = flat_files(app, 'genotype/') + app.config["GENODIR"] = flat_files(app, 'genotype/') # JSON genotypes are OBSOLETE - WEBQTL_JSON_GENODIR = flat_files(app, 'genotype/json/') - if not valid_path(WEBQTL_JSON_GENODIR): + JSON_GENODIR = flat_files(app, 'genotype/json/') + if not valid_path(JSON_GENODIR): # fall back on old location (move the dir, FIXME) - WEBQTL_JSON_GENODIR = flat_files('json') - app.config["WEBQTL_JSON_GENODIR"] = WEBQTL_JSON_GENODIR + JSON_GENODIR = flat_files('json') + app.config["JSON_GENODIR"] = JSON_GENODIR - app.config["WEBQTL_TEXTDIR"] = os.path.join( + app.config["TEXTDIR"] = os.path.join( app.config.get("GNSHARE", "/gnshare/gn/"), "web/ProbeSetFreeze_DataMatrix") # Are we using the following...? - app.config["WEBQTL_PORTADDR"] = "http://50.16.251.170" - app.config["WEBQTL_INFOPAGEHREF"] = '/dbdoc/%s.html' - app.config["WEBQTL_CGIDIR"] = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' + app.config["PORTADDR"] = "http://50.16.251.170" + app.config["INFOPAGEHREF"] = '/dbdoc/%s.html' + app.config["CGIDIR"] = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR' return app |