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-rw-r--r--wqflask/base/data_set/datasetgroup.py2
-rw-r--r--wqflask/base/data_set/utils.py4
-rw-r--r--wqflask/base/webqtlConfig.py35
-rw-r--r--wqflask/wqflask/correlation/pre_computes.py2
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py2
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py4
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py4
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py2
-rw-r--r--wqflask/wqflask/views.py4
9 files changed, 29 insertions, 30 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
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py
index 308614f0..c08b2d28 100644
--- a/wqflask/wqflask/correlation/pre_computes.py
+++ b/wqflask/wqflask/correlation/pre_computes.py
@@ -102,7 +102,7 @@ def fetch_text_file(dataset_name, conn, text_dir=None):
# checks first for recently generated textfiles if not use gn1 datamatrix
return __file_scanner__(text_dir, results[0]) or __file_scanner__(
- get_setting(app, "WEBQTL_TEXTDIR"), results[0])
+ get_setting(app, "TEXTDIR"), results[0])
except Exception:
pass
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 5848a756..2440b05d 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -225,7 +225,7 @@ def export_corr_matrix(corr_results):
''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
matrix_export_path = "{}{}.csv".format(
- get_setting(app, "WEBQTL_GENERATED_TEXT_DIR"), corr_matrix_filename)
+ get_setting(app, "GENERATED_TEXT_DIR"), corr_matrix_filename)
with open(matrix_export_path, "w+") as output_file:
output_file.write(
"Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index c544190a..48ccd93c 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -608,7 +608,7 @@ class DisplayMappingResults:
self.filename = webqtlUtil.genRandStr("Itvl_")
intCanvas.save(
"{}.png".format(
- os.path.join(get_setting(app, "WEBQTL_GENERATED_IMAGE_DIR"), self.filename)),
+ os.path.join(get_setting(app, "GENERATED_IMAGE_DIR"), self.filename)),
format='png')
intImg = HtmlGenWrapper.create_image_tag(
src="/image/{}.png".format(self.filename),
@@ -623,7 +623,7 @@ class DisplayMappingResults:
intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm, zoom=2)
intCanvasX2.save(
"{}.png".format(
- os.path.join(get_setting(app, "WEBQTL_GENERATED_IMAGE_DIR"),
+ os.path.join(get_setting(app, "GENERATED_IMAGE_DIR"),
self.filename + "X2")),
format='png')
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index bd3fdbc8..7d617f06 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -90,7 +90,7 @@ def write_covarstruct_file(cofactors: str) -> str:
writer.writerow([cofactor_name, datatype])
hash_of_file = get_hash_of_textio(covar_struct_file)
- file_path = get_setting(app, "WEBQTL_TMPDIR") + hash_of_file + ".csv"
+ file_path = get_setting(app, "TMPDIR") + hash_of_file + ".csv"
with open(file_path, "w") as fd:
covar_struct_file.seek(0)
@@ -133,7 +133,7 @@ def write_phenotype_file(trait_name: str,
writer.writerow(this_row)
hash_of_file = get_hash_of_textio(pheno_file)
- file_path = get_setting(app, "WEBQTL_TMPDIR") + hash_of_file + ".csv"
+ file_path = get_setting(app, "TMPDIR") + hash_of_file + ".csv"
with open(file_path, "w") as fd:
pheno_file.seek(0)
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index a478f875..f7ab8ddc 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -465,7 +465,7 @@ class RunMapping:
self.this_trait, self.dataset, self.vals, pheno_filename=output_filename)
rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (
- self.dataset.group.name, self.dataset.group.name, get_setting(app, "WEBQTL_TMPDIR"), plink_output_filename, self.this_trait.name, self.maf, get_setting(app, "WEBQTL_TMPDIR"), plink_output_filename)
+ self.dataset.group.name, self.dataset.group.name, get_setting(app, "TMPDIR"), plink_output_filename, self.this_trait.name, self.maf, get_setting(app, "TMPDIR"), plink_output_filename)
os.system(rqtl_command)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index de2e803a..c7f741c2 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -118,7 +118,7 @@ def index_page():
@app.route("/tmp/<img_path>")
def tmp_page(img_path):
initial_start_vars = request.form
- imgfile = open(get_setting(app, "WEBQTL_GENERATED_IMAGE_DIR") + img_path, 'rb')
+ imgfile = open(get_setting(app, "GENERATED_IMAGE_DIR") + img_path, 'rb')
imgdata = imgfile.read()
imgB64 = base64.b64encode(imgdata)
bytesarray = array.array('B', imgB64)
@@ -229,7 +229,7 @@ def docedit():
@app.route('/generated/<filename>')
def generated_file(filename):
- return send_from_directory(get_setting(app, "WEBQTL_GENERATED_IMAGE_DIR"), filename)
+ return send_from_directory(get_setting(app, "GENERATED_IMAGE_DIR"), filename)
@app.route("/help")
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-21 18:11:42 +0000