Restore configuration variables' names

The names had been changed when refactoring the code but can now be restored.

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")