Use Constants instead of initiating constants object

app.py

@@ -261,14 +261,14 @@
 callbacks.text_mining.callbacks.init_callback(app)
 
 # Create database table
-const = Constants()
-make_dir(const.TEMP)
+
+make_dir(Constants.TEMP)
 
 try:
-    connection = sqlite3.connect(const.FILE_STATUS_DB)
+    connection = sqlite3.connect(Constants.FILE_STATUS_DB)
     cursor = connection.cursor()
 
-    query = f'CREATE TABLE IF NOT EXISTS {const.FILE_STATUS_TABLE} (name TEXT, UNIQUE(name));'
+    query = f'CREATE TABLE IF NOT EXISTS {Constants.FILE_STATUS_TABLE} (name TEXT, UNIQUE(name));'
 
     cursor.execute(query)
     connection.commit()

callbacks/browse_loci/callbacks.py

@@ -11,7 +11,6 @@
 from ..file_util import *
 
 from ..constants import Constants
-const = Constants()
 
 
 def init_callback(app):
@@ -73,15 +72,15 @@ def handle_exception(e):
     @app.server.route('/genomes_nipponbare/<path:filename>')
     def send_genomes_nipponbare_url(filename):
         try:
-            return send_from_directory(const.GENOMES_NIPPONBARE, filename)
+            return send_from_directory(Constants.GENOMES_NIPPONBARE, filename)
         except FileNotFoundError:
             abort(404)
 
     @app.server.route('/annotations_nb/<nb_intervals_str>/<path:foldername>/<selected_interval_str>/<file_format>')
     def send_annotations_nb_url(nb_intervals_str, foldername, selected_interval_str, file_format):
         try:
             temp_output_folder_dir = get_path_to_temp(
-                nb_intervals_str, const.TEMP_IGV, foldername)
+                nb_intervals_str, Constants.TEMP_IGV, foldername)
 
             selected_interval_str_filename = convert_text_to_path(
                 selected_interval_str)
@@ -96,7 +95,7 @@ def send_annotations_nb_url(nb_intervals_str, foldername, selected_interval_str,
     @app.server.route('/open_chromatin_panicle/<path:filename>')
     def send_open_chromatin_panicle_url(filename):
         try:
-            return send_from_directory(const.OPEN_CHROMATIN_PANICLE, filename)
+            return send_from_directory(Constants.OPEN_CHROMATIN_PANICLE, filename)
 
         except FileNotFoundError:
             abort(404)

callbacks/browse_loci/util.py

@@ -1,17 +1,13 @@
 from ..lift_over import util
 import gffutils
-import pandas as pd
-import os
 from ..file_util import *
 from ..constants import Constants
 
-const = Constants()
-
 
 def write_igv_tracks_to_file(nb_intervals_str):
     # tracks found in igv
-    track_db = [[const.ANNOTATIONS_NB, 'IRGSPMSU.gff.db', 'gff'],
-                [const.OPEN_CHROMATIN_PANICLE, 'SRR7126116_ATAC-Seq_Panicles.bed', 'bed']]
+    track_db = [[Constants.ANNOTATIONS_NB, 'IRGSPMSU.gff.db', 'gff'],
+                [Constants.OPEN_CHROMATIN_PANICLE, 'SRR7126116_ATAC-Seq_Panicles.bed', 'bed']]
 
     # write to file the data for igv
     for db in track_db:
@@ -32,7 +28,7 @@ def write_gff_igv_track_to_file(source_dir, source_file, nb_intervals_str):
             nb_intervals_str)
 
         temp_folder = get_path_to_temp(
-            nb_intervals_str, const.TEMP_IGV, source_file)
+            nb_intervals_str, Constants.TEMP_IGV, source_file)
         make_dir(temp_folder)
 
         for i in range(len(loci_list)):

callbacks/coexpression/util.py

@@ -11,7 +11,6 @@
 
 from collections import namedtuple
 
-const = Constants()
 
 # Settings for the module detection algorithms:
 # - multiplier: Value multiplied to the parameter to get the name of the directory
@@ -60,7 +59,7 @@
 
 def get_user_facing_parameter(algo, parameter, network='OS-CX'):
     parameters = sorted(
-        map(int, os.listdir(f'{const.NETWORK_MODULES}/{network}/MSU/{algo}')))
+        map(int, os.listdir(f'{Constants.NETWORK_MODULES}/{network}/MSU/{algo}')))
 
     return parameters.index(parameter) + 1
 
@@ -90,7 +89,7 @@ def get_parameters_for_algo(algo, network='OS-CX'):
     """
     param_dict = {}
     parameters = sorted(
-        map(int, os.listdir(f'{const.NETWORK_MODULES}/{network}/MSU/{algo}')))
+        map(int, os.listdir(f'{Constants.NETWORK_MODULES}/{network}/MSU/{algo}')))
 
     # Display the user-facing parameters for the module detection algorithms
     for idx, parameter in enumerate(parameters):
@@ -124,10 +123,10 @@ def create_module_enrichment_results_dir(genomic_intervals, addl_genes, network,
     """
     if addl_genes:
         temp_output_folder_dir = get_path_to_temp(
-            genomic_intervals, const.TEMP_COEXPRESSION, f'{shorten_name(addl_genes)}/{network}/{algo}/{parameters}')
+            genomic_intervals, Constants.TEMP_COEXPRESSION, f'{shorten_name(addl_genes)}/{network}/{algo}/{parameters}')
     else:
         temp_output_folder_dir = get_path_to_temp(
-            genomic_intervals, const.TEMP_COEXPRESSION, f'{network}/{algo}/{parameters}')
+            genomic_intervals, Constants.TEMP_COEXPRESSION, f'{network}/{algo}/{parameters}')
 
     if not path_exists(temp_output_folder_dir):
         make_dir(temp_output_folder_dir)
@@ -180,7 +179,7 @@ def do_module_enrichment_analysis(implicated_gene_ids, genomic_intervals, addl_g
     if not path_exists(ENRICHED_MODULES_PATH):
         ENRICHED_MODULES_PATH_WITH_TIMESTAMP = append_timestamp_to_filename(
             ENRICHED_MODULES_PATH)
-        MODULES_PATH = f'{const.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv'
+        MODULES_PATH = f'{Constants.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv'
 
         # ====================================================================================
         # This replicates the logic of running the universal enrichment function `enricher()`
@@ -214,7 +213,7 @@ def do_module_enrichment_analysis(implicated_gene_ids, genomic_intervals, addl_g
 
             adj_p_values = false_discovery_control(p_values, method='bh')
             significant_adj_p_values = [(p_values_indices[idx], adj_p_value) for idx, adj_p_value in enumerate(
-                adj_p_values) if adj_p_value < const.P_VALUE_CUTOFF]
+                adj_p_values) if adj_p_value < Constants.P_VALUE_CUTOFF]
             significant_adj_p_values.sort(key=lambda x: x[1])
             significant_adj_p_values = [
                 f'{ID}\t{adj_p_value}' for ID, adj_p_value in significant_adj_p_values]
@@ -265,7 +264,7 @@ def convert_transcript_to_msu_id(transcript_ids_str, network):
     Returns:
     - Equivalent MSU accessions of the KEGG transcript IDs
     """
-    with open(f'{const.GENE_ID_MAPPING}/{network}/transcript-to-msu-id.pickle', 'rb') as f:
+    with open(f'{Constants.GENE_ID_MAPPING}/{network}/transcript-to-msu-id.pickle', 'rb') as f:
         mapping_dict = pickle.load(f)
 
     output_str = ''
@@ -279,14 +278,14 @@ def convert_transcript_to_msu_id(transcript_ids_str, network):
 
 
 def get_genes_in_module(module_idx, network, algo, parameters):
-    with open(f'{const.NETWORK_MODULES}/{network}/transcript/{algo}/{parameters}/{algo}-module-list.tsv') as f:
+    with open(f'{Constants.NETWORK_MODULES}/{network}/transcript/{algo}/{parameters}/{algo}-module-list.tsv') as f:
         for idx, module in enumerate(f):
             if idx + 1 == int(module_idx):
                 return set(module.split('\t'))
 
 
 def get_genes_in_pathway(pathway_id, network):
-    with open(f'{const.ENRICHMENT_ANALYSIS}/{network}/{const.KEGG_DOSA_GENESET}', 'rb') as f:
+    with open(f'{Constants.ENRICHMENT_ANALYSIS}/{network}/{Constants.KEGG_DOSA_GENESET}', 'rb') as f:
         genes_in_pathway = pickle.load(f)
 
     return genes_in_pathway[pathway_id]
@@ -298,7 +297,7 @@ def get_genes_in_module_and_pathway(pathway_id, module_idx, network, algo, param
 
 
 def get_kegg_pathway_name(pathway_id, network):
-    with open(f'{const.ENRICHMENT_ANALYSIS}/{network}/{const.KEGG_DOSA_PATHWAY_NAMES}') as pathways:
+    with open(f'{Constants.ENRICHMENT_ANALYSIS}/{network}/{Constants.KEGG_DOSA_PATHWAY_NAMES}') as pathways:
         for line in pathways:
             line = line.split('\t')
             if line[0].rstrip() == pathway_id:
@@ -408,7 +407,8 @@ def convert_to_df_pe(result, module_idx, network, algo, parameters):
     if result.empty:
         return create_empty_df_with_cols(cols)
 
-    result = result.loc[result['Adj. Combined p-value'] < const.P_VALUE_CUTOFF]
+    result = result.loc[result['Adj. Combined p-value']
+                        < Constants.P_VALUE_CUTOFF]
 
     # IMPORTANT: Do not change ordering of instructions
 
@@ -444,7 +444,8 @@ def convert_to_df_spia(result, network):
     if result.empty:
         return create_empty_df_with_cols(cols)
 
-    result = result.loc[result['Adj. Combined p-value'] < const.P_VALUE_CUTOFF]
+    result = result.loc[result['Adj. Combined p-value']
+                        < Constants.P_VALUE_CUTOFF]
 
     # Prettify display of ID
     result['ID'] = 'dosa' + result['ID']
@@ -486,7 +487,7 @@ def convert_to_df(active_tab, module_idx, network, algo, parameters):
     dir = enrichment_tabs[get_tab_index(active_tab)].path
     enrichment_type = dir.split('/')[-1]
 
-    file = f'{const.ENRICHMENT_ANALYSIS}/{network}/output/{algo}/{parameters}/{dir}/results/{enrichment_type}-df-{module_idx}.tsv'
+    file = f'{Constants.ENRICHMENT_ANALYSIS}/{network}/output/{algo}/{parameters}/{dir}/results/{enrichment_type}-df-{module_idx}.tsv'
 
     columns = {'go': ['ID', 'Gene Ontology Term', 'Gene Ratio',
                       'BG Ratio', 'p-value', 'Adj. p-value', 'q-value', 'Genes', 'Count'],
@@ -591,12 +592,12 @@ def load_module_graph(implicated_gene_ids, module, network, algo, parameters, la
     try:
         # Ignore the word "Module" at the start
         module_idx = int(module.split(' ')[1])
-        OUTPUT_DIR = f'{const.TEMP}/{network}/{algo}/modules/{parameters}'
+        OUTPUT_DIR = f'{Constants.TEMP}/{network}/{algo}/modules/{parameters}'
         coexpress_nw = f'{OUTPUT_DIR}/module-{module_idx}.tsv'
 
         if not path_exists(coexpress_nw):
-            NETWORK_FILE = f'{const.NETWORKS}/{network}.txt'
-            MODULE_FILE = f'{const.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv'
+            NETWORK_FILE = f'{Constants.NETWORKS}/{network}.txt'
+            MODULE_FILE = f'{Constants.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv'
 
             convert_modules_to_edgelist(
                 NETWORK_FILE, MODULE_FILE, module_idx, OUTPUT_DIR)
@@ -621,7 +622,7 @@ def load_module_graph(implicated_gene_ids, module, network, algo, parameters, la
 
 
 def count_modules(network, algo, parameters):
-    with open(f'{const.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv') as f:
+    with open(f'{Constants.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv') as f:
         return len(f.readlines())
 
 
@@ -637,7 +638,7 @@ def get_noun_for_active_tab(active_tab):
 
 
 def count_genes_in_module(implicated_genes, module_idx, network, algo, parameters):
-    with open(f'{const.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv') as modules:
+    with open(f'{Constants.NETWORK_MODULES}/{network}/MSU/{algo}/{parameters}/{algo}-module-list.tsv') as modules:
         for idx, module in enumerate(modules):
             if idx == module_idx - 1:
                 module_genes = module.strip().split('\t')

callbacks/file_util.py

@@ -5,8 +5,6 @@
 import time
 import sqlite3
 
-const = Constants()
-
 
 def path_exists(path):
     """
@@ -64,7 +62,7 @@ def get_path_to_temp(genomic_interval, analysis_type, *args):
 
     analysis_type = convert_text_to_path(analysis_type)
 
-    temp_dir = f'{const.TEMP}/{genomic_interval_foldername}/{analysis_type}'
+    temp_dir = f'{Constants.TEMP}/{genomic_interval_foldername}/{analysis_type}'
     for folder in args:
         temp_dir += f'/{convert_text_to_path(folder)}'
 
@@ -76,20 +74,21 @@ def get_path_to_temp(genomic_interval, analysis_type, *args):
 def get_path_to_text_mining_temp(analysis_type, *args):
     analysis_type = convert_text_to_path(analysis_type)
 
-    temp_dir = f'{const.TEMP}/{analysis_type}'
+    temp_dir = f'{Constants.TEMP}/{analysis_type}'
     for folder in args:
         temp_dir += f'/{convert_text_to_path(folder)}'
 
     temp_dir = re.sub(r'/+', '/', temp_dir)
-    
+
     return temp_dir
-
+
+
 def shorten_name(name):
     try:
-        connection = sqlite3.connect(const.FILE_STATUS_DB)
+        connection = sqlite3.connect(Constants.FILE_STATUS_DB)
         cursor = connection.cursor()
 
-        query = f'INSERT OR IGNORE INTO {const.FILE_STATUS_TABLE}(name) VALUES("{name}")'
+        query = f'INSERT OR IGNORE INTO {Constants.FILE_STATUS_TABLE}(name) VALUES("{name}")'
 
         cursor.execute(query)
         connection.commit()
@@ -100,10 +99,10 @@ def shorten_name(name):
         pass
 
     try:
-        connection = sqlite3.connect(const.FILE_STATUS_DB)
+        connection = sqlite3.connect(Constants.FILE_STATUS_DB)
         cursor = connection.cursor()
 
-        query = f'SELECT rowid FROM {const.FILE_STATUS_TABLE} WHERE name = "{name}"'
+        query = f'SELECT rowid FROM {Constants.FILE_STATUS_TABLE} WHERE name = "{name}"'
         cursor.execute(query)
         row_id = cursor.fetchall()[0][0]
 

callbacks/homepage/callbacks.py

@@ -8,8 +8,6 @@
 
 from ..style_util import *
 
-const = Constants()
-
 
 def init_callback(app):
 
@@ -72,7 +70,8 @@ def parse_input(nb_intervals_str, n_clicks, n_submit, dccStore_children, *_):
 
         if 'homepage-reset' == ctx.triggered_id:
             # clear data for items in dcc.Store found in session-container
-            dccStore_children = get_cleared_dccStore_data_excluding_some_data(dccStore_children)
+            dccStore_children = get_cleared_dccStore_data_excluding_some_data(
+                dccStore_children)
 
             return dccStore_children, None, {'display': 'none'}, False, ''
 
@@ -130,8 +129,7 @@ def set_input_fields_with_preset_input(example_genomic_interval_n_clicks):
             return get_example_genomic_interval(ctx.triggered_id['description'])
 
         raise PreventUpdate
-
-
+
     @app.callback(
         Output('homepage-genomic-intervals-saved-input',
                'data', allow_duplicate=True),
@@ -141,7 +139,6 @@ def set_input_fields_with_preset_input(example_genomic_interval_n_clicks):
     def set_input_fields(genomic_intervals):
         return genomic_intervals
 
-
     @app.callback(
         Output('homepage-results-container', 'style'),
         Input('homepage-is-submitted', 'data'),

callbacks/homepage/util.py

@@ -6,23 +6,22 @@
 
 import sqlite3
 
-const = Constants()
 
 example_genomic_intervals = {
     'pre-harvest': 'Chr01:1523625-1770814;Chr04:4662701-4670717',
     'anaerobic-germination': 'Chr07:6000000-6900000'}
 
 
 def clear_cache_folder():
-    if os.path.exists(const.TEMP):
-        shutil.rmtree(const.TEMP, ignore_errors=True)
+    if os.path.exists(Constants.TEMP):
+        shutil.rmtree(Constants.TEMP, ignore_errors=True)
 
     # Drop the table
     try:
-        connection = sqlite3.connect(const.FILE_STATUS_DB)
+        connection = sqlite3.connect(Constants.FILE_STATUS_DB)
         cursor = connection.cursor()
 
-        query = f'DROP TABLE {const.FILE_STATUS_TABLE}'
+        query = f'DROP TABLE {Constants.FILE_STATUS_TABLE}'
 
         cursor.execute(query)
         connection.commit()
@@ -33,13 +32,13 @@ def clear_cache_folder():
         pass
 
     # Recreate the database
-    make_dir(const.TEMP)
+    make_dir(Constants.TEMP)
 
     try:
-        connection = sqlite3.connect(const.FILE_STATUS_DB)
+        connection = sqlite3.connect(Constants.FILE_STATUS_DB)
         cursor = connection.cursor()
 
-        query = f'CREATE TABLE IF NOT EXISTS {const.FILE_STATUS_TABLE} (name TEXT, UNIQUE(name));'
+        query = f'CREATE TABLE IF NOT EXISTS {Constants.FILE_STATUS_TABLE} (name TEXT, UNIQUE(name));'
 
         cursor.execute(query)
         connection.commit()
@@ -59,10 +58,10 @@ def get_cleared_dccStore_data_excluding_some_data(dccStore_children, *args):
             for arg in args:
                 if arg in dccStore_ID:
                     flag = True
-                    
+
             if not flag:
                 dccStore_children[i]['props']['data'] = ''
-    
+
         else:
             dccStore_children[i]['props']['data'] = ''
 

callbacks/lift_over/callbacks.py

@@ -4,7 +4,6 @@
 from .util import *
 from ..constants import Constants
 from ..general_util import *
-const = Constants()
 
 
 def init_callback(app):