Merge pull request #9 from hippolyteblot/fixe-lcmodeldata

using env var for the cache folder

Author: axlbonnet

src/app.py

@@ -17,7 +17,7 @@
 
 # local imports
 from utils.settings import (APP_HOST, APP_PORT, APP_DEBUG, DEV_TOOLS_PROPS_CHECK, SSL_CERT_CHAIN, SSL_SERVER_KEY,
-                            get_DB, PRODUCTION)
+                            get_DB, PRODUCTION, CACHE_FOLDER)
 
 from components import navbar, footer
 from components.login import User, login_location
@@ -64,8 +64,8 @@ def serve_layout():
     local_app.layout = serve_layout  # set the layout to the serve_layout function
 
     # create a tmp folder if it does not exist
-    if not os.path.exists('src/tmp'):
-        os.makedirs('src/tmp')
+    if not os.path.exists(CACHE_FOLDER):
+        os.makedirs(CACHE_FOLDER)
 
     login_manager = LoginManager()
     login_manager.init_app(server)

src/models/home.py

@@ -16,23 +16,6 @@
 from utils.settings import get_DB, CACHE_FOLDER
 
 
-def load_exec_from_local() -> list:
-    """Load the executions from the local folder"""
-    folder = "src/data/spectro/"
-    exec_list = []
-    for group in ["A", "B"]:
-        for subfolder in os.listdir(folder + group):
-            voxel = subfolder.split("_Vox")[1]
-            exec_number = int(subfolder.split("_")[0].split("Rec")[1])
-
-            execution = {
-                "path": group + "/" + subfolder + "/",
-                "name": "parameters " + group + ", voxel " + voxel + ", execution " + str(exec_number)
-            }
-            exec_list.append(execution)
-    return exec_list
-
-
 def load_exp_from_db():
     """Load the experiments from the local folder"""
     # query = 'SELECT * FROM EXPERIMENTS INNER JOIN USERS U ON EXPERIMENTS.user_id = U.id WHERE EXPERIMENTS.single = 0'

src/models/spectro_utils.py

@@ -11,7 +11,7 @@
 from dash import html
 from pandas import DataFrame
 
-from utils.settings import get_GVC
+from utils.settings import get_GVC, CACHE_FOLDER
 from utils.spectro_reader import get_quest2, get_lcmodel, parse_lcmodel
 from utils.settings import get_DB
 
@@ -39,14 +39,14 @@ def get_cquest_experiment_data(experiment_id: int) -> pd.DataFrame:
 
 def read_cquest_file(file_uuid: str) -> DataFrame:
     """Read the file uploaded by the user using the uuid and return a dataframe"""
-    path = os.path.join("src", "tmp", "user_compare", str(file_uuid) + ".txt")
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(file_uuid) + ".txt")
     data = get_quest2(path)
     return data
 
 
 def read_lcmodel_file(file_uuid: str) -> DataFrame:
     """Read the file uploaded by the user using the uuid and return a dataframe"""
-    path = os.path.join("src", "tmp", "user_compare", str(file_uuid) + ".table")
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(file_uuid) + ".table")
     data, diag = get_lcmodel(path)
     data = parse_lcmodel(data, diag)
     return data
@@ -78,30 +78,30 @@ def get_metadata_cquest(exp_id: int) -> list:
 
 def get_files_in_folder(folder_id, extension='txt'):
     """Get the files in a folder from user's folder in local"""
-    path = os.path.join("src", "tmp", "user_compare", str(folder_id))
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(folder_id))
     files = os.listdir(path)
     files = [file for file in files if file.endswith(f".{extension}")]
     return files
 
 
 def read_file_in_folder_cquest(folder, file):
     """Read the file uploaded by the user using the uuid and return a dataframe"""
-    path = os.path.join("src", "tmp", "user_compare", str(folder), str(file))
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(folder), str(file))
     data = get_quest2(path)
     return data
 
 
 def read_file_in_folder_lcmodel(folder, file):
     """Read the file uploaded by the user using the uuid and return a dataframe"""
-    path = os.path.join("src", "tmp", "user_compare", str(folder), str(file))
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(folder), str(file))
     data, diag = get_lcmodel(path)
     data = parse_lcmodel(data, diag)
     return data
 
 
 def read_folder_cquest(folder):
     """Read all the files in a folder and return a dataframe containing all the data"""
-    path = os.path.join("src", "tmp", "user_compare", str(folder))
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(folder))
     files = os.listdir(path)
     files = [file for file in files if file.endswith(".txt")]
     data = pd.DataFrame()
@@ -114,7 +114,7 @@ def read_folder_cquest(folder):
 
 def read_folder_lcmodel(folder):
     """Read all the files in a folder and return a dataframe containing all the data"""
-    path = os.path.join("src", "tmp", "user_compare", str(folder))
+    path = os.path.join(CACHE_FOLDER, "user_compare", str(folder))
     files = os.listdir(path)
     files = [file for file in files if file.endswith(".table")]
     data = pd.DataFrame()

src/models/visualize_experiment_template.py

@@ -4,15 +4,17 @@
 
 import pandas as pd
 
+from settings import CACHE_FOLDER
+
 
 def read_file(filename):
     """Read a file from the tmp folder. The file can be a csv, xlsx or feather file."""
     ext = filename.split('.')[-1]
 
     if ext == 'feather':
-        data = pd.read_feather('src/tmp/' + filename)
+        data = pd.read_feather(CACHE_FOLDER + filename)
     elif ext == 'xlsx':
-        data = pd.read_excel('src/tmp/' + filename)
+        data = pd.read_excel(CACHE_FOLDER + filename)
     else:
-        data = pd.read_csv('src/tmp/' + filename)
+        data = pd.read_csv(CACHE_FOLDER + filename)
     return data

src/views/visualize_experiment_template.py

@@ -11,6 +11,7 @@
 import plotly.express as px
 
 from models.visualize_experiment_template import read_file
+from settings import CACHE_FOLDER
 
 
 def layout():
@@ -542,7 +543,7 @@ def update_dropdowns(contents, filename):
     md5 = hashlib.md5(b64).hexdigest()
     ext = filename[0].split('.')[-1]
     new_filename = md5 + '.' + ext
-    with open('src/tmp/' + new_filename, 'wb') as f:
+    with open(CACHE_FOLDER + new_filename, 'wb') as f:
         f.write(base64.b64decode(content_string))
     try:
         data = read_file(new_filename)