mitocube/App.py at master · hnolCol/mitocube · GitHub

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#import flask utils
from flask import Flask, request, jsonify, send_from_directory, render_template
from flask_restful import Resource, Api

#import internal helpers/resources
from backend.resources.resources import mitoCubeResources

from backend.helper.Data import Data, DBFeatures
from backend.helper.Token import Token
from backend.helper.FeatureFinder import FeatureFinder
from backend.helper.Email import EmailHelper
from backend.helper.Admin import AdminUsers
from backend.helper.Submission import Submission
from backend.helper.Performance import Performance
from backend.helper.PTM import PTMAnnotations, PTMManger
from backend.helper.Library import Libraries
#external package imports

from pathlib import Path
import os

from decouple import config

#internal imports
# set the project root directory as the static folder
app = Flask(__name__,
            static_folder='build/static',
            template_folder="build",
            )

api = Api(app)
#define improtant paths
pathToDataFolder = os.path.join(app.root_path,"backend","data")
pathToTokens = os.path.join(pathToDataFolder,"dynamic","tokens.json")
pathToUsers = os.path.join(pathToDataFolder,"dynamic","users.json")
pathToData = os.path.join(pathToDataFolder,"static","datasets")
pathToPerformanceData = os.path.join(pathToDataFolder,"dynamic","performance")
pathToDB = os.path.join(pathToDataFolder,"static","dbs","uniprot")
pathToSubmissionFolder =  os.path.join(pathToDataFolder,"dynamic","submissions")
pathToArchive =  os.path.join(pathToDataFolder,"archive")
pathToAPIConfig = os.path.join(app.root_path,"backend","config","docs") #should point to figure, and check for existance! ToDO
pathToStaticData = os.path.join(pathToDataFolder,"static")
pathToLibs = os.path.join(pathToStaticData,"dbs","library")

pathToStaticData = os.path.join(pathToDataFolder,"static")
pathToDynamicData = os.path.join(pathToDataFolder,"dynamic")
staticDatasets, staticUniprot = os.path.join(pathToStaticData,"datasets"), os.path.join(pathToStaticData,"dbs","uniprot")
pathToPerformance = os.path.join(pathToDynamicData,"performance")
pathToSubmission = os.path.join(pathToDynamicData,"submissions")
#creating folders if they do not exists, should actually only happen on first start.
for p in [pathToStaticData,pathToDynamicData,staticDatasets, staticUniprot, pathToPerformance, pathToSubmission, pathToArchive, pathToLibs]:
        if not os.path.exists(p):
                Path(p).mkdir(parents=True,exist_ok=True)

#define data helpers
dbManager = DBFeatures(pathToDB=pathToDB)
libManager = Libraries()
libManager.addLibsFromFolder(pathToLibs)
dataManger = Data(pathToData,pathToAPIConfig,pathToArchive,dbManager)
adminUserManager = AdminUsers(pathToUsers)
tokenManager = Token(pathToTokens,
        tokensValid = dataManger.getAPIParam("token-valid(h)"),
        shareTokensValid = dataManger.getAPIParam("share-token-valid(h)"))
performanceManager = Performance(pathToData = pathToPerformanceData,
                        performanceConfig = dataManger.getAPIParam("performance-runs"),
                        propertyOptions = dataManger.getAPIParam("performancePropertyOptions"),
                        mainGroup = dataManger.getAPIParam("performance-main-group"))

##update email settings
emailSettings = dataManger.getConfigParam("email-sever-settings")
for k,v in emailSettings.items():
        if v in [0,1]:
                app.config[k] = v == 1 #0 and 1 are transfered to True/False, might wort also with 0/1?
        else:
                app.config[k] = v
app.config["MAIL_PASSWORD"] = config("email-pw")

#init email and submission manager
emailHelper = EmailHelper(app)
submissionManager =  Submission(pathToSubmissionFolder,pathToArchive ,dataManger, emailHelper)
featureFinder = FeatureFinder(data = dataManger, DB = dbManager)
ptmManger = PTMManger(dataManger,featureFinder)
##put helpers in dict for easy init
helpers = {
        "data" :  dataManger,
        "featureFinder" : featureFinder,
        "db" : dbManager,
        "token" : tokenManager,
        "email" : emailHelper,
        "user" : adminUserManager,
        "submission" : submissionManager,
        "ptm" : ptmManger,
        "libs" : libManager,
        "performance" : performanceManager
}

# add resources
for resource in mitoCubeResources:
        resourceKwargs = dict()
        if len(resource["reqKwargs"]) > 0:
                resourceKwargs = dict([(k,helpers[k]) for k in resource["reqKwargs"]])
        api.add_resource(resource["obj"],resource["url"],resource_class_kwargs=resourceKwargs)


@app.route("/")
def build_index():
        return render_template("index.html")#

if __name__ == '__main__':
    app.run(host='0.0.0.0', port=5000, use_reloader = True)