commit 6cdf4d5197e5b122f4683a2c5c6a102ce6eda650 Author: Pablo <42.pablo.ms@gmail.com> Date: Mon Jul 13 01:07:56 2020 +0200 first commit diff --git a/.drone.yml b/.drone.yml new file mode 100644 index 0000000..12f0804 --- /dev/null +++ b/.drone.yml @@ -0,0 +1,12 @@ +kind: pipeline +type: exec +name: default + +platform: + os: linux + arch: amd64 + +steps: +- name: run + commands: + - docker-compose up -d --remove-orphans --build \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..268f784 --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +__pycache__/ +.vscode/ +TODO.md \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..5126449 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,11 @@ +FROM tiangolo/meinheld-gunicorn-flask:python3.7 + +RUN pip install flask + +COPY ./requirements.txt /app/requirements.txt + +WORKDIR /app + +RUN pip install -r requirements.txt + +COPY . /app \ No newline at end of file diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..e142a52 --- /dev/null +++ b/LICENSE @@ -0,0 +1,625 @@ +GNU GENERAL PUBLIC LICENSE + +Version 3, 29 June 2007 + +Copyright © 2007 Free Software Foundation, Inc. + +Everyone is permitted to copy and distribute verbatim copies of this license +document, but changing it is not allowed. + +Preamble + +The GNU General Public License is a free, copyleft license for software and +other kinds of works. + +The licenses for most software and other practical works are designed to take +away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + +If the program does terminal interaction, make it output a short notice like +this when it starts in an interactive mode: + + Copyright (C) + +This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + +This is free software, and you are welcome to redistribute it under certain +conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands might +be different; for a GUI interface, you would use an "about box". + +You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. For +more information on this, and how to apply and follow the GNU GPL, see . + +The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you may +consider it more useful to permit linking proprietary applications with the +library. If this is what you want to do, use the GNU Lesser General Public +License instead of this License. But first, please read . diff --git a/README.md b/README.md new file mode 100644 index 0000000..9b80e59 --- /dev/null +++ b/README.md @@ -0,0 +1,5 @@ +# sdc-lifecycle + +[![Build Status](https://drone.med.upct.es/api/badges/ocean/sdc-lifecycle/status.svg)](https://drone.med.upct.es/ocean/sdc-lifecycle) + +Web tool to upload, process and store data collected during the campaigns \ No newline at end of file diff --git a/dataset/.gitignore b/dataset/.gitignore new file mode 100644 index 0000000..78dc380 --- /dev/null +++ b/dataset/.gitignore @@ -0,0 +1,4 @@ +* +# Except this files +!.gitignore +!README.md diff --git a/dataset/README.md b/dataset/README.md new file mode 100644 index 0000000..bef6593 --- /dev/null +++ b/dataset/README.md @@ -0,0 +1,2 @@ +This folder contains all the sensor data uploaded to the server + diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..ca58d4f --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,27 @@ +version: '3.7' + +services: + + ## TODO: Add true proxy WSGI Server instead of running the builtin + uploadtool: + build: . + restart: unless-stopped + volumes: + - /mnt/storage/dataset-neo:/app/dataset + labels: + - traefik.enable=true + - traefik.http.routers.sdc-uploader.entryPoints=web-secure + - traefik.http.routers.sdc-uploader.rule=Host(`upload.med.upct.es`) + - traefik.http.routers.sdc-uploader.tls.certresolver=default + + download: + image: abiosoft/caddy + restart: unless-stopped + volumes: + - /mnt/storage/dataset-neo:/srv + labels: + - traefik.enable=true + - traefik.http.routers.sdc-download.entryPoints=web-secure + - traefik.http.routers.sdc-download.rule=Host(`download.med.upct.es`) + - traefik.http.routers.sdc-download.tls.certresolver=default + - traefik.http.services.sdc-download.loadbalancer.server.port=2015 \ No newline at end of file diff --git a/gunicorn_conf.py b/gunicorn_conf.py new file mode 100644 index 0000000..f26b4bf --- /dev/null +++ b/gunicorn_conf.py @@ -0,0 +1,46 @@ +# cat /gunicorn_conf.py inside container +# Copied to project so we can tune max_content_length +from __future__ import print_function + +import json +import multiprocessing +import os + +workers_per_core_str = os.getenv("WORKERS_PER_CORE", "2") +web_concurrency_str = os.getenv("WEB_CONCURRENCY", None) +host = os.getenv("HOST", "0.0.0.0") +port = os.getenv("PORT", "80") +bind_env = os.getenv("BIND", None) +use_loglevel = os.getenv("LOG_LEVEL", "info") +if bind_env: + use_bind = bind_env +else: + use_bind = "{host}:{port}".format(host=host, port=port) + +cores = multiprocessing.cpu_count() +workers_per_core = float(workers_per_core_str) +default_web_concurrency = workers_per_core * cores +if web_concurrency_str: + web_concurrency = int(web_concurrency_str) + assert web_concurrency > 0 +else: + web_concurrency = int(default_web_concurrency) + +# Gunicorn config variables +loglevel = use_loglevel +workers = web_concurrency +bind = use_bind +keepalive = 120 +errorlog = "-" + +# For debugging and testing +log_data = { + "loglevel": loglevel, + "workers": workers, + "bind": bind, + # Additional, non-gunicorn variables + "workers_per_core": workers_per_core, + "host": host, + "port": port, +} +print(json.dumps(log_data)) \ No newline at end of file diff --git a/main.py b/main.py new file mode 100644 index 0000000..50a99ec --- /dev/null +++ b/main.py @@ -0,0 +1,196 @@ +from flask import Flask, render_template, request +from datetime import datetime +from probeutils import utils as probeutils +import re +import fnmatch +import os +import meinheld + + +app = Flask(__name__) + +app.config['UPLOAD_FOLDER'] = "./dataset/" + +app.config['MAX_CONTENT_LENGTH'] = 10000000000 # 10GB +meinheld.set_max_content_length(100*1024*1024) + +app.config['DOWNLOADS_URL'] = "https://download.med.upct.es/" + +probes = [{ + 'sensor': 'SUNA', + 'img': 'suna.jpg', + 'active': ['SATSLF0037'], + 'stations': ['M1', 'M2', 'M3'] +}, { + 'sensor': 'FIRe', + 'img': 'fire.jpg', + 'active': ['SATFIS0006'], + 'stations': ['M1', 'M2', 'M3'] +}, { + 'sensor': 'PhycoCTD', + 'img': 'phycoctd.jpg', + 'active': ['phyco_v1', 'phyco_v2'], + 'stations': ['M1', 'M2', 'M3'] +}, { + 'sensor': 'CastAway', + 'img': 'castaway.jpg', + 'active': ['CC1326008'], + 'stations': ['M1', 'M2', 'M3'] +} +#,{ +# 'sensor': 'GoPro', +# 'img': 'gopro.png', +# 'active': ['gopro1'], +# 'stations': ['M1', 'M2', 'M3'] +#} +] + +# Return our beautiful Bootstrap webpage. That we totally have. +@app.route('/') +def upload(): + return render_template('upload.html', probes=probes) + +# What happens when the files just don't fit +@app.errorhandler(413) +def request_entity_too_large(error): + return 'File Too Thicc', 413 + +# What happens when we did an oopsie +@app.errorhandler(500) +def internal_server_error(error): + return render_template('error.html') + +# What happens when someone uploads a thingy +@app.route('/uploader', methods=['POST']) +def upload_file(): + if request.method == 'POST': + f = request.files['file'] + + # Get which probe the user uploaded + probe = request.form.get('probe') + + # Get selected probe + activeProbe = request.form.get('activeProbe') + + # Check if its a valid file to upload + # TODO: Implement this method + # probeutils.check(probe, f) + + # Check if folder exists + try: + if not os.path.exists( + os.path.join(app.config['UPLOAD_FOLDER'], probe)): + os.makedirs(os.path.join(app.config['UPLOAD_FOLDER'], probe)) + + if not os.path.exists( + os.path.join(app.config['UPLOAD_FOLDER'], probe, 'raw')): + os.makedirs(os.path.join( + app.config['UPLOAD_FOLDER'], probe, 'raw')) + except Exception: + return render_template('error.html') + + # Strip station + # if forceStation is checked, override all station parsing + if (request.form.get("forceStation" + probe) != None): + station = request.form.get("stations" + probe) + else: + if (fnmatch.fnmatch((f.filename).upper(), '*M1*') or fnmatch.fnmatch((f.filename).upper(), 'M1*')): + station = 'M1' + elif (fnmatch.fnmatch((f.filename).upper(), "*M2*") or fnmatch.fnmatch((f.filename).upper(), "M2*")): + station = 'M2' + elif (fnmatch.fnmatch((f.filename).upper(), "*M3*") or fnmatch.fnmatch((f.filename).upper(), "M3*")): + station = 'M3' + + # Date Parser of filename + match1 = re.search('\d{4}-\d{2}-\d{2}', f.filename) + if (match1 == None): + match1 = re.search('\d{2}-\d{2}-\d{4}', f.filename) + try: + date = datetime.strptime(match1.group(), '%d-%m-%Y').date() + except Exception: + # Error! More strange data format XD + match1 = re.search('\d{4}\d{2}\d{2}', f.filename) + if (match1 == None): + match1 = re.search('\d{2}\d{2}\d{4}', f.filename) + date = datetime.strptime(match1.group(), '%d%m%Y').date() + else: + date = datetime.strptime(match1.group(), '%Y%m%d').date() + else: + date = datetime.strptime(match1.group(), '%Y-%m-%d').date() + + # Crafting the real overpowered name!!!! + filename = probe + '-' + station + '-'+ activeProbe + '-'+ date.strftime("%Y-%m-%d") + '.csv' + #print(filename) + + # Setting the filePath and saving it + finalFilename = 'raw-'+filename + rawFilePath = os.path.join(app.config['UPLOAD_FOLDER'], probe, 'raw', finalFilename) + f.save(rawFilePath) + + # Start with probe definition + if (probe == 'CastAway'): + ''' CastAway Files ''' + + df_table = probeutils.process_castaway(rawFilePath) + + elif (probe == 'SUNA'): + ''' SUNA Files ''' + + df_table = probeutils.process_suna(rawFilePath) + + elif (probe == 'FIRe'): + ''' FIRe Files ''' + + df_table = probeutils.process_fire(rawFilePath) + + elif (probe == 'PhycoCTD'): + ''' PhycoCTD Files ''' + + df_table = probeutils.process_phyco(rawFilePath) + else: + ''' Empty probe ''' + + df_table = "
" + + # Save file on raw folder and create URL download + url_download = app.config['DOWNLOADS_URL'] + probe + "/" + finalFilename + + # Return success webpage + return render_template('successful.html', url=url_download, tables=df_table) + else: + # No POST Found + return render_template('error.html') + +## Force regenerate QC +@app.route('/regenerate') +def regenerate(): + error_list = [] + #for each file in raw folder, execute all QC + PATH = './dataset/FIRe/raw' + for filename in os.listdir(PATH): + try: + filename_nn = probeutils.execution_NN(filename) + probeutils.execution_PAR(filename_nn) + except Exception as err: + #print(filename) + #print(repr(err)) + error_list.append([filename, repr(err)]) + + #print('Regenerate FIRe done') + + PATH = './dataset/PhycoCTD/raw' + for filename in os.listdir(PATH): + try: + probeutils.check_if_old_phyco(filename) + probeutils.execution_pb_phyco(filename) + except Exception as err: + #print(filename) + #print(repr(err)) + error_list.append([filename, repr(err)]) + + #print('Regenerate Phyco done') + + return render_template('regenerate.html', error_list=error_list) + +if __name__ == '__main__': + app.run() diff --git a/probeutils/utils.py b/probeutils/utils.py new file mode 100644 index 0000000..dd352e8 --- /dev/null +++ b/probeutils/utils.py @@ -0,0 +1,293 @@ +from datetime import datetime +from shutil import copy2 +import pandas as pd +import numpy as np +import os, csv + +UPLOAD_FOLDER = './dataset/' +tableClass = 'table table-striped table-sm table-responsive' + +def get_date(probe, file): + ''' Test utils file ''' + return datetime.now().strftime("%Y-%m-%d-%H:%M:%S") + +# TODO: +# - Check if is a good file +# +#def checkUploadedFile(probe, file): +# return 1 + +# TODO: +# - clean the head of csv, need to extract info an remove the %% (maybe new file with metadata info?) [done] +# - create the empty csv, first row with headers [done] +# - desviation and more data things +def process_castaway(file): + + try: + # Copy raw file to process folder + with open(file) as CastAwayFile: + filename = os.path.basename(CastAwayFile.name).strip('raw-') + processFilePath = os.path.join( + UPLOAD_FOLDER, 'CastAway', filename) + #copy2(file, processFilePath) + + # Getting some metadata info + #with open(file, newline='') as castfile: + # lines = castfile.readlines() + # device = lines[0].split(',')[1].replace('\r\n', '') + # filename = lines[1].split(',')[1].replace('\r\n', '') + # start_latitude = lines[9].split(',')[1].replace('\r\n', '') + # start_longitude = lines[10].split(',')[1].replace('\r\n', '') + # start_altitude = lines[11].split(',')[1].replace('\r\n', '') + # castfile.close() + + # Opening the csv with pandas + df = pd.read_csv(file, skiprows=28) + + # Extract perfil bajada, el 1 es por el header + index_max = df['Depth (Meter)'].idxmax() + 1 + #df_perfilBajada = df[df['depth'].between(0, df['depth'].max())] # No funciona muy bien + # Limitamos a solo el perfil de bajada + df_perfilBajada = df[:index_max] + + # Guardamos solo el perfilBajada en carpeta PB + if not os.path.exists(os.path.join(UPLOAD_FOLDER, 'CastAway', 'PB')): + os.makedirs(os.path.join(UPLOAD_FOLDER, 'CastAway', 'PB')) + + filenamePB = filename.strip('.csv') + '-PB.csv' + perfilBajadaFilePath = os.path.join( + UPLOAD_FOLDER, 'CastAway', 'PB', filenamePB) + df_perfilBajada.to_csv(perfilBajadaFilePath, index=False) + + # Trying to show Dataframe on webpage + return df.to_html(classes=tableClass) + + except Exception as ex: + print('Exception: '+repr(ex)) + return ex + +def process_suna(file): + try: + df = pd.read_csv(file, encoding="ISO-8859-1", header=None) + + #df.columns = ['fechaHora', 'INSTRUMENT', 'Start-time', 'Nitrato(uMol/L)','Nitrato(MG/L)', 'ERROR', 'T_lamp', ] + + #if not os.path.exists(os.path.join(UPLOAD_FOLDER, 'SUNA', 'HEAD')): + # os.makedirs(os.path.join(UPLOAD_FOLDER, 'SUNA', 'HEAD')) + + # Return webpage + return df.to_html(classes=tableClass) + except Exception as ex: + print('Exception: '+repr(ex)) + return ex + +# TODO: +# - Ask for FIRe examples, actually only bin files found (done) +# - Extract file to process folder (done) +# - Save a File with PAR info +# - Headers on email (ask for new headers)[done] +# - Remove negative values (this, done) +# - Arrange similar windows depth and do measure +def process_fire(file): + ''' Processing FIRe ''' + + try: + # Copy raw file to process folder + with open(file) as FIReFile: + filename_raw = os.path.basename(FIReFile.name) + filename = os.path.basename(FIReFile.name).strip('raw-') + #raw_file_path = os.path.join(UPLOAD_FOLDER, 'FIRe', 'raw', filename_raw) + processFilePath = os.path.join( + UPLOAD_FOLDER, 'FIRe', filename) + #copy2(file, processFilePath) + + # First, need to check the csv headers + # Open the process file with pandas + df = pd.read_csv(file, header=None) + + # Headers (now working fine) + df.columns = ['fechaHora', 'estacion', 'fecha', 'hora', 'profundidad', 'Fo', 'Fm', 'Fv', 'Fv/Fm', 'p', 'Abs_rel', 'Abs_abs', 'led_light', 'ETR', 'coma1', 'coma2', 'coma3', 'coma4', 'coma5', 'coma6','error_norm', 'PAR', 'V', 'cero1', 'cero2', 'cero3', 'cero4', 'raro'] + df.loc[:, 'coma1'] = 0 + df.loc[:, 'coma2'] = 0 + df.loc[:, 'coma3'] = 0 + df.loc[:, 'coma4'] = 0 + df.loc[:, 'coma5'] = 0 + df.loc[:, 'coma6'] = 0 + + # Fixing empty values + #df.to_csv(os.path.join(UPLOAD_FOLDER, 'FIRe', 'raw', 'raw-'+filename), index=False) + + filename_nn = execution_NN(filename_raw) + + execution_PAR(filename_nn) + + return df.to_html(classes=tableClass) + + except Exception as ex: + print('Exception: '+repr(ex)) + return ex + +# TODO: +# - Only perfil bajada (done) +def process_phyco(file): + ''' Processing PhycoCTD''' + + try: + # Copy raw file to process folder + with open(file, "r+") as phycoFile: + # Sustract raw- of filename + filename_raw = os.path.basename(phycoFile.name) + filename = os.path.basename(phycoFile.name).strip('raw-') + processFilePath = os.path.join( + UPLOAD_FOLDER, 'PhycoCTD', filename) + #copy2(file, processFilePath) + + # Working with the process file + df = pd.read_csv(file, delimiter=';') + + check_if_old_phyco(filename_raw) + execution_pb_phyco(filename_raw) + + # Return webpage + return df.to_html(classes=tableClass) + except Exception as ex: + print('Exception: '+repr(ex)) + return ex + +def check_if_old_phyco(filename): + # Checking if old file csv + PATH = os.path.join(UPLOAD_FOLDER, 'PhycoCTD', 'raw', filename) + with open(PATH, "r+") as phycoFile: + # Check if old version + line = phycoFile.readline() + if (',' in line): + old = True + else: + old = False + + if (old == True): + df_old = pd.read_csv(PATH, header=None, skiprows=1) + if (len(df_old.columns) == 16): + df_old.columns = ['station', 'latitude', 'longitude', 'time', 'depth', 'temp1', 'temp2', 'cdom[gain]', + 'cdom[ppb]', 'cdom[mv]', 'pe[gain]', 'pe[ppb]', 'pe[mv]', 'chl[gain]', 'chl[ppb]', 'chl[mv]'] + else: + df_old.columns = ['station', 'time', 'depth', 'temp1', 'temp2', 'cdom[gain]', 'cdom[ppb]', + 'cdom[mv]', 'pe[gain]', 'pe[ppb]', 'pe[mv]', 'chl[gain]', 'chl[ppb]', 'chl[mv]'] + raw_path = os.path.join(UPLOAD_FOLDER, 'PhycoCTD', 'raw', filename) + df_old.to_csv(raw_path, index=False, sep=';') + +def execution_pb_phyco(filename): + # Guardamos solo el perfilBajada + if not os.path.exists(os.path.join(UPLOAD_FOLDER, 'PhycoCTD', 'PB')): + os.makedirs(os.path.join(UPLOAD_FOLDER, 'PhycoCTD', 'PB')) + + PATH = os.path.join(UPLOAD_FOLDER, 'PhycoCTD', 'raw', filename) + df = pd.read_csv(PATH, delimiter=';') + + # Checking if NaN values exists [for hack lab version csv upload] + if (df['temp2'].isnull().sum() > 0): + df.loc[:, 'temp2'] = 0 + df = df.dropna() + + # Extract perfil bajada, el 1 es por el header + index_max = df['depth'].idxmax() + 1 + #df_perfilBajada = df[df['depth'].between(0, df['depth'].max())] # No funciona muy bien + # Limitamos a solo el perfil de bajada + df_pb= df[:index_max] + + filename_pb = filename.strip('raw-').strip('.csv') + '-PB.csv' + pb_path = os.path.join(UPLOAD_FOLDER, 'PhycoCTD', 'PB', filename_pb) + df_pb.to_csv(pb_path, sep=';', index=False) + +def execution_NN(filename): + + PATH = os.path.join(UPLOAD_FOLDER, 'FIRe', 'raw', filename) + df = pd.read_csv(PATH, header=None) + + # Headers (now working fine) + df.columns = ['fechaHora', 'estacion', 'fecha', 'hora', 'profundidad', 'Fo', 'Fm', 'Fv', 'Fv/Fm', 'p', 'Abs_rel', 'Abs_abs', 'led_light', + 'ETR', 'coma1', 'coma2', 'coma3', 'coma4', 'coma5', 'coma6', 'error_norm', 'PAR', 'V', 'cero1', 'cero2', 'cero3', 'cero4', 'raro'] + df.loc[:, 'coma1'] = 0 + df.loc[:, 'coma2'] = 0 + df.loc[:, 'coma3'] = 0 + df.loc[:, 'coma4'] = 0 + df.loc[:, 'coma5'] = 0 + df.loc[:, 'coma6'] = 0 + + # NonNegative values rutine + if not os.path.exists(os.path.join(UPLOAD_FOLDER, 'FIRe', 'NN')): + os.makedirs(os.path.join(UPLOAD_FOLDER, 'FIRe', 'NN')) + + # Remove rows with negatives values + df_nn = df[(df.iloc[:, 4:27] >= 0).all(1)] + filename_nn = filename.strip('raw-').strip('.csv') + '-NN.csv' + nonnegative_path = os.path.join(UPLOAD_FOLDER, 'FIRe', 'NN', filename_nn) + df_nn.to_csv(nonnegative_path, index=False) + + return filename_nn + +def execution_PAR(filename): + # PAR rutine + if not os.path.exists(os.path.join(UPLOAD_FOLDER, 'FIRe', 'PAR')): + os.makedirs(os.path.join(UPLOAD_FOLDER, 'FIRe', 'PAR')) + + PATH = os.path.join(UPLOAD_FOLDER, 'FIRe', 'NN', filename) + df = pd.read_csv(PATH) + + # PAR execution + PAR_columns = ['estacion', 'fecha', 'profundidad', 'Fo', 'Fm', 'Fv', 'Fv/Fm', 'p', 'Abs_rel', 'Abs_abs', 'led_light', + 'ETR', 'error_norm', 'PAR'] + + df_PAR = pd.DataFrame(columns=PAR_columns) + + index_max = df['profundidad'].idxmax() + index_min = df['profundidad'].idxmin() + 1 + depth_list = df[index_max:index_min]['profundidad'].to_list() + + last_value = df['profundidad'].max() + similar_depth = [] + for i in range(len(depth_list)): + #print(depth_list[i]) + + if (abs(last_value - depth_list[i]) <= 2000): + last_value = depth_list[i] + similar_depth.append(depth_list[i]) + elif (abs(last_value - depth_list[i]) >= 6000): + ## Save the actual list to DataFrame + #print(similar_depth) + index_first = pd.to_numeric(df.index[df['profundidad'] == similar_depth[0]])[0] + index_last = pd.to_numeric(df.index[df['profundidad'] == similar_depth[-1]])[0] + 1 + df_range = df.iloc[index_first:index_last] + + # Working with df_range + estacion = df['estacion'][0] + fecha = df['fecha'][0] + profundidad = df_range['profundidad'].mean() + Fo = df_range['Fo'].mean() + Fm = df_range['Fm'].mean() + Fv = df_range['Fv'].mean() + FvFm = df_range['Fv/Fm'].mean() + p = df_range['p'].mean() + Abs_rel = df_range['Abs_rel'].mean() + Abs_abs = df_range['Abs_abs'].mean() + led_light = df_range['led_light'].mean() + ETR = df_range['ETR'].mean() + error_norm = df_range['error_norm'].mean() + PAR = df_range['PAR'].mean() + data = [estacion, fecha, profundidad, Fo, Fm, Fv, FvFm, p, Abs_rel, Abs_abs, led_light, ETR, error_norm, PAR] + row = pd.Series(data, index=PAR_columns) + df_PAR = df_PAR.append(row, ignore_index=True) + + ## Empty the list + similar_depth = [] + last_value = depth_list[i] + + ## Adding to the new list + similar_depth.append(depth_list[i]) + + # Saving the DataFrame + # TODO: check last values, around 400 depth + filenamePAR = filename.strip('-NN.csv') + '-PAR.csv' + PARFilePath = os.path.join(UPLOAD_FOLDER, 'FIRe', 'PAR', filenamePAR) + df_PAR.to_csv(PARFilePath, index=False) + diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..508dae9 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,3 @@ +Flask +pandas +meinheld \ No newline at end of file diff --git a/static/css/main.css b/static/css/main.css new file mode 100644 index 0000000..c1316d4 --- /dev/null +++ b/static/css/main.css @@ -0,0 +1,265 @@ +/*! HTML5 Boilerplate v7.3.0 | MIT License | https://html5boilerplate.com/ */ + +/* main.css 2.0.0 | MIT License | https://github.com/h5bp/main.css#readme */ +/* + * What follows is the result of much research on cross-browser styling. + * Credit left inline and big thanks to Nicolas Gallagher, Jonathan Neal, + * Kroc Camen, and the H5BP dev community and team. + */ + +/* ========================================================================== + Base styles: opinionated defaults + ========================================================================== */ + +html { + color: #222; + font-size: 1em; + line-height: 1.4; +} + +/* + * Remove text-shadow in selection highlight: + * https://twitter.com/miketaylr/status/12228805301 + * + * Vendor-prefixed and regular ::selection selectors cannot be combined: + * https://stackoverflow.com/a/16982510/7133471 + * + * Customize the background color to match your design. + */ + +::-moz-selection { + background: #b3d4fc; + text-shadow: none; +} + +::selection { + background: #b3d4fc; + text-shadow: none; +} + +/* + * A better looking default horizontal rule + */ + +hr { + display: block; + height: 1px; + border: 0; + border-top: 1px solid #ccc; + margin: 1em 0; + padding: 0; +} + +/* + * Remove the gap between audio, canvas, iframes, + * images, videos and the bottom of their containers: + * https://github.com/h5bp/html5-boilerplate/issues/440 + */ + +audio, +canvas, +iframe, +img, +svg, +video { + vertical-align: middle; +} + +/* + * Remove default fieldset styles. + */ + +fieldset { + border: 0; + margin: 0; + padding: 0; +} + +/* + * Allow only vertical resizing of textareas. + */ + +textarea { + resize: vertical; +} + +/* ========================================================================== + Browser Upgrade Prompt + ========================================================================== */ + +.browserupgrade { + margin: 0.2em 0; + background: #ccc; + color: #000; + padding: 0.2em 0; +} + +/* ========================================================================== + Author's custom styles + ========================================================================== */ + +/* ========================================================================== + Helper classes + ========================================================================== */ + +/* + * Hide visually and from screen readers + */ + +.hidden { + display: none !important; +} + +/* +* Hide only visually, but have it available for screen readers: +* https://snook.ca/archives/html_and_css/hiding-content-for-accessibility +* +* 1. For long content, line feeds are not interpreted as spaces and small width +* causes content to wrap 1 word per line: +* https://medium.com/@jessebeach/beware-smushed-off-screen-accessible-text-5952a4c2cbfe +*/ + +.sr-only { + border: 0; + clip: rect(0, 0, 0, 0); + height: 1px; + margin: -1px; + overflow: hidden; + padding: 0; + position: absolute; + white-space: nowrap; + width: 1px; + /* 1 */ +} + +/* +* Extends the .sr-only class to allow the element +* to be focusable when navigated to via the keyboard: +* https://www.drupal.org/node/897638 +*/ + +.sr-only.focusable:active, +.sr-only.focusable:focus { + clip: auto; + height: auto; + margin: 0; + overflow: visible; + position: static; + white-space: inherit; + width: auto; +} + +/* +* Hide visually and from screen readers, but maintain layout +*/ + +.invisible { + visibility: hidden; +} + +/* +* Clearfix: contain floats +* +* For modern browsers +* 1. The space content is one way to avoid an Opera bug when the +* `contenteditable` attribute is included anywhere else in the document. +* Otherwise it causes space to appear at the top and bottom of elements +* that receive the `clearfix` class. +* 2. The use of `table` rather than `block` is only necessary if using +* `:before` to contain the top-margins of child elements. +*/ + +.clearfix:before, +.clearfix:after { + content: " "; + /* 1 */ + display: table; + /* 2 */ +} + +.clearfix:after { + clear: both; +} + +/* ========================================================================== + EXAMPLE Media Queries for Responsive Design. + These examples override the primary ('mobile first') styles. + Modify as content requires. + ========================================================================== */ + +@media only screen and (min-width: 35em) { + /* Style adjustments for viewports that meet the condition */ +} + +@media print, + (-webkit-min-device-pixel-ratio: 1.25), + (min-resolution: 1.25dppx), + (min-resolution: 120dpi) { + /* Style adjustments for high resolution devices */ +} + +/* ========================================================================== + Print styles. + Inlined to avoid the additional HTTP request: + https://www.phpied.com/delay-loading-your-print-css/ + ========================================================================== */ + +@media print { + *, + *:before, + *:after { + background: transparent !important; + color: #000 !important; + /* Black prints faster */ + box-shadow: none !important; + text-shadow: none !important; + } + a, + a:visited { + text-decoration: underline; + } + a[href]:after { + content: " (" attr(href) ")"; + } + abbr[title]:after { + content: " (" attr(title) ")"; + } + /* + * Don't show links that are fragment identifiers, + * or use the `javascript:` pseudo protocol + */ + a[href^="#"]:after, + a[href^="javascript:"]:after { + content: ""; + } + pre { + white-space: pre-wrap !important; + } + pre, + blockquote { + border: 1px solid #999; + page-break-inside: avoid; + } + /* + * Printing Tables: + * https://web.archive.org/web/20180815150934/http://css-discuss.incutio.com/wiki/Printing_Tables + */ + thead { + display: table-header-group; + } + tr, + img { + page-break-inside: avoid; + } + p, + h2, + h3 { + orphans: 3; + widows: 3; + } + h2, + h3 { + page-break-after: avoid; + } +} + diff --git a/static/css/normalize.css b/static/css/normalize.css new file mode 100644 index 0000000..192eb9c --- /dev/null +++ b/static/css/normalize.css @@ -0,0 +1,349 @@ +/*! normalize.css v8.0.1 | MIT License | github.com/necolas/normalize.css */ + +/* Document + ========================================================================== */ + +/** + * 1. Correct the line height in all browsers. + * 2. Prevent adjustments of font size after orientation changes in iOS. + */ + +html { + line-height: 1.15; /* 1 */ + -webkit-text-size-adjust: 100%; /* 2 */ +} + +/* Sections + ========================================================================== */ + +/** + * Remove the margin in all browsers. + */ + +body { + margin: 0; +} + +/** + * Render the `main` element consistently in IE. + */ + +main { + display: block; +} + +/** + * Correct the font size and margin on `h1` elements within `section` and + * `article` contexts in Chrome, Firefox, and Safari. + */ + +h1 { + font-size: 2em; + margin: 0.67em 0; +} + +/* Grouping content + ========================================================================== */ + +/** + * 1. Add the correct box sizing in Firefox. + * 2. Show the overflow in Edge and IE. + */ + +hr { + box-sizing: content-box; /* 1 */ + height: 0; /* 1 */ + overflow: visible; /* 2 */ +} + +/** + * 1. 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Correct the odd `em` font sizing in all browsers. + */ + +code, +kbd, +samp { + font-family: monospace, monospace; /* 1 */ + font-size: 1em; /* 2 */ +} + +/** + * Add the correct font size in all browsers. + */ + +small { + font-size: 80%; +} + +/** + * Prevent `sub` and `sup` elements from affecting the line height in + * all browsers. + */ + +sub, +sup { + font-size: 75%; + line-height: 0; + position: relative; + vertical-align: baseline; +} + +sub { + bottom: -0.25em; +} + +sup { + top: -0.5em; +} + +/* Embedded content + ========================================================================== */ + +/** + * Remove the border on images inside links in IE 10. + */ + +img { + border-style: none; +} + +/* Forms + ========================================================================== */ + +/** + * 1. Change the font styles in all browsers. + * 2. Remove the margin in Firefox and Safari. + */ + +button, +input, +optgroup, +select, +textarea { + font-family: inherit; /* 1 */ + font-size: 100%; /* 1 */ + line-height: 1.15; /* 1 */ + margin: 0; /* 2 */ +} + +/** + * Show the overflow in IE. + * 1. Show the overflow in Edge. + */ + +button, +input { /* 1 */ + overflow: visible; +} + +/** + * Remove the inheritance of text transform in Edge, Firefox, and IE. + * 1. Remove the inheritance of text transform in Firefox. + */ + +button, +select { /* 1 */ + text-transform: none; +} + +/** + * Correct the inability to style clickable types in iOS and Safari. + */ + +button, +[type="button"], +[type="reset"], +[type="submit"] { + -webkit-appearance: button; +} + +/** + * Remove the inner border and padding in Firefox. + */ + +button::-moz-focus-inner, +[type="button"]::-moz-focus-inner, +[type="reset"]::-moz-focus-inner, +[type="submit"]::-moz-focus-inner { + border-style: none; + padding: 0; +} + +/** + * Restore the focus styles unset by the previous rule. + */ + +button:-moz-focusring, +[type="button"]:-moz-focusring, +[type="reset"]:-moz-focusring, +[type="submit"]:-moz-focusring { + outline: 1px dotted ButtonText; +} + +/** + * Correct the padding in Firefox. + */ + +fieldset { + padding: 0.35em 0.75em 0.625em; +} + +/** + * 1. Correct the text wrapping in Edge and IE. + * 2. Correct the color inheritance from `fieldset` elements in IE. + * 3. 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e.CSS){for(;o--;)if(e.CSS.supports(f(t[o]),r))return!0;return!1}if("CSSSupportsRule"in e){for(var i=[];o--;)i.push("("+f(t[o])+":"+r+")");return i=i.join(" or "),l("@supports ("+i+") { #modernizr { position: absolute; } }",function(e){return"absolute"===c(e,null,"position")})}return n}function p(e){return e.replace(/([a-z])-([a-z])/g,function(e,t,n){return t+n.toUpperCase()}).replace(/^-/,"")}function m(e,t,o,i){function a(){f&&(delete L.style,delete L.modElem)}if(i=!r(i,"undefined")&&i,!r(o,"undefined")){var l=d(e,o);if(!r(l,"undefined"))return l}for(var f,c,m,h,A,v=["modernizr","tspan","samp"];!L.style&&v.length;)f=!0,L.modElem=s(v.shift()),L.style=L.modElem.style;for(m=e.length,c=0;c + + + + + {% block title %}{% endblock %} - UPCT + + + + + + + + + + + + + + + + + + + + + + +
+
SDC Lifecycle 0.1
+ +
+ + + + {% block content %}{% endblock %} + + + + \ No newline at end of file diff --git a/templates/error.html b/templates/error.html new file mode 100644 index 0000000..93eebdc --- /dev/null +++ b/templates/error.html @@ -0,0 +1,11 @@ +{% extends "base.html" %} +{% block title %}ERROR{% endblock %} + +{% block content %} + +
+
+

ERROR en la subida

+
+ +{% endblock %} \ No newline at end of file diff --git a/templates/regenerate.html b/templates/regenerate.html new file mode 100644 index 0000000..bc1c714 --- /dev/null +++ b/templates/regenerate.html @@ -0,0 +1,22 @@ +{% extends "base.html" %} +{% block title %}DONE{% endblock %} + +{% block content %} + +
+
+

Control de calidad aplicado.

+ + + + {% for error in error_list %} + + + + + {% endfor %} +
{{ error[0] }}{{ error[1] }}
+ +
+ +{% endblock %} \ No newline at end of file diff --git a/templates/successful.html b/templates/successful.html new file mode 100644 index 0000000..06f6d6d --- /dev/null +++ b/templates/successful.html @@ -0,0 +1,33 @@ +{% extends "base.html" %} +{% block title %}OK{% endblock %} + +{% block content %} + +
+
+ +
+ +
+ Volver + + Descargar Archivo + +
+
+ {{ tables|safe }} +
+
+ +
+
+
+
+ +{% endblock %} \ No newline at end of file diff --git a/templates/upload.html b/templates/upload.html new file mode 100644 index 0000000..ce4ac8d --- /dev/null +++ b/templates/upload.html @@ -0,0 +1,127 @@ +{% extends "base.html" %} +{% block title %}Subida{% endblock %} + +{% block content %} + + +
+

Sensores

+
+ +
+
+ + +
+ {% for i in probes %} +
+
+
+

{{ i.sensor }}

+
+ +
+
+ ... +
+
+ + +
+
+ {% endfor%} +
+ + + {% for i in probes %} + + {% endfor %} + + +
+ +{% endblock %} \ No newline at end of file