fixed build script - now produces proper build

desktop/build.py

@@ -1,18 +1,26 @@
-from os import pathsep
+from os.path import realpath, dirname, join
+import shutil
 from os.path import realpath, dirname, join
 from subprocess import call
 
 ROOT = dirname(realpath(__file__))
 
 
 def main():
-    entry_point = join(root, 'src', 'mmonitor', '__main__.py')
-    placeholder = join(root, 'src', 'resources', 'images', '.placeholder')
+    entry_point = join(ROOT, 'src', 'mmonitor', '__main__.py')
+    placeholder = join(ROOT, 'src', 'resources', 'images', '.placeholder')
     images_dir_dest = join('resources', 'images')
-    r_script = join(root, 'src', 'resources', 'r', 'horizon.r')
+    r_script = join(ROOT, 'src', 'resources', 'r', 'horizon.r')
     r_dir_dest = join('resources', 'r')
 
-    call(f"pyinstaller -D {entry_point} --name mmonitor --add-data {placeholder}{pathsep}{images_dir_dest} --add-data {r_script}{pathsep}{r_dir_dest}".split())
+    # call(f"pyinstaller -D {entry_point} --name mmonitor --add-data {placeholder}{pathsep}{images_dir_dest} --add-data {r_script}{pathsep}{r_dir_dest}".split()) #use this for building new spec file
+    # remove old dist and built for faster rebuilding
+    try:
+        shutil.rmtree("/Users/timolucas/PycharmProjects/MMonitor/desktop/build/mmonitor/")
+        shutil.rmtree("/Users/timolucas/PycharmProjects/MMonitor/desktop/dist/mmonitor/")
+    except:
+        call(f"pyinstaller mmonitor.spec".split())  # use this for using edited spec file
+    call(f"pyinstaller mmonitor.spec".split())  # use this for using edited spec file
 
 
 if __name__ == '__main__':

desktop/src/mmonitor/dashapp/apps/correlations.py

@@ -1,12 +1,12 @@
 from typing import Tuple, Any, List, Iterable, Dict, Union
 
 import dash
-import dash_core_components as dcc
-import dash_html_components as html
 import plotly.express as px
+from dash import dash_table
+from dash import dcc as dcc
+from dash import html as html
 from dash.dependencies import Input, Output, State
 from dash.exceptions import PreventUpdate
-from dash_table import DataTable
 from pandas import DataFrame
 from plotly.graph_objects import Figure
 
@@ -141,14 +141,15 @@ def _init_layout(self) -> None:
         )
 
         # data table and its download element
-        correlations_tb = DataTable(id='table-correlations', data=[], columns=[])
+        correlations_tb = dash_table.DataTable(id='table-correlations', data=[], columns=[])
         download_tb = dcc.Download(id='download-tb')
 
         CONTENT_STYLE = {
 
             "margin-right": "2rem",
             "padding": "2rem 1rem",
-            'margin-bottom': '200px', 'background-color': 'gainsboro'
+            'margin-bottom': '200px',
+            'font-size': '25px'
         }
 
         container = html.Div(

desktop/src/mmonitor/dashapp/apps/horizon.py

@@ -1,7 +1,7 @@
 import uuid
 
-import dash_core_components as dcc
-import dash_html_components as html
+from dash import dcc
+from dash import html
 from dash.dependencies import Input, Output, State
 from dash.exceptions import PreventUpdate
 from flask import send_from_directory

desktop/src/mmonitor/dashapp/apps/kegg.py

@@ -2,8 +2,8 @@
 import glob
 
 import dash
-import dash_core_components as dcc
-import dash_html_components as html
+from dash import dcc
+from dash import html
 
 from mmonitor.dashapp.app import app
 from mmonitor.dashapp.base_app import BaseApp
@@ -28,7 +28,7 @@ def __init__(self):
 
     def _init_layout(self) -> None:
         self._static_image_route = "/static/"
-        self._samples = glob.glob("/resources/pipeline_out/*/")
+        self._samples = glob.glob("/Users/timolucas/PycharmProjects/MMonitor/desktop/src/resources/pipeline_out/*/")
         print(self._samples)
         header = html.H1("Functional mapping of annotated genomes to KEGG pathways")
         print(self._samples)

desktop/src/mmonitor/dashapp/apps/kraken.py

@@ -3,10 +3,10 @@
 from typing import List, Tuple, Set
 
 import dash
-import dash_core_components as dcc
-import dash_html_components as html
 import pandas as pd
 import plotly.express as px
+from dash import dcc
+from dash import html
 from dash.dependencies import Input, Output, State
 from dash.exceptions import PreventUpdate
 from plotly.graph_objects import Figure

desktop/src/mmonitor/dashapp/apps/taxonomy.py

@@ -1,9 +1,9 @@
 from typing import Tuple, List, Any, Dict
 
 import plotly.express as px
-import dash_core_components as dcc
-import dash_html_components as html
-from dash_table import DataTable
+from dash import dash_table
+from dash import dcc
+from dash import html
 from dash.dependencies import Input, Output
 from plotly.graph_objects import Figure
 
@@ -70,7 +70,7 @@ def _init_layout(self) -> None:
         # data table for debugging
         db_header = html.H4(children='SQLite Database')
         data, columns = self._generate_table_data_cols()
-        data_tb = DataTable(id='table-correlations', data=data, columns=columns)
+        data_tb = dash_table.DataTable(id='table-correlations', data=data, columns=columns)
 
         container = html.Div([maira_header, demo_dd, graph1, graph2, pie_chart_input, db_header, data_tb])
         self.layout = container

desktop/src/mmonitor/dashapp/base_app.py

@@ -1,4 +1,4 @@
-import dash_html_components as html
+from dash import html
 
 from mmonitor.database.mmonitor_db import MMonitorDBInterface
 

desktop/src/mmonitor/dashapp/index.py

@@ -1,11 +1,11 @@
-import dash_core_components as dcc
-import dash_html_components as html
+from dash import dcc
+from dash import html
 from dash.dependencies import Input, Output
 from dash.exceptions import PreventUpdate
 from flask import request
 
 from mmonitor.dashapp.app import app
-from mmonitor.dashapp.apps import correlations, taxonomy, kraken, horizon, kegg
+from mmonitor.dashapp.apps import correlations, taxonomy, horizon, kegg
 from mmonitor.dashapp.base_app import BaseApp
 from mmonitor.database.mmonitor_db import MMonitorDBInterface
 
@@ -44,13 +44,13 @@ def _init_apps(self) -> None:
             '/apps/correlations': {
                 'name': 'Correlations',
                 'app': correlations.Correlations(self._sql)
-            },
-            '/apps/kraken2': {
-                'name': 'Kraken2',
-                'app': kraken.Kraken(self._sql)
+                # },
+                # '/apps/kraken2': {
+                #     'name': 'Kraken2',
+                #     'app': kraken.Kraken(self._sql)
             },
             '/apps/kegg': {
-                'name': 'kegg',
+                'name': 'KEGG',
                 'app': kegg.Kegg()
             }
         }

desktop/src/mmonitor/database/mmonitor_db.py

@@ -96,17 +96,14 @@ def create_db(self, db_name):
             taxonomy TEXT,
             abundance INTEGER,
             sample_id INTEGER,
-            project_id INTEGER,
-            sample_date TEXT,
-            PRIMARY KEY ("read_id")
+            project_id INTEGER
         )"""
 
         # sample metadata
         cursor.execute(create_command)
         create_command = f"""CREATE TABLE IF NOT EXISTS metadata (
             "sample_id"	INTEGER PRIMARY KEY,
-            "data" TEXT,
-            PRIMARY KEY("sample_id")
+            "data" TEXT
         )"""
 
         cursor.execute(create_command)
@@ -115,7 +112,7 @@ def create_db(self, db_name):
         self._db_path = db_name
 
     def update_table_with_kraken_out(self, kraken_out_path: str, tax_rank: str, sample_name: str,
-                                     project_name: str) -> None:
+                                     project_name: str, sample_date):
         """
         Update MMonitor data from a file containing kraken output
         """
@@ -131,9 +128,11 @@ def update_table_with_kraken_out(self, kraken_out_path: str, tax_rank: str, samp
         )
         df = df.sort_values('Count', ascending=False)
         # format name
-        df['Name'] = df['Name'].apply(lambda s: s.strip())
+
+        # df['Name'] = df['Name'].apply(lambda s: s.strip())
         # add sample name
         df['Sample'] = sample_name
+        df['Sample_date'] = sample_date
         df = df[df['Rank'] == tax_rank]
         df = df.drop(columns='Rank')
         for index, row in df.iterrows():
@@ -145,7 +144,7 @@ def update_table_with_kraken_out(self, kraken_out_path: str, tax_rank: str, samp
                 # the same sample while sequencing) then add the abundance to the value in the database
                 if name_exists == 0:
                     insert_query = f"""INSERT INTO mmonitor
-                        (taxonomy, abundance, sample_id, project_id) 
+                        (taxonomy, abundance, sample_id, project_id, sample_date) 
                         VALUES 
                         ('{row['Name']}', {row['Count']}, '{sample_name}', '{project_name}')"""
                     cursor.execute(insert_query)

desktop/src/mmonitor/userside/centrifuge.py

@@ -1,8 +1,7 @@
-import os
 import logging
-import subprocess
 import multiprocessing
-import pathlib
+import os
+import subprocess
 
 
 class CentrifugeRunner:
@@ -32,15 +31,16 @@ def check_centrifuge(self):
     def run_centrifuge(self, sequence_list, centrifuge_index, sample_name):
         print(sequence_list)
         if sequence_list[0].lower().endswith(('.fq', '.fastq', '.fastq.gz', '.fq.gz')):
+            self.cent_out = f"/Users/timolucas/PycharmProjects/MMonitor/desktop/src/resources/pipeline_out/{sample_name}_cent_out"
             # if ".fastq" in sequence_list[0] or ".fq" in sequence_list[0] or ".fastq.gz" in sequence_list[0]:
-            self.cent_out = f"{pathlib.Path(__file__).parent.resolve()}/classifier_out/{sample_name}_cent_out"
-            cmd = f'centrifuge -x {centrifuge_index} -U {self.unpack_fastq_list(sequence_list)} -p {multiprocessing.cpu_count()} -S {pathlib.Path(__file__).parent.resolve()}/classifier_out/{sample_name}_cent_out'
+
+            cmd = f'centrifuge -x {centrifuge_index} -U {self.unpack_fastq_list(sequence_list)} -p {multiprocessing.cpu_count()} -S {self.cent_out}'
             print(cmd)
             os.system(cmd)
             return
         if ".fasta" in sequence_list[0] or ".fa" in sequence_list[0]:
-            self.cent_out = f"{pathlib.Path(__file__).parent.resolve()}/classifier_out/{sample_name}_cent_out"
-            cmd = f'centrifuge -x {centrifuge_index} -f {self.unpack_fastq_list(sequence_list)} -p {multiprocessing.cpu_count()} -S {pathlib.Path(__file__).parent.resolve()}/classifier_out/{sample_name}_cent_out'
+            self.cent_out = f"/Users/timolucas/PycharmProjects/MMonitor/desktop/src/resources/pipeline_out/{sample_name}_cent_out"
+            cmd = f'centrifuge -x {centrifuge_index} -f {self.unpack_fastq_list(sequence_list)} -p {multiprocessing.cpu_count()} -S {self.cent_out}'
             print(cmd)
             os.system(cmd)
             return

desktop/src/mmonitor/userside/functional_analysis.py

@@ -6,7 +6,6 @@
 import zipfile
 from os import path
 
-import pandas as pd
 import requests
 
 from build import ROOT

desktop/src/mmonitor/userside/view.py

@@ -1,4 +1,6 @@
 import tkinter as tk
+# from tkcalendar import Calendar
+from datetime import date
 from threading import Thread
 from time import sleep
 from tkinter import filedialog
@@ -33,22 +35,55 @@ def func_wrapper(*args):
 
 def require_centrifuge(func):
     """Decorator that ensures that a centrifuge index was selected by the user."""
+
     def func_wrapper(*args):
         obj: GUI = args[0]
         if obj.centrifuge_index is not None and len(obj.centrifuge_index) > 0:
             return func(*args)
         else:
             obj.open_popup("Please first select a centrifuge index before analyzing files.", "Centrifuge error")
+
     return func_wrapper
 
 
+def calendar_picker(but_exit=None):
+    tkobj = tk.Tk()
+    # setting up the geomentry
+    tkobj.geometry("400x400")
+    tkobj.title("Calendar picker")
+    # creating a calender object
+    tkc = Calendar(tkobj, selectmode="day", year=2022, month=1, date=1)
+    # display on main window
+    tkc.pack(pady=40)
+
+    # getting date from the calendar
+    def fetch_date():
+        date.config(text="Selected Date is: " + tkc.get_date())
+
+    # add button to load the date clicked on calendar
+    but = tk.Button(tkobj, text="Select Date", command=fetch_date, bg="black", fg='white')
+    # displaying button on the main display
+    but.pack()
+
+    but_exit = tk.Button(tkobj, text="Exit", command=tkobj.destroy, bg="black", fg='white')
+    # displaying button on the main display
+    but_exit.pack()
+
+    # Label for showing date on main display
+    date = tk.Label(tkobj, text="", bg='black', fg='white')
+    date.pack(pady=20)
+    # starting the object
+    tkobj.mainloop()
+    return tkc.get_date()
+
+
 class GUI:
 
     def __init__(self):
         # declare data base class variable, to be chosen by user with choose_project()
         self.db: MMonitorDBInterface = None
         self.db_path = None
-        self.centrifuge_index = None
+        self.centrifuge_index = "/Users/timolucas/Downloads/p_compressed_2018_4_15_2/p_compressed"
         self.cent = CentrifugeRunner()
         self.func = FunctionalAnalysisRunner()
         self.dashapp = None
@@ -65,28 +100,28 @@ def __init__(self):
     def init_layout(self):
 
         self.root.geometry("350x250")
-        self.root.title("MMonitor v0.1.0. alpha")
+        self.root.title("MMonitor v0.1.0 alpha")
         self.root.resizable(width=False, height=True)
         self.width = 20
         self.height = 1
         # create buttons
         tk.Button(self.root, text="Create Project", command=self.create_project,
-                  padx=10, pady=5, width=self.width, height=self.height, fg='white', bg='#254D25').pack()
+                  padx=10, pady=5, width=self.width, height=self.height, fg='black', bg='white').pack()
         tk.Button(self.root, text="Choose Project", command=self.choose_project,
-                  padx=10, pady=5, width=self.width, height=self.height, fg='white', bg='#254D25').pack()
+                  padx=10, pady=5, width=self.width, height=self.height, fg='black', bg='#254D25').pack()
         # tk.Button(self.root, text="Choose centrifuge index", command=self.choose_index,
         #           padx=10, pady=5, width=self.width,height=self.height, fg='white', bg='#254D25').pack()
         # # tk.Button(self.root, text="Analyze fastq in folder", command=self.analyze_fastq_in_folder,
         #           padx=10, pady=5, width=self.width,height=self.height, fg='white', bg='#254D25').pack()
         tk.Button(self.root, text="Add metadata from CSV", command=self.append_metadata,
-                  padx=10, pady=5, width=self.width, height=self.height, fg='white', bg='#254D25').pack()
+                  padx=10, pady=5, width=self.width, height=self.height, fg='black', bg='#254D25').pack()
         tk.Button(self.root, text="Run analysis pipeline", command=self.checkbox_popup,
-                  padx=10, pady=5, width=self.width, height=self.height, fg='white', bg='#254D25').pack()
+                  padx=10, pady=5, width=self.width, height=self.height, fg='black', bg='#254D25').pack()
 
         tk.Button(self.root, text="Start monitoring", command=self.start_monitoring,
-                  padx=10, pady=5, width=self.width, height=self.height, fg='white', bg='#254D25').pack()
+                  padx=10, pady=5, width=self.width, height=self.height, fg='black', bg='#254D25').pack()
         tk.Button(self.root, text="Quit",
-                  padx=10, pady=5, width=self.width, height=self.height, fg='white', bg='#254D25',
+                  padx=10, pady=5, width=self.width, height=self.height, fg='black', bg='#254D25',
                   command=self.stop_app).pack()
 
     def open_popup(self, text, title):
@@ -149,12 +184,18 @@ def analyze_fastq_in_folder(self):
             "What should the sample be called?",
             parent=self.root
         )
-        self.cent.run_centrifuge(files, self.centrifuge_index, sample_name)
 
+        # sample_date = calendar_picker()
+        sample_date = date.today()
+        self.cent.run_centrifuge(files, self.centrifuge_index, sample_name)
         self.cent.make_kraken_report(self.centrifuge_index)
-        self.db.update_table_with_kraken_out(f"classifier_out/{sample_name}_kraken_out", "S", sample_name, "project")
+
+        self.db.update_table_with_kraken_out(
+            f"/Users/timolucas/PycharmProjects/MMonitor/desktop/src/resources/pipeline_out/{sample_name}_kraken_out",
+            "S", sample_name, "project", sample_date)
 
     def checkbox_popup(self):
+
         # open checkbox to ask what the user wants to run (in case of rerunning)
         top = tk.Toplevel(self.root)
         top.geometry("400x300")

desktop/src/resources/r/horizon.r

@@ -6,7 +6,7 @@ bandwidth <- strtoi(Sys.getenv("HORI_BANDWIDTH"))
 library("latticeExtra")
 png(Sys.getenv("HORI_IMAGE"), width = width, height = height)
 horizonplot(ts(abundances), colorkey = TRUE, layout = c(1, ncol(abundances)),
-            strip.left = FALSE, xlab = "Sample ID", ylab = list(rev(colnames(abundances)), rot = 0, cex = 1.35),
-            horizonscale = bandwidth, origin = 0)
+            strip.left = FALSE, xlab = "Sample Date", ylab = list(rev(colnames(abundances)), rot = 0, cex = 1.35),
+            horizonscale = bandwidth, origin = 0, col.regions = hcl.colors(14, palette = "RdYlBu"),)
 
 dev.off()