Merge Template

.gitignore

@@ -24,6 +24,8 @@ workspaces-flashtaggerviewer
 **/__pycache__
 .DS_Store
 *-embed-amd64
+get-pip.py
+run_app.bat
+python*
+gdpr_consent/node_modules/
 *~
-
-

LICENSE

@@ -13,7 +13,7 @@ This software is released under a three-clause BSD license:
  * Neither the name of any author or any participating institution
    may be used to endorse or promote products derived from this software
    without specific prior written permission.
-For a full list of authors, refer to the file AUTHORS.
+For a full list of authors, refer to the git contributions.
 --------------------------------------------------------------------------
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

app.py

@@ -36,4 +36,4 @@
     }
 
     pg = st.navigation(pages, expanded=True)
-    pg.run()
+    pg.run()

docker-compose.yml

@@ -1,5 +1,3 @@
-version: '3.8'
-
 services:
   openms-streamlit-template:
     build:

requirements.txt

@@ -1,12 +1,140 @@
-# the requirements.txt file is intended for deployment on streamlit cloud and if the simple container is built
-# note that it is much more restricted in terms of installing third-parties / etc.
-# preferably use the batteries included or simple docker file for local hosting
-streamlit==1.43.0
-numpy==1.26.4 # pandas and numpy are dependencies of pyopenms, however, pyopenms needs numpy<=1.26.4
-plotly==5.22.0
+#
+# This file is autogenerated by pip-compile with Python 3.12
+# by the following command:
+#
+#    pip-compile --output-file=requirements.txt pyproject.toml
+#
+altair==5.5.0
+    # via streamlit
+attrs==25.3.0
+    # via
+    #   jsonschema
+    #   referencing
+blinker==1.9.0
+    # via streamlit
+cachetools==5.5.2
+    # via streamlit
 captcha==0.7.1
-pyopenms>=3.2.0
-pyarrow<16
-streamlit-js-eval
+    # via src (pyproject.toml)
+certifi==2025.1.31
+    # via requests
+charset-normalizer==3.4.1
+    # via requests
+click==8.1.8
+    # via streamlit
+contourpy==1.3.1
+    # via matplotlib
+cycler==0.12.1
+    # via matplotlib
+fonttools==4.56.0
+    # via matplotlib
+gitdb==4.0.12
+    # via gitpython
+gitpython==3.1.44
+    # via streamlit
+idna==3.10
+    # via requests
+jinja2==3.1.6
+    # via
+    #   altair
+    #   pydeck
+jsonschema==4.23.0
+    # via altair
+jsonschema-specifications==2024.10.1
+    # via jsonschema
+kiwisolver==1.4.8
+    # via matplotlib
+markupsafe==3.0.2
+    # via jinja2
+matplotlib==3.10.1
+    # via pyopenms
+narwhals==1.32.0
+    # via altair
+numpy==1.26.4
+    # via
+    #   contourpy
+    #   matplotlib
+    #   pandas
+    #   pydeck
+    #   pyopenms
+    #   src (pyproject.toml)
+    #   streamlit
+packaging==24.2
+    # via
+    #   altair
+    #   matplotlib
+    #   plotly
+    #   streamlit
+pandas==2.2.3
+    # via
+    #   pyopenms
+    #   pyopenms-viz
+    #   streamlit
+pillow==11.1.0
+    # via
+    #   captcha
+    #   matplotlib
+    #   streamlit
+plotly==5.22.0
+    # via src (pyproject.toml)
+protobuf==5.29.4
+    # via streamlit
+psutil==7.0.0
+    # via src (pyproject.toml)
+pyarrow==19.0.1
+    # via streamlit
+pydeck==0.9.1
+    # via streamlit
+pyopenms==3.3.0
+    # via src (pyproject.toml)
+pyopenms-viz==1.0.0
+    # via src (pyproject.toml)
+pyparsing==3.2.3
+    # via matplotlib
+python-dateutil==2.9.0.post0
+    # via
+    #   matplotlib
+    #   pandas
+pytz==2025.2
+    # via pandas
+referencing==0.36.2
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+requests==2.32.3
+    # via streamlit
+rpds-py==0.24.0
+    # via
+    #   jsonschema
+    #   referencing
+six==1.17.0
+    # via python-dateutil
+smmap==5.0.2
+    # via gitdb
+streamlit==1.49.0
+    # via
+    #   src (pyproject.toml)
+    #   streamlit-js-eval
+streamlit-js-eval==0.1.7
+    # via src (pyproject.toml)
+tenacity==9.0.0
+    # via
+    #   plotly
+    #   streamlit
+toml==0.10.2
+    # via streamlit
+tornado==6.4.2
+    # via streamlit
+typing-extensions==4.13.0
+    # via
+    #   altair
+    #   referencing
+    #   streamlit
+tzdata==2025.2
+    # via pandas
+urllib3==2.3.0
+    # via requests
+watchdog==6.0.0
+    # via streamlit
+xlsxwriter
 scipy>=1.15
-psutil

src/common/captcha_.py

@@ -1,14 +1,23 @@
-from pathlib import Path
 import streamlit as st
 import streamlit.components.v1 as st_components
-from streamlit.source_util import page_icon_and_name, calc_md5, get_pages, _on_pages_changed
 
+from streamlit.source_util import page_icon_and_name
 from captcha.image import ImageCaptcha
+from pathlib import Path
 
+import hashlib
 import random
 import string
 import os
 
+def calc_md5(string : str):
+    return hashlib.md5(string.encode()).hexdigest() 
+
+def get_pages():
+    return st.runtime.get_pages()
+
+def set_pages(pages : dict):
+    st.runtime.set_pages(pages)
 
 def delete_all_pages(main_script_path_str: str) -> None:
     """
@@ -22,7 +31,7 @@ def delete_all_pages(main_script_path_str: str) -> None:
 
     """
     # Get all pages from the app's configuration
-    current_pages = get_pages(main_script_path_str)
+    current_pages = get_pages()
 
     # Create a list to store keys pages to delete
     keys_to_delete = []
@@ -37,7 +46,7 @@ def delete_all_pages(main_script_path_str: str) -> None:
         del current_pages[key]
 
     # Refresh the pages configuration
-    _on_pages_changed.send()
+    set_pages(current_pages)
 
 
 def delete_page(main_script_path_str: str, page_name: str) -> None:
@@ -52,15 +61,15 @@ def delete_page(main_script_path_str: str, page_name: str) -> None:
         None
     """
     # Get all pages
-    current_pages = get_pages(main_script_path_str)
+    current_pages = get_pages()
 
     # Iterate over all pages and delete the desired page if found
     for key, value in current_pages.items():
         if value["page_name"] == page_name:
             del current_pages[key]
 
     # Refresh the pages configuration
-    _on_pages_changed.send()
+    set_pages(current_pages)
 
 
 def restore_all_pages(main_script_path_str: str) -> None:
@@ -74,7 +83,7 @@ def restore_all_pages(main_script_path_str: str) -> None:
         None
     """
     # Get all pages
-    pages = get_pages(main_script_path_str)
+    pages = get_pages()
 
     # Obtain the path to the main script
     main_script_path = Path(main_script_path_str)
@@ -126,7 +135,7 @@ def restore_all_pages(main_script_path_str: str) -> None:
         }
 
     # Refresh the page configuration
-    _on_pages_changed.send()
+    set_pages(pages)
 
 
 def add_page(main_script_path_str: str, page_name: str) -> None:
@@ -141,7 +150,7 @@ def add_page(main_script_path_str: str, page_name: str) -> None:
         None
     """
     # Get all pages
-    pages = get_pages(main_script_path_str)
+    pages = get_pages()
 
     # Obtain the path to the main script
     main_script_path = Path(main_script_path_str)
@@ -168,7 +177,7 @@ def add_page(main_script_path_str: str, page_name: str) -> None:
     }
 
     # Refresh the page configuration
-    _on_pages_changed.send()
+    set_pages(pages)
 
 
 length_captcha = 5

src/common/common.py

@@ -1,17 +1,18 @@
-import json
 import os
-import shutil
 import sys
 import uuid
+import json
 import time
+import psutil
+import shutil
+
+import pandas as pd
+import streamlit as st
+
 from typing import Any
 from pathlib import Path
 from streamlit.components.v1 import html
 
-import streamlit as st
-import pandas as pd
-import psutil
-
 try:
     from tkinter import Tk, filedialog
 
@@ -340,30 +341,25 @@ def render_sidebar(page: str = "") -> None:
         # The main page has workspace switcher
         # Display workspace switcher if workspace is enabled in local mode
         if st.session_state.settings["enable_workspaces"]:
-            with st.expander("🖥️ **Workspaces**"):
-                # Workspaces directory specified in the settings.json
-                if (
-                    st.session_state.settings["workspaces_dir"]
-                    and st.session_state.location == "local"
-                ):
-                    workspaces_dir = Path(
-                        st.session_state.settings["workspaces_dir"],
-                        "workspaces-" + st.session_state.settings["repository-name"],
-                    )
-                else:
-                    workspaces_dir = ".."
-                # Online: show current workspace name in info text and option to change to other existing workspace
-                if st.session_state.location == "local":
+            # Workspaces directory specified in the settings.json
+            if (
+                st.session_state.settings["workspaces_dir"]
+                and st.session_state.location == "local"
+            ):
+                workspaces_dir = Path(
+                    st.session_state.settings["workspaces_dir"],
+                    "workspaces-" + st.session_state.settings["repository-name"],
+                )
+            else:
+                workspaces_dir = ".."
+            # Online: show current workspace name in info text and option to change to other existing workspace
+            if st.session_state.location == "local":
+                with st.expander("🖥️ **Workspaces**"):
                     # Define callback function to change workspace
                     def change_workspace():
                         for key in params.keys():
-                            if key in ['controllo']:
-                                continue
                             if key in st.session_state.keys():
                                 del st.session_state[key]
-                        st.session_state.workspace = Path(
-                            workspaces_dir, st.session_state["chosen-workspace"]
-                        )
                         st.query_params.workspace = st.session_state["chosen-workspace"]
 
                     # Get all available workspaces as options