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Merged
t0mdavid-m merged 2 commits into from
Mar 19, 2025
Merged

feat: automatically load example data in pyOpenMS workflow #185

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3e0c71f
feat: automatically load example data in pyOpenMS workflow
achalbajpai Mar 15, 2025
78c4178
update : remove example data tab and associated code
achalbajpai Mar 19, 2025
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71 changes: 55 additions & 16 deletions content/file_upload.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,13 +3,26 @@
import streamlit as st
import pandas as pd

from src.common.common import page_setup, save_params, v_space, show_table, TK_AVAILABLE, tk_directory_dialog
from src.common.common import (
page_setup,
save_params,
v_space,
show_table,
TK_AVAILABLE,
tk_directory_dialog,
)
from src import fileupload

params = page_setup()

st.title("File Upload")

# Check if there are any files in the workspace
mzML_dir = Path(st.session_state.workspace, "mzML-files")
if not any(Path(mzML_dir).iterdir()):
# No files present, load example data
fileupload.load_example_mzML_files()

tabs = ["File Upload", "Example Data"]
if st.session_state.location == "local":
tabs.append("Files from local folder")
Expand Down Expand Up @@ -42,41 +55,67 @@
with st_cols[0]:
st.write("\n")
st.write("\n")
dialog_button = st.button("📁", key='local_browse', help="Browse for your local directory with MS data.", disabled=not TK_AVAILABLE)
dialog_button = st.button(
"📁",
key="local_browse",
help="Browse for your local directory with MS data.",
disabled=not TK_AVAILABLE,
)
if dialog_button:
st.session_state["local_dir"] = tk_directory_dialog("Select directory with your MS data", st.session_state["previous_dir"])
st.session_state["local_dir"] = tk_directory_dialog(
"Select directory with your MS data",
st.session_state["previous_dir"],
)
st.session_state["previous_dir"] = st.session_state["local_dir"]
with st_cols[1]:
# with st.form("local-file-upload"):
local_mzML_dir = st.text_input("path to folder with mzML files", value=st.session_state["local_dir"])
local_mzML_dir = st.text_input(
"path to folder with mzML files", value=st.session_state["local_dir"]
)
# raw string for file paths
local_mzML_dir = rf"{local_mzML_dir}"
cols = st.columns([0.65, 0.3, 0.4, 0.25], gap="small")
copy_button = cols[1].button("Copy files to workspace", type="primary", disabled=(local_mzML_dir == ""))
use_copy = cols[2].checkbox("Make a copy of files", key="local_browse-copy_files", value=True, help="Create a copy of files in workspace.")
copy_button = cols[1].button(
"Copy files to workspace", type="primary", disabled=(local_mzML_dir == "")
)
use_copy = cols[2].checkbox(
"Make a copy of files",
key="local_browse-copy_files",
value=True,
help="Create a copy of files in workspace.",
)
if not use_copy:
st.warning(
"**Warning**: You have deselected the `Make a copy of files` option. "
"This **_assumes you know what you are doing_**. "
"This means that the original files will be used instead. "
)
st.warning(
"**Warning**: You have deselected the `Make a copy of files` option. "
"This **_assumes you know what you are doing_**. "
"This means that the original files will be used instead. "
)
if copy_button:
fileupload.copy_local_mzML_files_from_directory(local_mzML_dir, use_copy)

mzML_dir = Path(st.session_state.workspace, "mzML-files")
if any(Path(mzML_dir).iterdir()):
v_space(2)
# Display all mzML files currently in workspace
df = pd.DataFrame({"file name": [f.name for f in Path(mzML_dir).iterdir() if "external_files.txt" not in f.name]})

df = pd.DataFrame(
{
"file name": [
f.name
for f in Path(mzML_dir).iterdir()
if "external_files.txt" not in f.name
]
}
)

# Check if local files are available
external_files = Path(mzML_dir, "external_files.txt")
if external_files.exists():
with open(external_files, "r") as f_handle:
external_files = f_handle.readlines()
external_files = [f.strip() for f in external_files]
df = pd.concat([df, pd.DataFrame({"file name": external_files})], ignore_index=True)

df = pd.concat(
[df, pd.DataFrame({"file name": external_files})], ignore_index=True
)

st.markdown("##### mzML files in current workspace:")
show_table(df)
v_space(1)
Expand Down
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