pycompound 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

app.py

@@ -4,6 +4,8 @@ from pycompound.spec_lib_matching import run_spec_lib_matching_on_HRMS_data
 from pycompound.spec_lib_matching import run_spec_lib_matching_on_NRMS_data 
 from pycompound.spec_lib_matching import tune_params_on_HRMS_data
 from pycompound.spec_lib_matching import tune_params_on_NRMS_data
+from pycompound.spec_lib_matching import tune_params_on_HRMS_data_shiny
+from pycompound.spec_lib_matching import tune_params_on_NRMS_data_shiny
 from pycompound.plot_spectra import generate_plots_on_HRMS_data
 from pycompound.plot_spectra import generate_plots_on_NRMS_data
 from pathlib import Path
@@ -20,10 +22,16 @@ import numpy as np
 import netCDF4 as nc
 from pyteomics import mgf, mzml
 import ast
+from numbers import Real
+
 
 
 _LOG_QUEUE: asyncio.Queue[str] = asyncio.Queue()
 
+def _run_with_redirects(fn, writer, *args, **kwargs):
+    with redirect_stdout(writer), redirect_stderr(writer):
+        return fn(*args, **kwargs)
+
 
 def strip_text(s):
     return [x.strip() for x in s.strip('[]').split(',') if x.strip()]
@@ -34,9 +42,23 @@ def strip_numeric(s):
 
 
 def strip_weights(s):
-    tuples = ast.literal_eval(s)
+    obj = ast.literal_eval(s) if isinstance(s, (str, bytes)) else s
     keys = ['Cosine', 'Shannon', 'Renyi', 'Tsallis']
-    return [dict(zip(keys,t)) for t in tuples]
+
+    if isinstance(obj, (list, tuple)):
+        if len(obj) == 4 and all(isinstance(x, Real) for x in obj):
+            tuples = [obj]
+        else:
+            tuples = list(obj)
+    else:
+        raise ValueError(f"Expected a 4-tuple or a sequence of 4-tuples, got {type(obj).__name__}")
+
+    out = []
+    for t in tuples:
+        if not (isinstance(t, (list, tuple)) and len(t) == 4):
+            raise ValueError(f"Each item must be a 4-tuple, got: {t!r}")
+        out.append(dict(zip(keys, t)))
+    return out
 
 
 def build_library(input_path=None, output_path=None):
@@ -177,7 +199,6 @@ def _open_plot_window(session, png_bytes: bytes, title: str = "plot.png"):
 
 
 def plot_spectra_ui(platform: str):
-    # Base inputs common to all platforms
     base_inputs = [
         ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
         ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
@@ -196,7 +217,7 @@ def plot_spectra_ui(platform: str):
             options={"placeholder": "Upload a library..."},
         ),
         ui.input_select("similarity_measure", "Select similarity measure:", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"]),
-        ui.input_text('weights', 'Weights for similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
+        ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
         ui.input_select(
             "high_quality_reference_library",
             "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.",
@@ -204,7 +225,6 @@ def plot_spectra_ui(platform: str):
         ),
     ]
 
-    # Extra inputs depending on platform
     if platform == "HRMS":
         extra_inputs = [
             ui.input_text(
@@ -224,7 +244,6 @@ def plot_spectra_ui(platform: str):
             )
         ]
 
-    # Numeric inputs
     numeric_inputs = [
         ui.input_numeric("mz_min", "Minimum m/z for filtering:", 0),
         ui.input_numeric("mz_max", "Maximum m/z for filtering:", 99999999),
@@ -237,18 +256,15 @@ def plot_spectra_ui(platform: str):
         ui.input_numeric("entropy_dimension", "Entropy dimension (Renyi/Tsallis only):", 1.1),
     ]
 
-    # Y-axis transformation select input
     select_input = ui.input_select(
         "y_axis_transformation",
         "Transformation to apply to intensity axis:",
         ["normalized", "none", "log10", "sqrt"],
     )
 
-    # Run and Back buttons
     run_button_plot_spectra = ui.download_button("run_btn_plot_spectra", "Run", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
 
-    # Layout base_inputs and extra_inputs in columns
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
             ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
@@ -266,7 +282,6 @@ def plot_spectra_ui(platform: str):
             col_widths=(3,3,3,3),
         )
 
-    # Combine everything
     return ui.div(
         ui.TagList(
             ui.h2("Plot Spectra"),
@@ -281,12 +296,11 @@ def plot_spectra_ui(platform: str):
 
 
 def run_spec_lib_matching_ui(platform: str):
-    # Base inputs common to all platforms
     base_inputs = [
         ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
         ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
         ui.input_select("similarity_measure", "Select similarity measure:", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"]),
-        ui.input_text('weights', 'Weights for similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
+        ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '0.25, 0.25, 0.25, 0.25'),
         ui.input_selectize(
             "spectrum_ID1",
             "Select spectrum ID 1 (only applicable for plotting; default is the first spectrum in the query library):",
@@ -308,7 +322,6 @@ def run_spec_lib_matching_ui(platform: str):
         )
     ]
 
-    # Extra inputs depending on platform
     if platform == "HRMS":
         extra_inputs = [
             ui.input_text(
@@ -328,7 +341,6 @@ def run_spec_lib_matching_ui(platform: str):
             )
         ]
 
-    # Numeric inputs
     numeric_inputs = [
         ui.input_numeric("mz_min", "Minimum m/z for filtering:", 0),
         ui.input_numeric("mz_max", "Maximum m/z for filtering:", 99999999),
@@ -343,12 +355,10 @@ def run_spec_lib_matching_ui(platform: str):
     ]
 
 
-    # Run and Back buttons
     run_button_spec_lib_matching = ui.download_button("run_btn_spec_lib_matching", "Run Spectral Library Matching", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     run_button_plot_spectra_within_spec_lib_matching = ui.download_button("run_btn_plot_spectra_within_spec_lib_matching", "Plot Spectra", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
 
-    # Layout base_inputs and extra_inputs in columns
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
             ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
@@ -372,7 +382,6 @@ def run_spec_lib_matching_ui(platform: str):
         style="max-height:300px; overflow:auto"
     )
 
-    # Combine everything
     return ui.div(
         ui.TagList(
             ui.h2("Run Spectral Library Matching"),
@@ -387,16 +396,14 @@ def run_spec_lib_matching_ui(platform: str):
 
 
 def run_parameter_tuning_ui(platform: str):
-    # Base inputs common to all platforms
     base_inputs = [
         ui.input_file("query_data", "Upload query dataset (mgf, mzML, cdf, msp, or csv):"),
         ui.input_file("reference_data", "Upload reference dataset (mgf, mzML, cdf, msp, or csv):"),
         ui.input_selectize("similarity_measure", "Select similarity measure(s):", ["cosine","shannon","renyi","tsallis","mixture","jaccard","dice","3w_jaccard","sokal_sneath","binary_cosine","mountford","mcconnaughey","driver_kroeber","simpson","braun_banquet","fager_mcgowan","kulczynski","intersection","hamming","hellinger"], multiple=True, selected='cosine'),
-        ui.input_text('weights', 'Weights for similarity measure (cosine, shannon, renyi, tsallis):', '((0.25, 0.25, 0.25, 0.25), (0.2, 0.3, 0.4, 0.1))'),
+        ui.input_text('weights', 'Weights for mixture similarity measure (cosine, shannon, renyi, tsallis):', '((0.25, 0.25, 0.25, 0.25))'),
         ui.input_text("high_quality_reference_library", "Indicate whether the reference library is considered high quality. If True, filtering and noise removal are only applied to the query spectra.", '[True]')
     ]
 
-    # Extra inputs depending on platform
     if platform == "HRMS":
         extra_inputs = [
             ui.input_text(
@@ -416,7 +423,6 @@ def run_parameter_tuning_ui(platform: str):
             )
         ]
 
-    # Numeric inputs
     numeric_inputs = [
         ui.input_text("mz_min", "Minimum m/z for filtering:", '[0]'),
         ui.input_text("mz_max", "Maximum m/z for filtering:", '[99999999]'),
@@ -430,11 +436,9 @@ def run_parameter_tuning_ui(platform: str):
     ]
 
 
-    # Run and Back buttons
     run_button_parameter_tuning = ui.download_button("run_btn_parameter_tuning", "Tune parameters", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
     back_button = ui.input_action_button("back", "Back to main menu", style="font-size:16px; padding:15px 30px; width:200px; height:80px")
 
-    # Layout base_inputs and extra_inputs in columns
     if platform == "HRMS":
         inputs_columns = ui.layout_columns(
             ui.div(base_inputs[0:6], style="display:flex; flex-direction:column; gap:10px;"),
@@ -458,7 +462,6 @@ def run_parameter_tuning_ui(platform: str):
         style="max-height:300px; overflow:auto"
     )
 
-    # Combine everything
     return ui.div(
         ui.TagList(
             ui.h2("Tune parameters"),
@@ -494,6 +497,9 @@ def server(input, output, session):
     match_log_rv = reactive.Value("")
     is_matching_rv = reactive.Value(False)
     is_any_job_running = reactive.Value(False)
+    latest_csv_path_rv = reactive.Value("")
+    latest_df_rv = reactive.Value(None)
+    is_running_rv = reactive.Value(False)
 
     query_ids_rv = reactive.Value([])
     query_file_path_rv = reactive.Value(None)
@@ -508,7 +514,63 @@ def server(input, output, session):
     converted_reference_path_rv = reactive.Value(None)
 
 
-    #def _drain_queue_nowait(q: asyncio.Queue[str]) -> list[str]:
+    def _reset_plot_spectra_state():
+        query_status_rv.set("")
+        reference_status_rv.set("")
+        query_ids_rv.set([])
+        reference_ids_rv.set([])
+        query_file_path_rv.set(None)
+        reference_file_path_rv.set(None)
+        query_result_rv.set(None)
+        reference_result_rv.set(None)
+        converted_query_path_rv.set(None)
+        converted_reference_path_rv.set(None)
+        try:
+            ui.update_selectize("spectrum_ID1", choices=[], selected=None)
+            ui.update_selectize("spectrum_ID2", choices=[], selected=None)
+        except Exception:
+            pass
+
+
+    def _reset_spec_lib_matching_state():
+        match_log_rv.set("")
+        is_matching_rv.set(False)
+        is_any_job_running.set(False)
+        try:
+            ui.update_selectize("spectrum_ID1", choices=[], selected=None)
+            ui.update_selectize("spectrum_ID2", choices=[], selected=None)
+        except Exception:
+            pass
+
+
+    def _reset_parameter_tuning_state():
+        match_log_rv.set("")
+        is_tuning_running.set(False)
+        is_any_job_running.set(False)
+
+
+    @reactive.effect
+    @reactive.event(input.back)
+    def _clear_on_back_from_pages():
+        page = current_page()
+        if page == "plot_spectra":
+            _reset_plot_spectra_state()
+        elif page == "run_spec_lib_matching":
+            _reset_spec_lib_matching_state()
+        elif page == "run_parameter_tuning":
+            _reset_parameter_tuning_state()
+
+    @reactive.effect
+    def _clear_on_enter_pages():
+        page = current_page()
+        if page == "plot_spectra":
+            _reset_plot_spectra_state()
+        elif page == "run_spec_lib_matching":
+            _reset_spec_lib_matching_state()
+        elif page == "run_parameter_tuning":
+            _reset_parameter_tuning_state()
+
+
     def _drain_queue_nowait(q: asyncio.Queue) -> list[str]:
         out = []
         try:
@@ -519,12 +581,23 @@ def server(input, output, session):
         return out
 
 
+    class ReactiveWriter(io.TextIOBase):
+        def __init__(self, loop: asyncio.AbstractEventLoop):
+            self._loop = loop
+        def write(self, s: str):
+            if not s:
+                return 0
+            self._loop.call_soon_threadsafe(_LOG_QUEUE.put_nowait, s)
+            return len(s)
+        def flush(self):
+            pass
+
+
     @reactive.effect
     async def _pump_logs():
-        if not is_any_job_running.get():
+        if not (is_any_job_running.get() or is_tuning_running.get() or is_matching_rv.get()):
             return
-
-        reactive.invalidate_later(0.1)
+        reactive.invalidate_later(0.05)
         msgs = _drain_queue_nowait(_LOG_QUEUE)
         if msgs:
             match_log_rv.set(match_log_rv.get() + "".join(msgs))
@@ -593,24 +666,6 @@ def server(input, output, session):
         return match_log_rv.get()
 
 
-    class ReactiveWriter(io.TextIOBase):
-        def __init__(self, rv):
-            self.rv = rv
-        def write(self, s: str):
-            if not s:
-                return 0
-            self.rv.set(self.rv.get() + s)
-            try:
-                loop = asyncio.get_running_loop()
-                loop.create_task(reactive.flush())
-            except RuntimeError:
-                pass
-            return len(s)
-        def flush(self):
-            pass
-
-
-
     @reactive.Effect
     def _():
         if input.plot_spectra() > plot_clicks.get():
@@ -629,8 +684,6 @@ def server(input, output, session):
 
     @render.image
     def image():
-        from pathlib import Path
-
         dir = Path(__file__).resolve().parent
         img: ImgData = {"src": str(dir / "www/emblem.png"), "width": "320px", "height": "250px"}
         return img
@@ -726,9 +779,6 @@ def server(input, output, session):
     @reactive.effect
     @reactive.event(input.query_data)
     async def _populate_ids_from_query_upload():
-        #if current_page() != "plot_spectra":
-        #    return
-
         files = input.query_data()
         if not files:
             return
@@ -736,7 +786,6 @@ def server(input, output, session):
         in_path = Path(files[0]["datapath"])
         suffix = in_path.suffix.lower()
 
-        # Decide what CSV to read IDs from
         try:
             if suffix == ".csv":
                 csv_path = in_path
@@ -745,17 +794,14 @@ def server(input, output, session):
                 query_status_rv.set(f"Converting {in_path.name} → CSV …")
                 await reactive.flush()
 
-                # Choose an output temp path next to the upload
                 tmp_csv_path = in_path.with_suffix(".converted.csv")
 
                 out_obj = await asyncio.to_thread(build_library, str(in_path), str(tmp_csv_path))
 
-                # out_obj may be a path (str/PathLike) OR a DataFrame. Normalize to a path.
                 if isinstance(out_obj, (str, os.PathLike, Path)):
                     csv_path = Path(out_obj)
                 elif isinstance(out_obj, pd.DataFrame):
-                    # Write the DF to our chosen path
-                    out_obj.to_csv(tmp_csv_path, index=False)
+                    out_obj.to_csv(tmp_csv_path, index=False, sep='\t')
                     csv_path = tmp_csv_path
                 else:
                     raise TypeError(f"build_library returned unsupported type: {type(out_obj)}")
@@ -765,16 +811,12 @@ def server(input, output, session):
             query_status_rv.set(f"Reading IDs from: {csv_path.name} …")
             await reactive.flush()
 
-            # Extract IDs from the CSV’s first column
             ids = await asyncio.to_thread(extract_first_column_ids, str(csv_path))
             query_ids_rv.set(ids)
 
-            # Update dropdowns
             ui.update_selectize("spectrum_ID1", choices=ids, selected=(ids[0] if ids else None))
 
-            query_status_rv.set(
-                f"✅ Loaded {len(ids)} IDs from {csv_path.name}" if ids else f"⚠️ No IDs found in {csv_path.name}"
-            )
+            query_status_rv.set(f"✅ Loaded {len(ids)} IDs from {csv_path.name}" if ids else f"⚠️ No IDs found in {csv_path.name}")
             await reactive.flush()
 
         except Exception as e:
@@ -786,9 +828,6 @@ def server(input, output, session):
     @reactive.effect
     @reactive.event(input.reference_data)
     async def _populate_ids_from_reference_upload():
-        #if current_page() != "plot_spectra":
-        #    return
-
         files = input.reference_data()
         if not files:
             return
@@ -796,7 +835,6 @@ def server(input, output, session):
         in_path = Path(files[0]["datapath"])
         suffix = in_path.suffix.lower()
 
-        # Decide what CSV to read IDs from
         try:
             if suffix == ".csv":
                 csv_path = in_path
@@ -805,17 +843,14 @@ def server(input, output, session):
                 reference_status_rv.set(f"Converting {in_path.name} → CSV …")
                 await reactive.flush()
 
-                # Choose an output temp path next to the upload
                 tmp_csv_path = in_path.with_suffix(".converted.csv")
 
                 out_obj = await asyncio.to_thread(build_library, str(in_path), str(tmp_csv_path))
 
-                # out_obj may be a path (str/PathLike) OR a DataFrame. Normalize to a path.
                 if isinstance(out_obj, (str, os.PathLike, Path)):
                     csv_path = Path(out_obj)
                 elif isinstance(out_obj, pd.DataFrame):
-                    # Write the DF to our chosen path
-                    out_obj.to_csv(tmp_csv_path, index=False)
+                    out_obj.to_csv(tmp_csv_path, index=False, sep='\t')
                     csv_path = tmp_csv_path
                 else:
                     raise TypeError(f"build_library returned unsupported type: {type(out_obj)}")
@@ -825,11 +860,9 @@ def server(input, output, session):
             reference_status_rv.set(f"Reading IDs from: {csv_path.name} …")
             await reactive.flush()
 
-            # Extract IDs from the CSV’s first column
             ids = await asyncio.to_thread(extract_first_column_ids, str(csv_path))
             reference_ids_rv.set(ids)
 
-            # Update dropdowns
             ui.update_selectize("spectrum_ID2", choices=ids, selected=(ids[0] if ids else None))
 
             reference_status_rv.set(
@@ -851,11 +884,18 @@ def server(input, output, session):
         weights = [float(weight.strip()) for weight in input.weights().split(",") if weight.strip()]
         weights = {'Cosine':weights[0], 'Shannon':weights[1], 'Renyi':weights[2], 'Tsallis':weights[3]}
 
+        high_quality_reference_library_tmp2 = False
+        if input.high_quality_reference_library() != 'False':
+            high_quality_reference_library_tmp2 = True
+
+        print(input.high_quality_reference_library())
+        print(high_quality_reference_library_tmp2)
+
         if input.chromatography_platform() == "HRMS":
-            fig = generate_plots_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), weights=weights, spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=input.high_quality_reference_library(), mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), window_size_centroiding=input.window_size_centroiding(), window_size_matching=input.window_size_matching(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
+            fig = generate_plots_on_HRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), weights=weights, spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), window_size_centroiding=input.window_size_centroiding(), window_size_matching=input.window_size_matching(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
             plt.show()
         elif input.chromatography_platform() == "NRMS":
-            fig = generate_plots_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=input.high_quality_reference_library(), mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
+            fig = generate_plots_on_NRMS_data(query_data=input.query_data()[0]['datapath'], reference_data=input.reference_data()[0]['datapath'], spectrum_ID1=spectrum_ID1, spectrum_ID2=spectrum_ID2, similarity_measure=input.similarity_measure(), spectrum_preprocessing_order=input.spectrum_preprocessing_order(), high_quality_reference_library=high_quality_reference_library_tmp2, mz_min=input.mz_min(), mz_max=input.mz_max(), int_min=input.int_min(), int_max=input.int_max(), noise_threshold=input.noise_threshold(), wf_mz=input.wf_mz(), wf_intensity=input.wf_int(), LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(), y_axis_transformation=input.y_axis_transformation(), return_plot=True)
             plt.show()
         with io.BytesIO() as buf:
             fig.savefig(buf, format="png", dpi=150, bbox_inches="tight")
@@ -863,34 +903,10 @@ def server(input, output, session):
             yield buf.getvalue()
 
 
-    @render.text
-    def status_output():
-        return run_status_plot_spectra.get()
-        return run_status_spec_lib_matching.get()
-        return run_status_parameter_tuning.get()
-
-
-    class ReactiveWriter(io.TextIOBase):
-        def __init__(self, rv: reactive.Value, loop: asyncio.AbstractEventLoop):
-            self.rv = rv
-            self.loop = loop
-
-        def write(self, s: str):
-            if not s:
-                return 0
-            def _apply():
-                self.rv.set(self.rv.get() + s)
-                self.loop.create_task(reactive.flush())
-            self.loop.call_soon_threadsafe(_apply)
-            return len(s)
 
-        def flush(self):
-            pass
-
-
-    @render.download(filename="identification_output.csv")
+    @render.download(filename="identification_output.txt")
     async def run_btn_spec_lib_matching():
-        match_log_rv.set("Starting identification...\n")
+        match_log_rv.set("Running identification...\n")
         await reactive.flush()
 
         hq = input.high_quality_reference_library()
@@ -916,14 +932,14 @@ def server(input, output, session):
             wf_mz=input.wf_mz(), wf_intensity=input.wf_int(),
             LET_threshold=input.LET_threshold(), entropy_dimension=input.entropy_dimension(),
             n_top_matches_to_save=input.n_top_matches_to_save(),
-            print_id_results=True,  # ensure the library actually prints
-            output_identification=str(Path.cwd() / "identification_output.csv"),
-            output_similarity_scores=str(Path.cwd() / "similarity_scores.csv"),
+            print_id_results=True,
+            output_identification=str(Path.cwd() / "identification_output.txt"),
+            output_similarity_scores=str(Path.cwd() / "similarity_scores.txt"),
             return_ID_output=True,
         )
 
         loop = asyncio.get_running_loop()
-        rw = ReactiveWriter(match_log_rv, loop)
+        rw = ReactiveWriter(loop)
 
         try:
             with redirect_stdout(rw), redirect_stderr(rw):
@@ -943,7 +959,7 @@ def server(input, output, session):
             await reactive.flush()
             raise
 
-        yield df_out.to_csv(index=True)
+        yield df_out.to_csv(index=True, sep='\t')
 
 
 
@@ -998,62 +1014,12 @@ def server(input, output, session):
             yield buf.getvalue()
 
 
-    '''
-    @render.download(filename="parameter_tuning_output.csv")
-    async def run_btn_parameter_tuning():
-        match_log_rv.set("Running grid search of all parameters specified...\n")
-
-        similarity_measure_tmp = list(input.similarity_measure())
-        high_quality_reference_library_tmp = [x.strip().lower() == "true" for x in input.high_quality_reference_library().strip().strip("[]").split(",") if x.strip()]
-        spectrum_preprocessing_order_tmp = strip_text(input.spectrum_preprocessing_order())
-        mz_min_tmp = strip_numeric(input.mz_min())
-        mz_max_tmp = strip_numeric(input.mz_max())
-        int_min_tmp = strip_numeric(input.int_min())
-        int_max_tmp = strip_numeric(input.int_max())
-        noise_threshold_tmp = strip_numeric(input.noise_threshold())
-        wf_mz_tmp = strip_numeric(input.wf_mz())
-        wf_int_tmp = strip_numeric(input.wf_int())
-        LET_threshold_tmp = strip_numeric(input.LET_threshold())
-        entropy_dimension_tmp = strip_numeric(input.entropy_dimension())
-        weights_tmp = strip_weights(input.weights())
-
-        common_kwargs = dict(
-            query_data=input.query_data()[0]["datapath"],
-            reference_data=input.reference_data()[0]["datapath"],
-            output_path=str(Path.cwd() / "parameter_tuning_output.csv"),
-            return_output=True
-        )
-
-        loop = asyncio.get_running_loop()
-        rw = ReactiveWriter(match_log_rv, loop)
-
-        try:
-            with redirect_stdout(rw), redirect_stderr(rw):
-                if input.chromatography_platform() == "HRMS":
-                    window_size_centroiding_tmp = strip_numeric(input.window_size_centroiding())
-                    window_size_matching_tmp = strip_numeric(input.window_size_matching())
-                    grid={'similarity_measure':similarity_measure_tmp, 'weight':weights_tmp, 'spectrum_preprocessing_order':spectrum_preprocessing_order_tmp, 'mz_min':mz_min_tmp, 'mz_max':mz_max_tmp, 'int_min':int_min_tmp, 'int_max':int_max_tmp, 'noise_threshold':noise_threshold_tmp, 'wf_mz':wf_mz_tmp, 'wf_int':wf_int_tmp, 'LET_threshold':LET_threshold_tmp, 'entropy_dimension':entropy_dimension_tmp, 'high_quality_reference_library':high_quality_reference_library_tmp, 'window_size_centroiding':window_size_centroiding_tmp, 'window_size_matching':window_size_matching_tmp}
-                    df_out = await asyncio.to_thread(tune_params_on_HRMS_data, **common_kwargs, grid=grid)
-                else:
-                    grid={'similarity_measure':similarity_measure_tmp, 'weight':weights_tmp, 'spectrum_preprocessing_order':spectrum_preprocessing_order_tmp, 'mz_min':mz_min_tmp, 'mz_max':mz_max_tmp, 'int_min':int_min_tmp, 'int_max':int_max_tmp, 'noise_threshold':noise_threshold_tmp, 'wf_mz':wf_mz_tmp, 'wf_int':wf_int_tmp, 'LET_threshold':LET_threshold_tmp, 'entropy_dimension':entropy_dimension_tmp, 'high_quality_reference_library':high_quality_reference_library_tmp}
-                    df_out = await asyncio.to_thread(tune_params_on_NRMS_data, **common_kwargs, grid=grid)
-            match_log_rv.set(match_log_rv.get() + "\n✅ Parameter tuning finished.\n")
-            #await reactive.flush()
-        except Exception as e:
-            match_log_rv.set(match_log_rv.get() + f"\n❌ Error: {e}\n")
-            #await reactive.flush()
-            raise
-
-        yield df_out.to_csv(index=False)
-    '''
-
-
-    @render.download(filename="parameter_tuning_output.csv")
+    @render.download(filename="parameter_tuning_output.txt")
     async def run_btn_parameter_tuning():
         is_any_job_running.set(True)
         is_tuning_running.set(True)
         match_log_rv.set("Running grid search of all parameters specified...\n")
-        _drain_queue_nowait(_LOG_QUEUE) 
+        await reactive.flush()
 
         similarity_measure_tmp = list(input.similarity_measure())
         high_quality_reference_library_tmp = [x.strip().lower() == "true" for x in input.high_quality_reference_library().strip().strip("[]").split(",") if x.strip()]
@@ -1072,23 +1038,52 @@ def server(input, output, session):
         common_kwargs = dict(
             query_data=input.query_data()[0]["datapath"],
             reference_data=input.reference_data()[0]["datapath"],
-            output_path=str(Path.cwd() / "parameter_tuning_output.csv"),
-            return_output=True
+            output_path=str(Path.cwd() / "parameter_tuning_output.txt"),
+            return_output=True,
         )
 
         loop = asyncio.get_running_loop()
-        rw = ReactiveWriter(match_log_rv,loop)
+        rw = ReactiveWriter(loop)
 
         try:
-            with redirect_stdout(ReactiveWriter(match_log_rv, asyncio.get_running_loop())), redirect_stderr(ReactiveWriter(match_log_rv, asyncio.get_running_loop())):
-                if input.chromatography_platform() == "HRMS":
-                    window_size_centroiding_tmp = strip_numeric(input.window_size_centroiding())
-                    window_size_matching_tmp = strip_numeric(input.window_size_matching())
-                    grid={'similarity_measure':similarity_measure_tmp, 'weight':weights_tmp, 'spectrum_preprocessing_order':spectrum_preprocessing_order_tmp, 'mz_min':mz_min_tmp, 'mz_max':mz_max_tmp, 'int_min':int_min_tmp, 'int_max':int_max_tmp, 'noise_threshold':noise_threshold_tmp, 'wf_mz':wf_mz_tmp, 'wf_int':wf_int_tmp, 'LET_threshold':LET_threshold_tmp, 'entropy_dimension':entropy_dimension_tmp, 'high_quality_reference_library':high_quality_reference_library_tmp, 'window_size_centroiding':window_size_centroiding_tmp, 'window_size_matching':window_size_matching_tmp}
-                    df_out = await asyncio.to_thread(tune_params_on_HRMS_data, **common_kwargs, grid=grid)
-                else:
-                    grid={'similarity_measure':similarity_measure_tmp, 'weight':weights_tmp, 'spectrum_preprocessing_order':spectrum_preprocessing_order_tmp, 'mz_min':mz_min_tmp, 'mz_max':mz_max_tmp, 'int_min':int_min_tmp, 'int_max':int_max_tmp, 'noise_threshold':noise_threshold_tmp, 'wf_mz':wf_mz_tmp, 'wf_int':wf_int_tmp, 'LET_threshold':LET_threshold_tmp, 'entropy_dimension':entropy_dimension_tmp, 'high_quality_reference_library':high_quality_reference_library_tmp}
-                    df_out = await asyncio.to_thread(tune_params_on_NRMS_data, **common_kwargs, grid=grid)
+            if input.chromatography_platform() == "HRMS":
+                window_size_centroiding_tmp = strip_numeric(input.window_size_centroiding())
+                window_size_matching_tmp = strip_numeric(input.window_size_matching())
+                grid = {
+                    'similarity_measure': similarity_measure_tmp,
+                    'weight': weights_tmp,
+                    'spectrum_preprocessing_order': spectrum_preprocessing_order_tmp,
+                    'mz_min': mz_min_tmp,
+                    'mz_max': mz_max_tmp,
+                    'int_min': int_min_tmp,
+                    'int_max': int_max_tmp,
+                    'noise_threshold': noise_threshold_tmp,
+                    'wf_mz': wf_mz_tmp,
+                    'wf_int': wf_int_tmp,
+                    'LET_threshold': LET_threshold_tmp,
+                    'entropy_dimension': entropy_dimension_tmp,
+                    'high_quality_reference_library': high_quality_reference_library_tmp,
+                    'window_size_centroiding': window_size_centroiding_tmp,
+                    'window_size_matching': window_size_matching_tmp,
+                }
+                df_out = await asyncio.to_thread(_run_with_redirects, tune_params_on_HRMS_data_shiny, rw, **common_kwargs, grid=grid)
+            else:
+                grid = {
+                    'similarity_measure': similarity_measure_tmp,
+                    'weight': weights_tmp,
+                    'spectrum_preprocessing_order': spectrum_preprocessing_order_tmp,
+                    'mz_min': mz_min_tmp,
+                    'mz_max': mz_max_tmp,
+                    'int_min': int_min_tmp,
+                    'int_max': int_max_tmp,
+                    'noise_threshold': noise_threshold_tmp,
+                    'wf_mz': wf_mz_tmp,
+                    'wf_int': wf_int_tmp,
+                    'LET_threshold': LET_threshold_tmp,
+                    'entropy_dimension': entropy_dimension_tmp,
+                    'high_quality_reference_library': high_quality_reference_library_tmp,
+                }
+                df_out = await asyncio.to_thread(_run_with_redirects, tune_params_on_NRMS_data_shiny, rw, **common_kwargs, grid=grid)
 
             match_log_rv.set(match_log_rv.get() + "\n✅ Parameter tuning finished.\n")
         except Exception as e:
@@ -1097,37 +1092,12 @@ def server(input, output, session):
         finally:
             is_tuning_running.set(False)
             is_any_job_running.set(False)
-            trailing = _drain_queue_nowait(_LOG_QUEUE)
-            if trailing:
-                match_log_rv.set(match_log_rv.get() + "".join(trailing))
             await reactive.flush()
 
-        #yield df_out.to_csv(index=False)
-        csv_bytes = df_out.to_csv(index=False).encode('utf-8')
-        yield csv_bytes
+        yield df_out.to_csv(index=False).encode("utf-8", sep='\t')
 
 
 
-    @render.text
-    def status_output():
-        return run_status_plot_spectra.get()
-        return run_status_spec_lib_matching.get()
-        return run_status_parameter_tuning.get()
-
-
-    class ReactiveWriter(io.TextIOBase):
-        def __init__(self, rv: reactive.Value, loop: asyncio.AbstractEventLoop):
-            self._rv = rv
-            self._loop = loop
-
-        def write(self, s: str):
-            if not s:
-                return 0
-            self._loop.call_soon_threadsafe(_LOG_QUEUE.put_nowait, s)
-            return len(s)
-
-        def flush(self):
-            pass
 
 
     @reactive.effect
@@ -1142,7 +1112,6 @@ def server(input, output, session):
             await reactive.flush()
 
 
-
     @render.text
     def status_output():
         return run_status_plot_spectra.get()
@@ -1150,7 +1119,6 @@ def server(input, output, session):
         return run_status_parameter_tuning.get()
 
 
-
 app = App(app_ui, server)