Remove extra atlas return in rt_alignment run() function

metatlas/datastructures/metatlas_dataset.py

@@ -147,8 +147,8 @@ class MetatlasDataset(HasTraits):
     keep_nonmatches: bool = Bool(default_value=True)
     ids: analysis_ids.AnalysisIdentifiers = Instance(klass=analysis_ids.AnalysisIdentifiers)
     atlas: metob.Atlas = Instance(klass=metob.Atlas)
-    rt_min_delta = Int(allow_none=True, default_value=None)
-    rt_max_delta = Int(allow_none=True, default_value=None)
+    rt_min_delta = Float(allow_none=True, default_value=None)
+    rt_max_delta = Float(allow_none=True, default_value=None)
     _atlas_df: Optional[pd.DataFrame] = Instance(klass=pd.DataFrame, allow_none=True, default_value=None)
     # _all_data contanis all data in experiement before any filtering
     _all_data: Optional[SampleSet] = traitlets.Tuple(allow_none=True, default_value=None)

metatlas/datastructures/metatlas_objects.py

@@ -186,7 +186,7 @@ def clone(self, recursive=False):
         obj: MetatlasObject
             Cloned object.
         """
-        #logger.debug('Cloning instance of %s with recursive=%s', self.__class__.__name__, recursive)
+        logger.debug('Cloning instance of %s with recursive=%s', self.__class__.__name__, recursive)
         obj = self.__class__()
         for (tname, trait) in self.traits().items():
             if tname.startswith('_') or trait.metadata.get('readonly', False):

metatlas/plots/dill2plots.py

@@ -251,6 +251,7 @@ class adjust_rt_for_selected_compound(object):
     def __init__(self,
                  data,
                  msms_sorting_method=None,
+                 msms_radio_buttons=None,
                  include_lcmsruns=None,
                  exclude_lcmsruns=None,
                  include_groups=None,
@@ -308,6 +309,7 @@ def __init__(self,
         logger.debug("Initializing new instance of %s.", self.__class__.__name__)
         self.data = data
         self.msms_hits, _ = sp.sort_msms_hits(msms_hits, sorting_method=msms_sorting_method)
+        self.msms_radio_buttons = msms_radio_buttons
         self.color_me = or_default(color_me, [('black', '')])
         self.compound_idx = compound_idx
         self.width = width
@@ -509,24 +511,32 @@ def display_eic_data(self):
                                  picker=True, pickradius=5, color=color, label=label)
 
     def configure_flags(self):
-        default_peak = ['keep',
-                        'remove',
-                        'keep, unresolvable isomers',
-                        'keep, poor peak shape']
 
-        default_msms = ['no selection',
+        if self.msms_radio_buttons is None or self.msms_radio_buttons == 'new':
+            default_peak = ['keep','remove','keep, unresolvable isomers','keep, poor peak shape']
 
-                        '-1.0, poor match, should remove',
-                        '0.0, no match or no MSMS collected',
-                        '0.5, partial or putative match of fragments',
-                        '1.0, good match',
-
-                        '0.5, co-isolated precursor, partial match',
-                        '1.0, co-isolated precursor, good match',
+            default_msms = ['no selection',
+                            '-1.0, poor match, should remove',
+                            '0.0, no match or no MSMS collected',
+                            '0.5, partial or putative match of fragments',
+                            '1.0, good match',
+                            '0.5, co-isolated precursor, partial match',
+                            '1.0, co-isolated precursor, good match',
+                            '0.5, single ion match, no evidence',
+                            '1.0, single ion match, ISTD/ref evidence']
+        elif self.msms_radio_buttons == 'old':
+            default_peak = ['keep','remove','unresolvable isomers','poor peak shape']
 
-                        '0.5, single ion match, no evidence',
-                        '1.0, single ion match, ISTD/ref evidence']
-
+            default_msms = ['no selection',
+                            '-1, bad match - should remove compound',
+                            '0, no ref match available or no MSMS collected',
+                            '0.5, partial match of fragments',
+                            '1, perfect match to internal reference library',
+                            '1, perfect match to external reference library',
+                            '1, co-isolated precursor but all reference ions are in sample spectrum']
+        else:
+            logger.warning('Unknown value for msms_radio_buttons: %s. Must use "old" or "new" or remove.', self.msms_radio_buttons)
+
         if self.peak_flags is None or self.peak_flags == '':
             self.peak_flags = default_peak
         if self.msms_flags is None or self.msms_flags == '':

metatlas/targeted/process.py

@@ -76,6 +76,7 @@ def annotation_gui(
     peak_flags=None,
     msms_flags=None,
     msms_sorting_method: str = None,
+    msms_radio_buttons: str = None,
 ) -> Optional[dp.adjust_rt_for_selected_compound]:
     """
     Opens the interactive GUI for setting RT bounds and annotating peaks
@@ -96,6 +97,7 @@ def annotation_gui(
     return dp.adjust_rt_for_selected_compound(
         data,
         msms_sorting_method=msms_sorting_method,
+        msms_radio_buttons=msms_radio_buttons,
         msms_hits=data.hits,
         color_me=colors,
         compound_idx=compound_idx,

metatlas/targeted/rt_alignment.py

@@ -107,6 +107,7 @@ def generate_rt_alignment_models(
     Returns a tuple with linear, polynomial and offset models
     """
     params = workflow.rt_alignment.parameters
+    logger.info("Generating RT alignment models with QC atlas %s and RT expansion of %s and %s", workflow.rt_alignment.atlas.name, params.rt_min_delta, params.rt_max_delta)
     rts_df = get_rts(data)
     actual, pred = subset_data_for_model_input(
         params.dependent_data_source, rts_df, data.atlas_df, params.inchi_keys_not_in_model
@@ -447,7 +448,7 @@ def write_notebooks(
                         before processing of the config file
     Returns a list of Paths to notebooks
     """
-    parameters_not_to_forward = ["rt_min_delta", "rt_max_delta"]
+    parameters_not_to_forward = []
     out = []
     for atlas, analysis in zip(atlases, workflow.analyses):
         source = repo_path() / "notebooks" / "reference" / "Targeted.ipynb"
@@ -474,7 +475,7 @@ def run(
     configuration: Config,
     workflow: Workflow,
     set_parameters: dict,
-) -> tuple[MetatlasDataset, list]:
+) -> MetatlasDataset:
     """Generates RT alignment model, applies to atlases, and generates all outputs"""
     params = workflow.rt_alignment.parameters
     ids = AnalysisIdentifiers(
@@ -488,6 +489,6 @@ def run(
     )
     shutil.copy2(params.config_file_name, ids.output_dir)
     ids.set_output_state(params, "rt_alignment")
-    metatlas_dataset = MetatlasDataset(ids=ids, max_cpus=params.max_cpus)
-    atlases = generate_outputs(metatlas_dataset, workflow, set_parameters)
-    return metatlas_dataset, atlases
+    metatlas_dataset = MetatlasDataset(ids=ids, max_cpus=params.max_cpus, rt_min_delta=params.rt_min_delta, rt_max_delta=params.rt_max_delta)
+    generate_outputs(metatlas_dataset, workflow, set_parameters)
+    return metatlas_dataset

metatlas/tools/config.py

@@ -67,8 +67,6 @@ class BaseNotebookParameters(BaseModel):
     include_lcmsruns: OutputLists = OutputLists()
     exclude_lcmsruns: OutputLists = OutputLists()
     groups_controlled_vocab: List[str] = []
-    rt_min_delta: Optional[float] = None
-    rt_max_delta: Optional[float] = None
     mz_tolerance_default: float = 10  # units of ppm
     mz_tolerance_override: Optional[float] = None  # units of ppm
     frag_mz_tolerance: Optional[float] = 0.02  # units of Daltons
@@ -120,6 +118,7 @@ class AnalysisNotebookParameters(BaseNotebookParameters):
     slurm_execute: bool = False
     clear_cache: bool = False
     msms_sorting_method: Optional[str] = None
+    msms_radio_buttons: Optional[str] = None
     # these are populated from the workflow's RTAlignment if None
     google_folder: Optional[str] = None
     msms_refs: Optional[Path] = None
@@ -135,7 +134,8 @@ class RTAlignmentNotebookParameters(BaseNotebookParameters):
     stop_before: Optional[str] = None
     google_folder: str
     msms_refs: Path
-
+    rt_min_delta: Optional[float] = None
+    rt_max_delta: Optional[float] = None
 
 class Atlas(BaseModel):
     """Atlas specification"""

notebooks/reference/Targeted.ipynb

@@ -198,6 +198,11 @@
     "# If True, then include MSMS fragment ions in the output documents\n",
     "export_msms_fragment_ions = None\n",
     "\n",
+    "# One of 'old', 'new', or None. If 'old', use the old version of the\n",
+    "# MSMS (and MS) radio button selections in the GUI. If 'new' or None, use the \n",
+    "# new version of the MSMS (and MS) radio button selections in the GUI.\n",
+    "msms_radio_buttons = None\n",
+    "\n",
     "# Setting this to True will remove the cache of MSMS hits\n",
     "# if you don't see MSMS data for any of your compounds in RT adjuster GUI,\n",
     "# then you might want to try settings this to True. However, it will\n",
@@ -318,7 +323,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "agui = annotation_gui(data=metatlas_dataset, compound_idx=0, width=15, height=3, colors=analysis.parameters.line_colors, msms_sorting_method=analysis.parameters.msms_sorting_method)"
+    "agui = annotation_gui(data=metatlas_dataset, \n",
+    "                      compound_idx=0, width=15, height=3, \n",
+    "                      colors=analysis.parameters.line_colors, \n",
+    "                      msms_sorting_method=analysis.parameters.msms_sorting_method, \n",
+    "                      msms_radio_buttons=analysis.parameters.msms_radio_buttons)"
    ]
   },
   {