def build_method_step_table_editor(known_solution_names=None):
""" Build a custom table editor to control a list of MethodSteps
"""
if known_solution_names is None:
known_solution_names = []
editor = TableEditor(
columns=[
ObjectColumn(name='name', label="Step Name"),
ObjectColumn(name='step_type', label='Step Type'),
ObjectColumn(name='_solutions0_name', label='Solution A',
editor=EnumEditor(values=known_solution_names)),
ObjectColumn(name='_solutions1_name', label='Solution B',
editor=EnumEditor(values=known_solution_names)),
UnitScalarColumn(name='flow_rate', label='Flow Rate',
editor=UnitScalarEditor()),
UnitScalarColumn(name='volume', label='Volume',
editor=UnitScalarEditor()),
],
deletable=True,
auto_size=True,
row_factory=MethodStep,
row_factory_kw={"name": "New Step"},
show_toolbar=True,
sortable=False,
)
return editor
def default_traits_view(self):
view = View(
VGroup(
HGroup(
Item('model.name', width=300),
Spring(),
Item('model.product_type', style="readonly", label="Type"),
),
Item("model.description", style="custom"),
Item('model.pI', editor=UnitScalarEditor(), label="pI"),
VGroup(Item('model.product_components',
show_label=False,
editor=COMPONENT_TABLE_EDITOR),
show_border=True,
label="Product components"),
VGroup(Item('model.product_component_concentration_exps',
editor=COMPONENT_CONC_EXPRESSION_EDITOR,
show_label=False),
show_border=True,
label="Product component concentration expressions"),
VGroup(Item('product_component_assays',
editor=ASSAY_TABLE_EDITOR,
show_label=False),
show_border=True,
label="Assays"),
),
resizable=True,
)
return view
def default_traits_view(self):
pka_tooltip = ("Negative logarithm of the acidity constant of the "
"component")
view = View(
Item("model.name"),
Item("model.charge", label="Charge",
editor=UnitScalarEditor()),
Item("model.pKa", label="pKa", tooltip=pka_tooltip,
editor=UnitScalarEditor()),
# Relevant when used as standalone view:
resizable=True, buttons=OKCancelButtons,
title="Configure component"
)
return view
def build_assay_list_editor(known_assays_names):
""" Build a table editor to display a list of product assays.
Parameters
----------
known_assays_names : list(str)
List of assay names available, if wanting to allow users to add assays.
"""
if known_assays_names:
row_factory = ProductAssay
default_name = known_assays_names[0]
else:
row_factory = False
default_name = ""
editor = TableEditor(
columns=[
ObjectColumn(name='name',
editor=EnumEditor(values=known_assays_names)),
UnitScalarColumn(name='proportion', editor=UnitScalarEditor())
],
editable=True,
sortable=False,
deletable=True,
row_factory=row_factory,
row_factory_kw={"name": default_name},
)
return editor
def default_traits_view(self):
prod = self.model.product
all_assays = prod.product_component_assays
assay_names = [assay for assay in all_assays
if assay != STRIP_COMP_NAME]
if self.datasource:
component_names = self.datasource.get_object_names_by_type(
"components"
)
else:
component_names = []
view = View(
Item('model.name', label='Name'),
Item('model.product_concentration', label='Product Concentration',
editor=UnitScalarEditor()),
Item('model.conductivity', label='Conductivity',
editor=UnitScalarEditor()),
Item('model.pH', label='pH', editor=UnitScalarEditor()),
VGroup(
Item('product_assays', show_label=False,
editor=build_assay_list_editor(assay_names)),
VGroup(
VGroup(
Item("_strip_desc", editor=LabelWithHyperlinks(),
style="readonly", show_label=False,
resizable=True)
),
Item('model.strip_mass_fraction',
editor=UnitScalarEditor(), style="readonly"),
visible_when="_has_strip"),
label='Product assay fractions', show_border=True,
),
VGroup(
Item('chemical_components', show_label=False,
editor=build_chemical_component_editor(component_names)),
label='Chemical Components', show_border=True,
),
# Relevant when used as standalone view only:
resizable=True, buttons=OKCancelButtons, width=400,
title="Configure the solution"
)
return view
def default_traits_view(self):
view = View(Tabbed(
VGroup(Item("model.name", label="System Name"),
Item("model.system_number", label="System ID"),
Item("model.abs_path_length",
editor=UnitScalarEditor(),
label="Absorbance Detector Path Length"),
Item("model.holdup_volume", editor=UnitScalarEditor()),
label="System in use"),
VGroup(Item("_system_type_view",
editor=InstanceEditor(),
style="custom",
show_label=False,
enabled_when="_allow_type_editing"),
label="System type"),
),
buttons=OKCancelButtons)
return view
def default_traits_view(self):
view = View(
Item("model.name", label="Resin Name"),
Item("model.resin_type", label="Resin Type"),
Item("model.lot_id", label="Resin Lot ID"),
Item("model.average_bead_diameter",
label="Avg. Bead Diameter",
editor=UnitScalarEditor()),
Item("model.ligand_density",
label="Ligand Density",
editor=UnitScalarEditor()),
Item("model.settled_porosity",
label="Settled Porosity",
editor=UnitScalarEditor()),
# Relevant when used as standalone view:
resizable=True,
buttons=OKCancelButtons,
title="Configure component")
return view
def default_traits_view(self):
known_component_names = [comp.name for comp in self.known_components]
buff_comp_editor = build_buffer_component_table_editor(
known_component_names)
view = View(
Item('model.name'),
Item('model.pH', label='pH', editor=UnitScalarEditor()),
Item('model.conductivity',
label='Conductivity',
editor=UnitScalarEditor()),
VGroup(
Item('buffer_components',
editor=buff_comp_editor,
label='Buffer Components')),
# Relevant when used as standalone view:
resizable=True,
buttons=OKCancelButtons,
title="Configure buffer")
return view
def default_traits_view(self):
view = View(VGroup(
Item("model.name"),
Item("model.manufacturer", label="Manufacturer"),
Item("model.manufacturer_name", label="Manufacturer Model"),
Item("model.num_inlets", label="Number of Inlets"),
Item("model.num_channels", label="Number of Channels"),
HGroup(
Item("system_type_flow_range_min",
editor=UnitScalarEditor(),
label="Min Flow"),
Item("system_type_flow_range_max",
editor=UnitScalarEditor(),
label="Max Flow"),
),
label="System Type",
show_border=True,
),
buttons=OKCancelButtons)
return view
def default_traits_view(self):
view = KromView(
Item("model.name",
tooltip=COMPONENT_NAME_TOOLTIP,
editor=TextEditor(invalid='_invalid_name'),
enabled_when='name_editable'),
Item("model.target_product",
enabled_when="target_product_editable"),
Item("model.extinction_coefficient",
editor=UnitScalarEditor(),
width=200),
Item("model.molecular_weight",
editor=UnitScalarEditor(),
tooltip="Molecular weight of the component in kilo-Daltons "
"(1 kDa=1 kg/mol)"),
# Relevant when used as standalone view:
buttons=OKCancelButtons,
title=self.title)
return view
def build_performance_data_table_editor():
""" Build a table editor to display a list of PerformanceParameters of
Simulations modeling the provided product.
"""
pool_conc_tooltip = 'Sum of concentration of all product components'
purity_tooltip = 'Purities (c_comp/c_all_comps * 100) of all product ' \
'components.'
columns = [
ObjectColumn(name='name',
label='Simulation Name',
editor=NoAutoTextEditor()),
UnitScalarColumn(name='start_collect_time',
label='Start Collect Time',
editor=UnitScalarEditor()),
UnitScalarColumn(name='stop_collect_time',
label='Stop Collect Time',
editor=UnitScalarEditor()),
UnitScalarColumn(name='pool_volume',
label='Pool Volume',
editor=UnitScalarEditor()),
UnitScalarColumn(name='step_yield',
label='Yield',
editor=UnitScalarEditor()),
UnitScalarColumn(name='pool_concentration',
label='Pool Concentration',
tooltip=pool_conc_tooltip,
editor=UnitScalarEditor()),
ObjectColumn(name='pool_purities',
label='Pool Product Component Purities',
tooltip=purity_tooltip),
]
editor = TableEditor(columns=columns,
deletable=False,
auto_size=True,
sortable=True,
editable=False)
return editor
def default_traits_view(self):
view = View(
VGroup(
Item("model.name", label="Column Model"),
Item("model.manufacturer", label="Column Manufacturer"),
Item("model.manufacturer_name",
label="Manufacturer Model Number"),
Item("model.diameter",
label="Column Diameter",
editor=UnitScalarEditor()),
Item("column_type_bed_height_min",
editor=UnitScalarEditor(),
label="Min Bed Height"),
Item("column_type_bed_height_max",
editor=UnitScalarEditor(),
label="Max Bed Height"),
Item("model.bed_height_adjust_method",
label="Bed Height Adjustment Method"),
),
# Relevant when used as standalone view:
resizable=True,
buttons=OKCancelButtons,
title="Configure Column Type")
return view
def build_chemical_component_editor(known_component_names):
""" Build a table editor to display a list of chemical components.
"""
if known_component_names:
row_factory = ChemicalComponent
default_name = known_component_names[0]
else:
row_factory = False
default_name = ""
editor = TableEditor(
columns=[
ObjectColumn(name='name',
editor=EnumEditor(values=known_component_names)),
UnitScalarColumn(name='concentration', editor=UnitScalarEditor())
],
editable=True,
sortable=False,
deletable=True,
row_factory=row_factory,
row_factory_kw={"name": default_name},
)
return editor
def default_traits_view(self):
known_component_names = [comp.name for comp in self.known_components]
chem_comp_editor = build_chemical_component_table_editor(
known_component_names)
# FIXME: How do we want to 'create' this object in the UI?
# i.e. what traits should be editable and what should be read only
# Note: Current traits not in view of Chemical are 'component_list',
# and 'component_atom_counts' which will be picked up by Tree
view = View(Item('model.name'),
Item('model.state'),
Item('model.formula', style='readonly'),
Item('model.molecular_weight',
label='Molecular Weight',
editor=UnitScalarEditor()),
VGroup(
Item('chemical_components',
editor=chem_comp_editor,
label='Chemical Components')),
resizable=True,
buttons=OKCancelButtons,
title="Configure Chemical")
return view
def default_traits_view(self):
landing_text = r"Strip contribution estimation for Experiment " \
r"'<i>{}</i>' (load '<i>{}</i>'), from the specified " \
r"load concentration, method step <br>start times and "\
r"estimated product extinction coefficient:"
landing_text = landing_text.format(self.model.experim.name,
self._load_solution_name)
formula = "strip_fraction = 1 - mass_eluting_before_strip / " \
"loaded_mass"
view = KromView(
VGroup(
VGroup(Label(landing_text),
HGroup(
Spring(),
Label(formula),
Spring(),
),
show_border=True),
VGroup(HGroup(
VGroup(
Item("object.model.load_concentration",
editor=UnitScalarEditor()),
Item("object.model.loaded_volume",
editor=UnitScalarEditor())),
Spring(),
VGroup(
Spring(),
Item("object.model.loaded_mass",
editor=UnitScalarEditor(),
style="readonly"),
Spring(),
),
),
show_border=True,
label="Product loaded into the column"),
HGroup(VGroup(
Item("object.model.product_ext_coeff",
editor=UnitScalarEditor(),
label="Est. product extinction coef."),
Item("object.model.load_start",
label="Load start time",
editor=UnitScalarEditor()),
Item("object.model.strip_start",
label="Strip start time",
editor=UnitScalarEditor()),
),
Spring(),
VGroup(
Spring(),
Item("object.model.integrated_mass_before_strip",
label="Mass eluting before strip",
editor=UnitScalarEditor(),
style="readonly"), Spring()),
show_border=True,
label="Product recovered before Strip"),
HGroup(
Spring(),
Item("object.model.strip_mass_fraction",
editor=UnitScalarEditor(),
label="Proposed Strip Mass Fraction"),
Item("_current_strip_mass_fraction",
editor=UnitScalarEditor(),
style="readonly",
label="Current Strip Mass Fraction"), Spring()),
),
title="Strip Fraction Estimation Assistant",
buttons=[ResetButton, ApplyButton],
handler=StripFractionCalculatorHandler(),
)
return view
def traits_view(self):
col_pattern_editor = build_col_name_editor(self.all_col_names)
filename = basename(self.akta_filepath)
spinner_editor = RangeEditor(low=5, high=9999, mode='spinner')
time_orig = 'AKTA time from which to import AKTA data and name' \
' of the corresponding step (typically the load).'
search_instructions = 'Hit {}-f to search for a word'
search_instructions = search_instructions.format(get_ctrl())
view = KromView(
Tabbed(
VGroup(
VGroup(
Label(time_orig),
HGroup(
Item('time_of_origin', editor=UnitScalarEditor(),
show_label=False),
Item("akta_start_method_step",
label="Method step @ t=0"),
),
Item('origin_error_msg', emphasized=True,
visible_when='origin_error_msg',
style='readonly', label="Note"),
show_border=True, label="Time of origin"
),
VGroup(
Item('patterns_as_list', editor=col_pattern_editor,
show_label=False, height=200),
Item('pattern_error_msg', emphasized=True,
visible_when='pattern_error_msg',
style='readonly', label="Error"),
show_border=True, label="AKTA Column Types"
),
label="AKTA File Settings"
),
VGroup(
Item('file_preview', editor=CodeEditor(),
show_label=False, tooltip=search_instructions),
VGroup(Item('length_of_preview', editor=spinner_editor)),
show_border=True,
label="AKTA File Preview".format(filename),
),
VGroup(
# Information used to evaluate the loaded product mass
Item("mass_bal_analyzer", editor=InstanceEditor(),
style="custom", show_label=False),
VGroup(
HGroup(
Item("mass_bal_msg", emphasized=True,
style='readonly', show_label=False),
),
Item("mass_bal_strategy",
label="Adjustment strategy",
enabled_when="not mass_balanced"),
HGroup(
Item("mass_bal_strategy_msg", emphasized=True,
style='readonly', show_label=False,
enabled_when="not mass_balanced"),
),
visible_when="target_experiment and pure_protein_exp"
),
label="UV and Mass Balance",
),
),
buttons=OKCancelButtons,
title="Experiment Importer: {}".format(self.experiment_name),
width=900,
)
return view
def traits_view(self):
component_descr_simple_editor = build_component_descr_editor(False)
component_descr_expert_editor = build_component_descr_editor(True)
known_products = self.datasource.get_object_names_by_type('products')
name_editor = TextWithExcludedValuesEditor(
forbidden_values=set(known_products)
)
expert_mode_tooltip = "Expert mode: customize assay names, and " \
"control concentration expressions."
strip_label = 'Strip component, automatically added to account for' \
' load mass eluting during the Strip step, if any.'
view = KromView(
VGroup(
HGroup(
Item('name', editor=name_editor, width=300),
Item('product_type'),
),
Item("description", style="custom"),
Item('pI', editor=UnitScalarEditor(), label="pI"),
HGroup(
Spring(),
Item('expert_mode', tooltip=expert_mode_tooltip),
),
VGroup(
Item('component_descs', show_label=False,
editor=component_descr_simple_editor),
Item('_add_comp_button', show_label=False),
HGroup(
Spring(),
Item('add_strip', tooltip=expert_mode_tooltip),
),
VGroup(
Label(strip_label),
HGroup(
Item('strip_component_descs', style='readonly',
editor=component_descr_simple_editor,
show_label=False, height=40),
Item('_edit_strip_comp_button', show_label=False),
),
visible_when="add_strip"
),
label="Product component names",
show_border=True, visible_when="not expert_mode"
),
VGroup(
Item('component_descs', show_label=False,
editor=component_descr_expert_editor,
visible_when="expert_mode"),
Item('_add_comp_button', show_label=False),
label="Product components and concentration expressions",
show_border=True, visible_when="expert_mode"
),
VGroup(
Item('component_assay_names', editor=ASSAY_TABLE_EDITOR,
show_label=False),
Item("_add_assay_button", show_label=False),
label="Component assay values",
show_border=True, visible_when="expert_mode"
),
),
width=600, height=600, title="Specify New Product Characteristics",
buttons=OKCancelButtons
)
return view
def default_traits_view(self):
bed_height_actual_tooltip = ("Must be within the range set by the "
"Column Type")
bed_height_actual_label = "Bed Height"
col_type_bed_height_set = (self.model.column_type is not None
and self.model.column_type.bed_height_range
is not None)
if col_type_bed_height_set:
height_range = self.model.column_type.bed_height_range.tolist()
bed_height_actual_tooltip += ": {}.".format(height_range)
# bed_height_units = self.model.column_type.bed_height_range.units
# bed_height_actual_label += " ({})".format(bed_height_units.label)
hetp_tooltip = "Height Equivalent to a Theoretical Plate (HETP)"
compress_factor_tooltip = "Compression Factor (settled vol/packed vol)"
view = View(
VGroup(
Item("model.name", label="Column Name"),
Item("model.column_lot_id", label="Column Lot ID"),
Item("model.bed_height_actual",
label=bed_height_actual_label,
editor=UnitScalarEditor(),
tooltip=bed_height_actual_tooltip),
Item("model.volume",
editor=UnitScalarEditor(),
style="readonly"),
Item("model.compress_factor",
label="Compression Factor",
editor=UnitScalarEditor(),
tooltip=compress_factor_tooltip),
Item("model.hetp",
label="HETP",
editor=UnitScalarEditor(),
tooltip=hetp_tooltip),
Item("model.hetp_asymmetry",
label="HETP Asymmetry",
editor=UnitScalarEditor()),
label="Packed Column",
show_border=True,
),
VGroup(
Item("column_type_view",
editor=InstanceEditor(),
style="custom",
show_label=False),
label="Column Type",
show_border=True,
),
VGroup(Item("resin_view",
editor=InstanceEditor(),
style="custom",
show_label=False),
label="Resin",
show_border=True),
# Relevant when used as standalone view:
resizable=True,
buttons=OKCancelButtons,
title="Configure column")
return view