def test_simple_deserialization(valid_data):
"""Ensure that a deserialized Process Spec looks sane."""
process_spec: ProcessSpec = ProcessSpec.build(valid_data)
assert process_spec.uids == {'id': valid_data['uids']['id']}
assert process_spec.tags == ['baking::cakes', 'danger::low']
assert process_spec.parameters[0] == Parameter(name='oven temp',
value=UniformReal(
195, 205, ''),
origin='specified')
assert process_spec.conditions == []
assert process_spec.template == \
ProcessTemplate('the template', uids={'id': valid_data['template']['uids']['id']},
parameters=[
[ParameterTemplate('oven temp template',
bounds=RealBounds(175, 225, ''),
uids={'id': valid_data['template']['parameters'][0][0]['uids']['id']}),
RealBounds(175, 225, '')]
],
description='a long description',
allowed_labels=['a', 'b'],
allowed_names=['a name'])
assert process_spec.name == 'Process 1'
assert process_spec.notes == 'make sure to use oven mitts'
assert process_spec.file_links == [
FileLink('cake_recipe.txt', 'www.baking.com')
]
assert process_spec.typ == 'process_spec'
assert process_spec.audit_info == AuditInfo(**valid_data['audit_info'])
def test_invalid_assignment():
"""Invalid assignments to `material` or `spec` throw a TypeError."""
with pytest.raises(TypeError):
MeasurementRun("name",
spec=Condition("value of pi",
value=NominalReal(3.14159, '')))
with pytest.raises(TypeError):
MeasurementRun("name", material=FileLink("filename", "url"))
with pytest.raises(TypeError):
MeasurementRun() # Name is required
def test_material_soft_link():
"""Test that a measurement run can link to a material run, and that it survives serde."""
dye = MaterialRun("rhodamine",
file_links=FileLink(filename='a.csv', url='/a/path'))
assert dye.measurements == [], "default value of .measurements should be an empty list"
# The .measurements member should not be settable
with pytest.raises(AttributeError):
dye.measurements = [MeasurementRun("Dummy")]
absorbance = MeasurementRun(name="Absorbance",
uids={'id': str(uuid4())},
properties=[
Property(name='Abs at 500 nm',
value=NominalReal(0.1, ''))
])
assert absorbance.material is None, "Measurements should have None as the material by default"
absorbance.material = dye
assert absorbance.material == dye, "Material not set correctly for measurement"
assert dye.measurements == [
absorbance
], "Soft-link from material to measurement not created"
fluorescence = MeasurementRun(name="Fluorescence",
uids={'id': str(uuid4())},
properties=[
Property(name='PL counts at 550 nm',
value=NominalReal(30000, ''))
],
material=dye)
assert fluorescence.material == dye, "Material not set correctly for measurement"
assert dye.measurements == [absorbance, fluorescence], \
"Soft-link from material to measurements not created"
assert loads(dumps(absorbance)) == absorbance, \
"Measurement should remain unchanged when serialized"
assert loads(dumps(fluorescence)) == fluorescence, \
"Measurement should remain unchanged when serialized"
assert 'measurements' in repr(dye)
assert 'material' in repr(fluorescence)
assert 'material' in repr(absorbance)
subbed = substitute_links(dye)
assert 'measurements' in repr(subbed)
def test_cake_sigs():
"""Verify that all arguments for create methods work as expected."""
templates = make_cake_templates()
tmpl_snap = dumps(templates)
specs = make_cake_spec(templates)
spec_snap = dumps(specs)
assert dumps(templates) == tmpl_snap
cake1 = make_cake(seed=27, cake_spec=specs, tmpl=templates)
assert dumps(templates) == tmpl_snap
assert dumps(specs) == spec_snap
filelink = FileLink(filename='The name of the file', url='www.file.gov')
cake2 = make_cake(seed=27, cake_spec=specs, tmpl=templates, toothpick_img=filelink)
assert filelink.filename not in dumps(cake1)
assert filelink.filename in dumps(cake2)
assert cake1.uids == cake2.uids
def __init__(self, filename: str, url: str):
GEMDFileLink.__init__(self, filename, url)
self.typ = GEMDFileLink.typ
def make_cake(seed=None, tmpl=None, cake_spec=None, toothpick_img=None):
"""Define all objects that go into making a demo cake."""
import struct
import hashlib
if seed is not None:
random.seed(seed)
# Code to generate quasi-repeatable run annotations
# Note there are potential machine dependencies
md5 = hashlib.md5()
for x in random.getstate()[1]:
md5.update(struct.pack(">I", x))
run_key = md5.hexdigest()
######################################################################
# Parent Objects
if tmpl is None:
tmpl = make_cake_templates()
if cake_spec is None:
cake_spec = make_cake_spec(tmpl)
######################################################################
# Objects
cake_obj = make_instance(cake_spec)
operators = ['gwash', 'jadams', 'thomasj', 'jmadison', 'jmonroe']
producers = ['Fresh Farm', 'Sunnydale', 'Greenbrook']
drygoods = ['Acme', 'A1', 'Reliable', "Big Box"]
cake_obj.process.source = PerformedSource(
performed_by=random.choice(operators), performed_date='2015-03-14')
def _randomize_object(item):
# Add in the randomized particular values
if not isinstance(item, (MaterialRun, ProcessRun, IngredientRun)):
return
item.add_uid(DEMO_SCOPE, '{}-{}'.format(item.spec.uids[DEMO_SCOPE],
run_key))
if item.spec.tags is not None:
item.tags = list(item.spec.tags)
if item.spec.notes: # Neither None or empty string
item.notes = 'The spec says "{}"'.format(item.spec.notes)
if isinstance(item, MaterialRun):
if 'raw material' in item.tags:
if 'produce' in item.tags:
supplier = random.choice(producers)
else:
supplier = random.choice(drygoods)
item.name = "{} {}".format(supplier, item.spec.name)
if isinstance(item, ProcessRun):
if item.template.name == "Procuring":
item.source = PerformedSource(performed_by='hamilton',
performed_date='2015-02-17')
item.name = "{} {}".format(item.template.name,
item.output_material.name)
else:
item.source = cake_obj.process.source
if isinstance(item, IngredientRun):
fuzz = 0.95 + 0.1 * random.random()
if item.spec.absolute_quantity is not None:
item.absolute_quantity = \
NormalReal(mean=fuzz * item.spec.absolute_quantity.nominal,
std=0.05 * item.spec.absolute_quantity.nominal,
units=item.spec.absolute_quantity.units)
if item.spec.volume_fraction is not None:
# The only element here is dry mix, and it's almost entirely flour
item.volume_fraction = \
NormalReal(mean=0.01 * (fuzz - 0.5) + item.spec.volume_fraction.nominal,
std=0.005,
units=item.spec.volume_fraction.units)
if item.spec.mass_fraction is not None:
item.mass_fraction = \
UniformReal(lower_bound=(fuzz - 0.05) * item.spec.mass_fraction.nominal,
upper_bound=(fuzz + 0.05) * item.spec.mass_fraction.nominal,
units=item.spec.mass_fraction.units)
if item.spec.number_fraction is not None:
item.number_fraction = \
NormalReal(mean=fuzz * item.spec.number_fraction.nominal,
std=0.05 * item.spec.number_fraction.nominal,
units=item.spec.number_fraction.units)
recursive_foreach(cake_obj, _randomize_object)
frosting = \
next(x.material for x in cake_obj.process.ingredients if 'rosting' in x.name)
baked = \
next(x.material for x in cake_obj.process.ingredients if 'aked' in x.name)
def _find_name(name, material):
"""Recursively search for the right material."""
if name in material.name:
return material
for ingredient in material.process.ingredients:
result = _find_name(name, ingredient.material)
if result:
return result
return
flour = _find_name('Flour', cake_obj)
salt = _find_name('Salt', cake_obj)
sugar = _find_name('Sugar', cake_obj)
# Add measurements
cake_taste = MeasurementRun(name='Final Taste', material=cake_obj)
cake_appearance = MeasurementRun(name='Final Appearance',
material=cake_obj)
frosting_taste = MeasurementRun(name='Frosting Taste', material=frosting)
frosting_sweetness = MeasurementRun(name='Frosting Sweetness',
material=frosting)
baked_doneness = MeasurementRun(name='Baking doneness', material=baked)
flour_content = MeasurementRun(name='Flour nutritional analysis',
material=flour)
salt_content = MeasurementRun(name='Salt elemental analysis',
material=salt)
sugar_content = MeasurementRun(name='Sugar elemental analysis',
material=sugar)
if toothpick_img is not None:
baked_doneness.file_links.append(toothpick_img)
# and spec out the measurements
cake_taste.spec = MeasurementSpec(name='Taste',
template=tmpl['Taste test'])
cake_appearance.spec = MeasurementSpec(name='Appearance')
frosting_taste.spec = cake_taste.spec # Taste
frosting_sweetness.spec = MeasurementSpec(name='Sweetness')
baked_doneness.spec = MeasurementSpec(name='Doneness',
template=tmpl["Doneness"])
flour_content.spec = MeasurementSpec(name='Nutritional analysis',
template=tmpl["Nutritional Analysis"])
salt_content.spec = MeasurementSpec(name='Elemental analysis',
template=tmpl["Elemental Analysis"])
sugar_content.spec = salt_content.spec
# Note that while specs are regenerated each make_cake invocation, they are all identical
for msr in (cake_taste, cake_appearance, frosting_taste,
frosting_sweetness, baked_doneness, flour_content,
salt_content, sugar_content):
msr.spec.add_uid(DEMO_SCOPE, msr.spec.name.lower())
msr.add_uid(
DEMO_SCOPE,
'{}--{}-{}'.format(msr.spec.uids[DEMO_SCOPE],
msr.material.spec.uids[DEMO_SCOPE], run_key))
######################################################################
# Let's add some attributes
baked.process.conditions.append(
Condition(name='Cooking time',
template=tmpl['Cooking time'],
origin=Origin.MEASURED,
value=NominalReal(nominal=48, units='min')))
baked.process.conditions.append(
Condition(name='Oven temperature',
origin="measured",
value=NominalReal(nominal=362, units='degF')))
cake_taste.properties.append(
Property(name='Tastiness',
origin=Origin.MEASURED,
template=tmpl['Tastiness'],
value=UniformInteger(4, 5)))
cake_appearance.properties.append(
Property(name='Visual Appeal',
origin=Origin.MEASURED,
value=NominalInteger(nominal=5)))
frosting_taste.properties.append(
Property(name='Tastiness',
origin=Origin.MEASURED,
template=tmpl['Tastiness'],
value=NominalInteger(nominal=4)))
frosting_sweetness.properties.append(
Property(name='Sweetness (Sucrose-basis)',
origin=Origin.MEASURED,
value=NominalReal(nominal=1.7, units='')))
baked_doneness.properties.append(
Property(name='Toothpick test',
origin="measured",
template=tmpl["Toothpick test"],
value=NominalCategorical("crumbs")))
baked_doneness.properties.append(
Property(name='Color',
origin="measured",
template=tmpl["Color"],
value=DiscreteCategorical({
"Pale": 0.05,
"Golden brown": 0.65,
"Deep brown": 0.3
})))
flour_content.properties.append(
Property(name='Nutritional Information',
value=NominalComposition({
"dietary-fiber":
1 * (0.99 + 0.02 * random.random()),
"sugars":
1 * (0.99 + 0.02 * random.random()),
"other-carbohydrate":
20 * (0.99 + 0.02 * random.random()),
"protein":
4 * (0.99 + 0.02 * random.random()),
"other":
4 * (0.99 + 0.02 * random.random())
}),
template=tmpl["Nutritional Information"],
origin="measured"))
flour_content.conditions.append(
Condition(name='Sample Mass',
value=NormalReal(mean=99 + 2 * random.random(),
std=1.5,
units='mg'),
template=tmpl["Sample Mass"],
origin="measured"))
flour_content.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
flour_content.spec.conditions.append(
Condition(name='Sample Mass',
value=NominalReal(nominal=100, units='mg'),
template=tmpl["Sample Mass"],
origin="specified"))
flour_content.spec.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
salt_content.properties.append(
Property(name="Composition",
value=EmpiricalFormula(
formula="NaClCa0.006Si0.006O0.018K0.000015I0.000015"),
template=tmpl["Chemical Formula"],
origin="measured"))
salt_content.conditions.append(
Condition(name='Sample Mass',
value=NormalReal(mean=99 + 2 * random.random(),
std=1.5,
units='mg'),
template=tmpl["Sample Mass"],
origin="measured"))
salt_content.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
salt_content.spec.conditions.append(
Condition(name='Sample Mass',
value=NominalReal(nominal=100, units='mg'),
template=tmpl["Sample Mass"],
origin="specified"))
sugar_content.properties.append(
Property(
name="Composition",
value=EmpiricalFormula(formula='C11.996H21.995O10.997S0.00015'),
template=tmpl["Chemical Formula"],
origin="measured"))
sugar_content.conditions.append(
Condition(name='Sample Mass',
value=NormalReal(mean=99 + 2 * random.random(),
std=1.5,
units='mg'),
template=tmpl["Sample Mass"],
origin="measured"))
sugar_content.spec.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
cake_obj.notes = cake_obj.notes + "; Très délicieux! 😀"
cake_obj.file_links = [
FileLink(
filename="Photo",
url='https://storcpdkenticomedia.blob.core.windows.net/media/'
'recipemanagementsystem/media/recipe-media-files/recipes/retail/x17/'
'16730-beckys-butter-cake-600x600.jpg?ext=.jpg')
]
return cake_obj
def make_cake_spec(tmpl=None):
"""Define a recipe for making a cake."""
###############################################################################################
# Templates
if tmpl is None:
tmpl = make_cake_templates()
def _make_ingredient(*, material, process, **kwargs):
"""Convenience method to utilize material fields in creating an ingredient's arguments."""
return IngredientSpec(name=material.name.lower(),
tags=list(material.tags),
material=material,
process=process,
uids={
DEMO_SCOPE:
"{}--{}".format(material.uids[DEMO_SCOPE],
process.uids[DEMO_SCOPE])
},
**kwargs)
def _make_material(*, material_name, template, process_tmpl_name,
process_kwargs, **material_kwargs):
"""Convenience method to reuse material name in creating a material's arguments."""
process_name = "{} {}".format(process_tmpl_name, material_name)
return MaterialSpec(
name=material_name,
uids={DEMO_SCOPE: material_name.lower().replace(' ', '-')},
template=template,
process=ProcessSpec(
name=process_name,
uids={DEMO_SCOPE: process_name.lower().replace(' ', '-')},
template=tmpl[process_tmpl_name],
**process_kwargs),
**material_kwargs)
###############################################################################################
# Objects
cake_obj = _make_material(
material_name="Cake",
process_tmpl_name="Icing",
process_kwargs={
"tags": ['spreading'],
"notes": 'The act of covering a baked output with frosting'
},
template=tmpl["Dessert"],
properties=[
PropertyAndConditions(
Property(name="Tastiness",
value=NominalInteger(5),
template=tmpl["Tastiness"],
origin="specified"))
],
file_links=FileLink(
filename="Becky's Butter Cake",
url='https://www.landolakes.com/recipe/16730/becky-s-butter-cake/'
),
tags=['cake::butter cake', 'dessert::baked::cake', 'iced::chocolate'],
notes=
'Butter cake recipe reminiscent of the 1-2-3-4 cake that Grandma may have baked.'
)
########################
frosting = _make_material(
material_name="Frosting",
process_tmpl_name="Mixing",
process_kwargs={
"tags": ['mixing'],
"parameters": [
Parameter(name='Mixer speed setting',
template=tmpl['Mixer speed setting'],
origin='specified',
value=NominalInteger(2))
],
"notes":
'Combining ingredients to make a sweet frosting'
},
template=tmpl["Dessert"],
tags=['frosting::chocolate', 'topping::chocolate'],
notes='Chocolate frosting')
_make_ingredient(material=frosting,
notes='Seems like a lot of frosting',
labels=['coating'],
process=cake_obj.process,
absolute_quantity=NominalReal(nominal=0.751, units='kg'))
baked_cake = _make_material(
material_name="Baked Cake",
process_tmpl_name="Baking",
process_kwargs={
"tags": ['oven::baking'],
"conditions": [
Condition(name='Cooking time',
template=tmpl['Cooking time'],
origin=Origin.SPECIFIED,
value=NormalReal(mean=50, std=5, units='min'))
],
"parameters": [
Parameter(name='Oven temperature setting',
template=tmpl['Oven temperature setting'],
origin="specified",
value=NominalReal(nominal=350, units='degF'))
],
"notes":
'Using heat to convert batter into a solid matrix'
},
template=tmpl["Baked Good"],
properties=[
PropertyAndConditions(
property=Property(name="Toothpick test",
value=NominalCategorical("completely clean"),
template=tmpl["Toothpick test"])),
PropertyAndConditions(
property=Property(name="Color",
value=NominalCategorical("Golden brown"),
template=tmpl["Color"],
origin="specified"))
],
tags=['substrate'],
notes='The cakey part of the cake')
_make_ingredient(material=baked_cake,
labels=['substrate'],
process=cake_obj.process)
########################
batter = _make_material(
material_name="Batter",
process_tmpl_name="Mixing",
process_kwargs={
"tags": ['mixing'],
"parameters": [
Parameter(name='Mixer speed setting',
template=tmpl['Mixer speed setting'],
origin='specified',
value=NominalInteger(2))
],
"notes":
'Combining ingredients to make a baking feedstock'
},
template=tmpl["Generic Material"],
tags=['mixture'],
notes='The fluid that converts to cake with heat')
_make_ingredient(material=batter,
labels=['precursor'],
process=baked_cake.process)
########################
wetmix = _make_material(
material_name="Wet Ingredients",
process_tmpl_name="Mixing",
process_kwargs={
"tags": ['mixing'],
"parameters": [
Parameter(name='Mixer speed setting',
template=tmpl['Mixer speed setting'],
origin='specified',
value=NominalInteger(2))
],
"notes":
'Combining wet ingredients to make a baking feedstock'
},
template=tmpl["Generic Material"],
tags=["mixture"],
notes='The wet fraction of a batter')
_make_ingredient(material=wetmix, labels=['wet'], process=batter.process)
drymix = _make_material(
material_name="Dry Ingredients",
process_tmpl_name="Mixing",
process_kwargs={
"tags": ['mixing'],
"notes": 'Combining dry ingredients to make a baking feedstock'
},
template=tmpl["Generic Material"],
tags=["mixture"],
notes='The dry fraction of a batter')
_make_ingredient(material=drymix,
labels=['dry'],
process=batter.process,
absolute_quantity=NominalReal(nominal=3.052,
units='cups'))
########################
flour = _make_material(
material_name="Flour",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::dry-goods'],
"notes": 'Purchasing all purpose flour'
},
template=tmpl["Nutritional Material"],
properties=[
PropertyAndConditions(
property=Property(name="Nutritional Information",
value=NominalComposition({
"dietary-fiber":
1,
"sugars":
1,
"other-carbohydrate":
20,
"protein":
4,
"other":
4
}),
template=tmpl["Nutritional Information"],
origin="specified"),
conditions=Condition(name="Serving Size",
value=NominalReal(30, 'g'),
template=tmpl["Sample Mass"],
origin="specified"))
],
tags=['raw material', 'flour', 'dry-goods'],
notes='All-purpose flour')
_make_ingredient(
material=flour,
labels=['dry'],
process=drymix.process,
volume_fraction=NominalReal(nominal=0.9829, units='') # 3 cups
)
baking_powder = _make_material(
material_name="Baking Powder",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::dry-goods'],
"notes": 'Purchasing baking powder'
},
template=tmpl["Generic Material"],
tags=['raw material', 'leavening', 'dry-goods'],
notes='Leavening agent for cake')
_make_ingredient(
material=baking_powder,
labels=['leavening', 'dry'],
process=drymix.process,
volume_fraction=NominalReal(nominal=0.0137, units='') # 2 teaspoons
)
salt = _make_material(material_name="Salt",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::dry-goods'],
"notes": 'Purchasing salt'
},
template=tmpl["Formulaic Material"],
tags=['raw material', 'seasoning', 'dry-goods'],
notes='Plain old NaCl',
properties=[
PropertyAndConditions(
Property(name='Formula',
value=EmpiricalFormula("NaCl")))
])
_make_ingredient(
material=salt,
labels=['dry', 'seasoning'],
process=drymix.process,
volume_fraction=NominalReal(nominal=0.0034, units='') # 1/2 teaspoon
)
sugar = _make_material(
material_name="Sugar",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::dry-goods'],
"notes": 'Purchasing granulated sugar'
},
template=tmpl["Formulaic Material"],
tags=['raw material', 'sweetener', 'dry-goods'],
notes='Sugar',
properties=[
PropertyAndConditions(
Property(name="Formula", value=EmpiricalFormula("C12H22O11"))),
PropertyAndConditions(
Property(name='SMILES',
value=Smiles(
"C(C1C(C(C(C(O1)OC2(C(C(C(O2)CO)O)O)CO)O)O)O)O"),
template=tmpl["Molecular Structure"]))
])
_make_ingredient(material=sugar,
labels=['wet', 'sweetener'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=2, units='cups'))
butter = _make_material(
material_name="Butter",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::produce'],
"notes": 'Purchasing butter'
},
template=tmpl["Generic Material"],
tags=['raw material', 'produce', 'shortening', 'dairy'],
notes='Shortening for making rich, buttery baked goods')
_make_ingredient(material=butter,
labels=['wet', 'shortening'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=1, units='cups'))
_make_ingredient(
material=butter,
labels=['shortening'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.1434,
units='') # 1/2 c @ 0.911 g/cc
)
eggs = _make_material(material_name="Eggs",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::produce'],
"notes": 'Purchasing eggs'
},
template=tmpl["Generic Material"],
tags=[
'raw material',
'produce',
],
notes='A custard waiting to happen')
_make_ingredient(material=eggs,
labels=['wet'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=4, units=''))
vanilla = _make_material(
material_name="Vanilla",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::solution'],
"notes": 'Purchasing vanilla'
},
template=tmpl["Generic Material"],
tags=['raw material', 'seasoning'],
notes=
'Vanilla Extract is mostly alcohol but the most important component '
'is vanillin (see attached structure)',
properties=[
PropertyAndConditions(
Property(
name='Component Structure',
value=InChI(
"InChI=1S/C8H8O3/c1-11-8-4-6(5-9)2-3-7(8)10/h2-5,10H,1H3"
),
template=tmpl["Molecular Structure"]))
])
_make_ingredient(material=vanilla,
labels=['wet', 'flavoring'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=2,
units='teaspoons'))
_make_ingredient(
material=vanilla,
labels=['flavoring'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.0231,
units='') # 2 tsp @ 0.879 g/cc
)
milk = _make_material(material_name="Milk",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::produce'],
"notes": 'Purchasing milk'
},
template=tmpl["Generic Material"],
tags=['raw material', 'produce', 'dairy'],
notes='')
_make_ingredient(material=milk,
labels=['wet'],
process=batter.process,
absolute_quantity=NominalReal(nominal=1, units='cup'))
_make_ingredient(
material=milk,
labels=[],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.0816,
units='') # 1/4 c @ 1.037 g/cc
)
chocolate = _make_material(material_name="Chocolate",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::dry-goods'],
"notes": 'Purchasing chocolate'
},
template=tmpl["Generic Material"],
tags=['raw material'],
notes='')
_make_ingredient(
material=chocolate,
labels=['flavoring'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.1132, units='') # 3 oz.
)
powder_sugar = _make_material(
material_name="Powdered Sugar",
process_tmpl_name="Procuring",
process_kwargs={
"tags": ['purchase::dry-goods'],
"notes": 'Purchasing powdered sugar'
},
template=tmpl["Generic Material"],
tags=['raw material', 'sweetener', 'dry-goods'],
notes='Granulated sugar mixed with corn starch')
_make_ingredient(
material=powder_sugar,
labels=['flavoring'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.6387,
units='') # 4 c @ 30 g/ 0.25 cups
)
return cake_obj
def make_cake(seed=None, tmpl=None, cake_spec=None):
"""Define all objects that go into making a demo cake."""
import struct
import hashlib
if seed is not None:
random.seed(seed)
######################################################################
# Parent Objects
if tmpl is None:
tmpl = make_cake_templates()
if cake_spec is None:
cake_spec = make_cake_spec(tmpl)
######################################################################
# Objects
cake = make_instance(cake_spec)
operators = ['gwash', 'jadams', 'thomasj', 'jmadison', 'jmonroe']
cake.process.source = PerformedSource(
performed_by=random.choice(operators), performed_date='2015-03-14')
# Replace Abstract/In General
queue = [cake]
while queue:
item = queue.pop(0)
if item.spec.tags is not None:
item.tags = list(item.spec.tags)
if item.spec.notes: # None or empty string
item.notes = 'The spec says "{}"'.format(item.spec.notes)
if isinstance(item, MaterialRun):
item.name = item.name.replace('Abstract ', '')
queue.append(item.process)
elif isinstance(item, ProcessRun):
item.name = item.name.replace(', in General', '')
queue.extend(item.ingredients)
if item.template.name == "Procurement":
item.source = PerformedSource(performed_by='hamilton',
performed_date='2015-02-17')
else:
item.source = cake.process.source
elif isinstance(item, IngredientRun):
queue.append(item.material)
fuzz = 0.95 + 0.1 * random.random()
if item.spec.absolute_quantity is not None:
item.absolute_quantity = \
NormalReal(mean=fuzz * item.spec.absolute_quantity.nominal,
std=0.05 * item.spec.absolute_quantity.nominal,
units=item.spec.absolute_quantity.units)
if item.spec.volume_fraction is not None:
# The only element here is dry mix, and it's almost entirely flour
item.volume_fraction = \
NormalReal(mean=0.01 * (fuzz - 0.5) + item.spec.volume_fraction.nominal,
std=0.005,
units=item.spec.volume_fraction.units)
if item.spec.mass_fraction is not None:
item.mass_fraction = \
UniformReal(lower_bound=(fuzz - 0.05) * item.spec.mass_fraction.nominal,
upper_bound=(fuzz + 0.05) * item.spec.mass_fraction.nominal,
units=item.spec.mass_fraction.units)
if item.spec.number_fraction is not None:
item.number_fraction = \
NormalReal(mean=fuzz * item.spec.number_fraction.nominal,
std=0.05 * item.spec.number_fraction.nominal,
units=item.spec.number_fraction.units)
else:
raise TypeError("Unexpected object in the queue")
frosting = \
next(x.material for x in cake.process.ingredients if 'rosting' in x.name)
baked = \
next(x.material for x in cake.process.ingredients if 'aked' in x.name)
def find_name(name, material):
# Recursively search for the right material
if name == material.name:
return material
for ingredient in material.process.ingredients:
result = find_name(name, ingredient.material)
if result:
return result
return
flour = find_name('Flour', cake)
salt = find_name('Salt', cake)
sugar = find_name('Sugar', cake)
# Add measurements
cake_taste = MeasurementRun(name='Final Taste', material=cake)
cake_appearance = MeasurementRun(name='Final Appearance', material=cake)
frosting_taste = MeasurementRun(name='Frosting Taste', material=frosting)
frosting_sweetness = MeasurementRun(name='Frosting Sweetness',
material=frosting)
baked_doneness = MeasurementRun(name='Baking doneness', material=baked)
flour_content = MeasurementRun(name='Flour nutritional analysis',
material=flour)
salt_content = MeasurementRun(name='Salt elemental analysis',
material=salt)
sugar_content = MeasurementRun(name='Sugar elemental analysis',
material=sugar)
# and spec out the measurements
cake_taste.spec = MeasurementSpec(name='Taste',
template=tmpl['Taste test'])
cake_appearance.spec = MeasurementSpec(name='Appearance')
frosting_taste.spec = cake_taste.spec # Taste
frosting_sweetness.spec = MeasurementSpec(name='Sweetness')
baked_doneness.spec = MeasurementSpec(name='Doneness',
template=tmpl["Doneness"])
flour_content.spec = MeasurementSpec(name='Nutritional analysis',
template=tmpl["Nutritional Analysis"])
salt_content.spec = MeasurementSpec(name='Elemental analysis',
template=tmpl["Elemental Analysis"])
sugar_content.spec = salt_content.spec
for msr in (cake_taste, cake_appearance, frosting_taste,
frosting_sweetness, baked_doneness, flour_content,
salt_content, sugar_content):
msr.spec.add_uid(DEMO_SCOPE, msr.spec.name)
######################################################################
# Let's add some attributes
baked.process.conditions.append(
Condition(name='Cooking time',
template=tmpl['Cooking time'],
origin=Origin.MEASURED,
value=NominalReal(nominal=48, units='min')))
baked.spec.process.conditions.append(
Condition(name='Cooking time',
template=tmpl['Cooking time'],
origin=Origin.SPECIFIED,
value=NormalReal(mean=50, std=5, units='min')))
baked.process.conditions.append(
Condition(name='Oven temperature',
origin="measured",
value=NominalReal(nominal=362, units='degF')))
baked.spec.process.parameters.append(
Parameter(name='Oven temperature setting',
template=tmpl['Oven temperature setting'],
origin="specified",
value=NominalReal(nominal=350, units='degF')))
cake_taste.properties.append(
Property(name='Tastiness',
origin=Origin.MEASURED,
template=tmpl['Tastiness'],
value=UniformInteger(4, 5)))
cake_appearance.properties.append(
Property(name='Visual Appeal',
origin=Origin.MEASURED,
value=NominalInteger(nominal=5)))
frosting_taste.properties.append(
Property(name='Tastiness',
origin=Origin.MEASURED,
template=tmpl['Tastiness'],
value=NominalInteger(nominal=4)))
frosting_sweetness.properties.append(
Property(name='Sweetness (Sucrose-basis)',
origin=Origin.MEASURED,
value=NominalReal(nominal=1.7, units='')))
baked_doneness.properties.append(
Property(name='Toothpick test',
origin="measured",
template=tmpl["Toothpick test"],
value=NominalCategorical("crumbs")))
baked_doneness.properties.append(
Property(name='Color',
origin="measured",
template=tmpl["Color"],
value=DiscreteCategorical({
"Pale": 0.05,
"Golden brown": 0.65,
"Deep brown": 0.3
})))
flour_content.properties.append(
Property(name='Nutritional Information',
value=NominalComposition({
"dietary-fiber":
1 * (0.99 + 0.02 * random.random()),
"sugars":
1 * (0.99 + 0.02 * random.random()),
"other-carbohydrate":
20 * (0.99 + 0.02 * random.random()),
"protein":
4 * (0.99 + 0.02 * random.random()),
"other":
4 * (0.99 + 0.02 * random.random())
}),
template=tmpl["Nutritional Information"],
origin="measured"))
flour_content.conditions.append(
Condition(name='Sample Mass',
value=NormalReal(mean=99 + 2 * random.random(),
std=1.5,
units='mg'),
template=tmpl["Sample Mass"],
origin="measured"))
flour_content.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
flour_content.spec.conditions.append(
Condition(name='Sample Mass',
value=NominalReal(nominal=100, units='mg'),
template=tmpl["Sample Mass"],
origin="specified"))
flour_content.spec.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
salt_content.properties.append(
Property(name="Composition",
value=EmpiricalFormula(
formula="NaClCa0.006Si0.006O0.018K0.000015I0.000015"),
template=tmpl["Chemical Formula"],
origin="measured"))
salt_content.conditions.append(
Condition(name='Sample Mass',
value=NormalReal(mean=99 + 2 * random.random(),
std=1.5,
units='mg'),
template=tmpl["Sample Mass"],
origin="measured"))
salt_content.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
salt_content.spec.conditions.append(
Condition(name='Sample Mass',
value=NominalReal(nominal=100, units='mg'),
template=tmpl["Sample Mass"],
origin="specified"))
sugar_content.properties.append(
Property(
name="Composition",
value=EmpiricalFormula(formula='C11.996H21.995O10.997S0.00015'),
template=tmpl["Chemical Formula"],
origin="measured"))
sugar_content.conditions.append(
Condition(name='Sample Mass',
value=NormalReal(mean=99 + 2 * random.random(),
std=1.5,
units='mg'),
template=tmpl["Sample Mass"],
origin="measured"))
sugar_content.spec.parameters.append(
Parameter(name='Expected Sample Mass',
value=NominalReal(nominal=0.1, units='g'),
template=tmpl["Expected Sample Mass"],
origin="specified"))
# Code to generate quasi-repeatable run annotations
# Note there are potential machine dependencies
md5 = hashlib.md5()
for x in random.getstate()[1]:
md5.update(struct.pack(">I", x))
run_key = md5.hexdigest()
# Crawl tree and annotate with uids; only add ids if there's nothing there
recursive_foreach(
cake,
lambda obj: obj.uids or obj.add_uid(DEMO_SCOPE, obj.name + run_key))
cake.notes = cake.notes + "; Très délicieux! 😀"
cake.file_links = [
FileLink(
filename="Photo",
url='https://www.landolakes.com/RecipeManagementSystem/media/'
'Recipe-Media-Files/Recipes/Retail/x17/16730-beckys-butter-cake-600x600.jpg?ext=.jpg'
)
]
return cake
def make_cake_spec(tmpl=None):
"""Define a recipe for making a cake."""
###############################################################################################
# Templates
if tmpl is None:
tmpl = make_cake_templates()
count = dict()
def ingredient_kwargs(material):
# Pulls the elements of a material that all ingredients consume out
count[material.name] = count.get(material.name, 0) + 1
return {
"name":
"{} input{}".format(material.name.replace('Abstract ', ''),
" (Again)" * (count[material.name] - 1)),
"tags":
list(material.tags),
"material":
material
}
###############################################################################################
# Objects
cake = MaterialSpec(
name="Abstract Cake",
template=tmpl["Dessert"],
process=ProcessSpec(
name='Icing Cake, in General',
template=tmpl["Icing"],
tags=['spreading'],
notes='The act of covering a baked output with frosting'),
properties=[
PropertyAndConditions(
Property(name="Tastiness",
value=NominalInteger(5),
template=tmpl["Tastiness"],
origin="specified"))
],
file_links=FileLink(
filename="Becky's Butter Cake",
url='https://www.landolakes.com/recipe/16730/becky-s-butter-cake/'
),
tags=['cake::butter cake', 'dessert::baked::cake', 'iced::chocolate'],
notes=
'Butter cake recipe reminiscent of the 1-2-3-4 cake that Grandma may have baked.'
)
########################
frosting = MaterialSpec(
name="Abstract Frosting",
template=tmpl["Dessert"],
process=ProcessSpec(
name='Mixing Frosting, in General',
template=tmpl["Mixing"],
tags=['mixing'],
notes='Combining ingredients to make a sweet frosting'),
tags=['frosting::chocolate', 'topping::chocolate'],
notes='Chocolate frosting')
IngredientSpec(**ingredient_kwargs(frosting),
notes='Seems like a lot of frosting',
labels=['coating'],
process=cake.process,
absolute_quantity=NominalReal(nominal=0.751, units='kg'))
baked_cake = MaterialSpec(
name="Abstract Baked Cake",
template=tmpl["Generic Material"],
process=ProcessSpec(
name='Baking, in General',
template=tmpl["Baking in an oven"],
tags=['oven::baking'],
notes='Using heat to convert batter into a solid matrix'),
tags=[],
notes='The cakey part of the cake')
IngredientSpec(**ingredient_kwargs(baked_cake),
labels=['substrate'],
process=cake.process)
########################
batter = MaterialSpec(
name="Abstract Batter",
template=tmpl["Generic Material"],
process=ProcessSpec(
name='Mixing Batter, in General',
template=tmpl["Mixing"],
tags=['mixing'],
notes='Combining ingredients to make a baking feedstock'),
tags=[],
notes='The fluid that converts to cake with heat')
IngredientSpec(**ingredient_kwargs(batter),
labels=['precursor'],
process=baked_cake.process)
########################
wetmix = MaterialSpec(
name="Abstract Wet Mix",
template=tmpl["Generic Material"],
process=ProcessSpec(
name='Mixing Wet, in General',
template=tmpl["Mixing"],
tags=['mixing'],
notes='Combining wet ingredients to make a baking feedstock'),
tags=[],
notes='The wet fraction of a batter')
IngredientSpec(**ingredient_kwargs(wetmix),
labels=['wet'],
process=batter.process)
drymix = MaterialSpec(
name="Abstract Dry Mix",
template=tmpl["Generic Material"],
process=ProcessSpec(
name='Mixing Dry, in General',
template=tmpl["Mixing"],
tags=['mixing'],
notes='Combining dry ingredients to make a baking feedstock'),
tags=[],
notes='The dry fraction of a batter')
IngredientSpec(**ingredient_kwargs(drymix),
labels=['dry'],
process=batter.process,
absolute_quantity=NominalReal(nominal=3.052, units='cups'))
########################
flour = MaterialSpec(
name="Abstract Flour",
template=tmpl["Nutritional Material"],
properties=[
PropertyAndConditions(
property=Property(name="Nutritional Information",
value=NominalComposition({
"dietary-fiber":
1,
"sugars":
1,
"other-carbohydrate":
20,
"protein":
4,
"other":
4
}),
template=tmpl["Nutritional Information"],
origin="specified"),
conditions=Condition(name="Serving Size",
value=NominalReal(30, 'g'),
template=tmpl["Sample Mass"],
origin="specified"))
],
process=ProcessSpec(name='Buying Flour, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing all purpose flour'),
tags=[],
notes='All-purpose flour')
IngredientSpec(
**ingredient_kwargs(flour),
labels=['dry'],
process=drymix.process,
volume_fraction=NominalReal(nominal=0.9829, units='') # 3 cups
)
baking_powder = MaterialSpec(name="Abstract Baking Powder",
template=tmpl["Generic Material"],
process=ProcessSpec(
name='Buying Baking Powder, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing baking powder'),
tags=[],
notes='Leavening agent for cake')
IngredientSpec(
**ingredient_kwargs(baking_powder),
labels=['leavening', 'dry'],
process=drymix.process,
volume_fraction=NominalReal(nominal=0.0137, units='') # 2 teaspoons
)
salt = MaterialSpec(name="Abstract Salt",
template=tmpl["Formulaic Material"],
process=ProcessSpec(name='Buying Salt, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing salt'),
tags=[],
notes='Plain old NaCl',
properties=[
PropertyAndConditions(
Property(name='Formula',
value=EmpiricalFormula("NaCl")))
])
IngredientSpec(
**ingredient_kwargs(salt),
labels=['dry', 'seasoning'],
process=drymix.process,
volume_fraction=NominalReal(nominal=0.0034, units='') # 1/2 teaspoon
)
sugar = MaterialSpec(
name="Abstract Sugar",
template=tmpl["Formulaic Material"],
process=ProcessSpec(name='Buying Sugar, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing all purpose flour'),
tags=[],
notes='Sugar',
properties=[
PropertyAndConditions(
Property(name="Formula", value=EmpiricalFormula("C12H22O11"))),
PropertyAndConditions(
Property(name='SMILES',
value=Smiles(
"C(C1C(C(C(C(O1)OC2(C(C(C(O2)CO)O)O)CO)O)O)O)O"),
template=tmpl["Molecular Structure"]))
])
IngredientSpec(**ingredient_kwargs(sugar),
labels=['wet', 'sweetener'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=2, units='cups'))
butter = MaterialSpec(
name="Abstract Butter",
template=tmpl["Generic Material"],
process=ProcessSpec(name='Buying Butter, in General',
template=tmpl["Procurement"],
tags=['purchase::produce'],
notes='Purchasing butter'),
tags=[],
notes='Shortening for making rich, buttery baked goods')
IngredientSpec(**ingredient_kwargs(butter),
labels=['wet', 'shortening'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=1, units='cups'))
IngredientSpec(
**ingredient_kwargs(butter),
labels=['shortening'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.1434,
units='') # 1/2 c @ 0.911 g/cc
)
eggs = MaterialSpec(name="Abstract Eggs",
template=tmpl["Generic Material"],
process=ProcessSpec(name='Buying Eggs, in General',
template=tmpl["Procurement"],
tags=['purchase::produce'],
notes='Purchasing eggs'),
tags=[],
notes='')
IngredientSpec(**ingredient_kwargs(eggs),
labels=['wet'],
absolute_quantity=NominalReal(nominal=4, units=''))
vanilla = MaterialSpec(
name="Abstract Vanilla",
template=tmpl["Generic Material"],
process=ProcessSpec(name='Buying Vanilla, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing vanilla'),
tags=[],
notes=
'Vanilla Extract is mostly alcohol but the most important component '
'is vanillin (see attached structure)',
properties=[
PropertyAndConditions(
Property(
name='Component Structure',
value=InChI(
"InChI=1S/C8H8O3/c1-11-8-4-6(5-9)2-3-7(8)10/h2-5,10H,1H3"
),
template=tmpl["Molecular Structure"]))
])
IngredientSpec(**ingredient_kwargs(vanilla),
labels=['wet', 'flavoring'],
process=wetmix.process,
absolute_quantity=NominalReal(nominal=2, units='teaspoons'))
IngredientSpec(
**ingredient_kwargs(vanilla),
labels=['flavoring'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.0231,
units='') # 2 tsp @ 0.879 g/cc
)
milk = MaterialSpec(name="Abstract Milk",
template=tmpl["Generic Material"],
process=ProcessSpec(name='Buying Milk, in General',
template=tmpl["Procurement"],
tags=['purchase::produce'],
notes='Purchasing milk'),
tags=[],
notes='')
IngredientSpec(**ingredient_kwargs(milk),
labels=['wet'],
process=batter.process,
absolute_quantity=NominalReal(nominal=1, units='cup'))
IngredientSpec(
**ingredient_kwargs(milk),
labels=[],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.0816,
units='') # 1/4 c @ 1.037 g/cc
)
chocolate = MaterialSpec(name="Abstract Chocolate",
template=tmpl["Generic Material"],
process=ProcessSpec(
name='Buying Chocolate, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing chocolate'),
tags=[],
notes='')
IngredientSpec(
**ingredient_kwargs(chocolate),
labels=['flavoring'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.1132, units='') # 3 oz.
)
powder_sugar = MaterialSpec(
name="Abstract Powdered Sugar",
template=tmpl["Generic Material"],
process=ProcessSpec(name='Buying Powdered Sugar, in General',
template=tmpl["Procurement"],
tags=['purchase::dry-goods'],
notes='Purchasing powdered sugar'),
tags=[],
notes='Granulated sugar mixed with corn starch')
IngredientSpec(
**ingredient_kwargs(powder_sugar),
labels=['flavoring'],
process=frosting.process,
mass_fraction=NominalReal(nominal=0.6387,
units='') # 4 c @ 30 g/ 0.25 cups
)
# Crawl tree and annotate with uids; only add ids if there's nothing there
recursive_foreach(
cake, lambda obj: obj.uids or obj.add_uid(DEMO_SCOPE, obj.name))
return cake