This PR reflects an old change in the data model, where material iden…

…tifiers become attributes instead of a list of subnodes. (#434)

* first steps to fix identifier

* making progress

* fix the problems

* fixing pytest tests

* fix spelling

* working through doctest

* fix CI

* fix doctests

* fix notebooks

* another fix

* fix simulation

.trunk/configs/.cspell.json

@@ -121,6 +121,7 @@
     "doctest",
     "Doctest",
     "Doctests",
-    "linenums"
+    "linenums",
+    "XLYOFNOQVPJJNP"
   ]
 }

docs/examples/simulation.md

@@ -361,23 +361,13 @@ bulk.output_data = [final_data]
 
 ## Create a virtual Material
 
-First, we'll create a virtual material and add some
-[`Identifiers`](../../nodes/primary_nodes/material/#cript.nodes.primary_nodes.material.Material.identifier)
-to the material to make it easier to identify and search.
+First, we'll create a virtual material with identifiers to make it easier to search for.
 
 ```python
-# create identifier dictionaries and put it in `identifiers` variable
-identifiers = [{"names": ["poly(styrene)", "poly(vinylbenzene)"]}]
-identifiers += [{"bigsmiles": "[H]{[>][<]C(C[>])c1ccccc1[<]}C(C)CC"}]
-identifiers += [{"chem_repeat": ["C8H8"]}]
-
 # create a material node object with identifiers
-polystyrene = cript.Material(name="virtual polystyrene", identifier=identifiers)
+polystyrene = cript.Material(name="virtual polystyrene", bigsmiles="[H]{[>][<]C(C[>])c1ccccc1[<]}C(C)CC", names = ["poly(styrene)", "poly(vinylbenzene)"], chem_repeat= ["C8H8"])
 ```
 
-!!! note "Identifier keys"
-    The allowed [`Identifiers`](../../nodes/primary_nodes/material/#cript.nodes.primary_nodes.material.Material.identifier) keys are listed in the [material identifier keys](https://app.criptapp.org/vocab/material_identifier_key) in the CRIPT controlled vocabulary.
-
 ## Add [`Property`](../../nodes/subobjects/property) sub-objects
 Let's also add some [`Property`](../../nodes/subobjects/property) nodes to the [`Material`](../../nodes/primary_nodes/material), which represent its physical or virtual (in the case of a simulated material) properties.
 

docs/examples/synthesis.md

@@ -116,26 +116,20 @@ They are for example the chemical you buy commercially and use as input into you
 For this we create this inventory by adding the [Material](../../nodes/primary_nodes/material) we need one by one.
 
 ```python
-# create a list of identifiers as dictionaries to
-# identify your material to the community and your team
-my_solution_material_identifiers = [
-    {"chemical_id": "598-30-1"}
-]
-
 solution = cript.Material(
     name="SecBuLi solution 1.4M cHex",
-    identifier=my_solution_material_identifiers
+    chemical_id = "598-30-1",
 )
 ```
 
 These materials are simple, notice how we use the SMILES notation here as an identifier for the material.
 Similarly, we can create more initial materials.
 
 ```python
-toluene = cript.Material(name="toluene", identifier=[{"smiles": "Cc1ccccc1"}, {"pubchem_cid": 1140}])
-styrene = cript.Material(name="styrene", identifier=[{"smiles": "c1ccccc1C=C"}, {"inchi": "InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2"}])
-butanol = cript.Material(name="1-butanol", identifier=[{"smiles": "OCCCC"}, {"inchi_key": "InChIKey=LRHPLDYGYMQRHN-UHFFFAOYSA-N"}])
-methanol = cript.Material(name="methanol", identifier=[{"smiles": "CO"}, {"names": ["Butan-1-ol", "Butyric alcohol", "Methylolpropane", "n-Butan-1-ol", "methanol"]}])
+toluene = cript.Material(name="toluene", smiles="Cc1ccccc1", pubchem_cid = 1140)
+styrene = cript.Material(name="styrene", smiles = "c1ccccc1C=C", inchi = "InChI=1S/C8H8/c1-2-8-6-4-3-5-7-8/h2-7H,1H2")
+butanol = cript.Material(name="1-butanol", smiles = "OCCCC", inchi_key = "InChIKey=LRHPLDYGYMQRHN-UHFFFAOYSA-N")
+methanol = cript.Material(name="methanol", smiles = "CO", names = ["Butan-1-ol", "Butyric alcohol", "Methylolpropane", "n-Butan-1-ol", "methanol"])
 ```
 
 Now that we defined those materials, we can combine them into an inventory
@@ -250,20 +244,15 @@ that will serve as our product. We give the material a `name` attribute and add
 [Project]((../../nodes/primary_nodes/project).
 
 ```python
-polystyrene = cript.Material(name="polystyrene", identifier=[])
+polystyrene = cript.Material(name="polystyrene", bigsmiles="[H]{[>][<]C(C[>])c1ccccc1[<]}C(C)CC")
 project.material += [polystyrene]
 ```
 
 Let's add some `Identifiers` to the material to make it easier to identify and search.
 
 ```python
-# create a name identifier
-polystyrene.identifier += [{"names": ["poly(styrene)", "poly(vinylbenzene)"]}]
-
-# create a BigSMILES identifier
-polystyrene.identifier += [{"bigsmiles": "[H]{[>][<]C(C[>])c1ccccc1[<]}C(C)CC"}]
 # create a chemical repeat unit identifier
-polystyrene.identifier += [{"chem_repeat": ["C8H8"]}]
+polystyrene.chem_repeat = ["C8H8"]
 ```
 
 Next, we'll add some [Property](../../nodes/subobjects/property) nodes to the

mkdocs.yml

@@ -38,7 +38,6 @@ nav:
       - Computational Forcefield: nodes/subobjects/computational_forcefield.md
       - Condition: nodes/subobjects/condition.md
       - Equipment: nodes/subobjects/equipment.md
-      #      - Identifier: nodes/subobjects/identifier.md
       - Ingredient: nodes/subobjects/ingredient.md
       - Parameter: nodes/subobjects/parameter.md
       - Property: nodes/subobjects/property.md

src/cript/api/api.py

@@ -824,7 +824,7 @@ def delete(self, node) -> None:
         >>> import cript
         >>> my_material_node = cript.Material(
         ...     name="my component material 1",
-        ...     identifier=[{"amino_acid": "component 1 alternative name"}],
+        ...     names = ["component 1 alternative name"],
         ... )
         >>> api.delete(node=my_material_node) # doctest: +SKIP
 

src/cript/api/valid_search_modes.py

@@ -16,7 +16,7 @@ class SearchModes(Enum):
     UUID : str
         Search by node UUID.
     BIGSMILES: str
-        search materials by bigsmiles identifier.
+        search materials by bigsmiles.
 
     Examples
     -------

src/cript/nodes/core.py

@@ -293,10 +293,10 @@ def get_expanded_json(self, **kwargs) -> str:
         >>> my_project = cript.Project(name=f"my_Project")
         >>> my_collection = cript.Collection(name="my collection")
         >>> my_material_1 = cript.Material(
-        ...     name="my material 1", identifier=[{"bigsmiles": "my material 1 bigsmiles"}]
+        ...     name="my material 1", bigsmiles = "my material 1 bigsmiles"
         ... )
         >>> my_material_2 = cript.Material(
-        ...     name="my material 2", identifier=[{"bigsmiles": "my material 2 bigsmiles"}]
+        ...     name="my material 2", bigsmiles = "my material 2 bigsmiles"
         ... )
         >>> my_inventory = cript.Inventory(
         ...     name="my inventory", material=[my_material_1, my_material_2]
@@ -511,10 +511,10 @@ def find_children(self, search_attr: dict, search_depth: int = -1, handled_nodes
         >>> my_project = cript.Project(name=f"my_Project")
         >>> my_collection = cript.Collection(name="my collection")
         >>> my_material_1 = cript.Material(
-        ...     name="my material 1", identifier=[{"bigsmiles": "my material 1 bigsmiles"}]
+        ...     name="my material 1", bigsmiles = "my material 1 bigsmiles"
         ... )
         >>> my_material_2 = cript.Material(
-        ...     name="my material 2", identifier=[{"bigsmiles": "my material 2 bigsmiles"}]
+        ...     name="my material 2", bigsmiles = "my material 2 bigsmiles"
         ... )
         >>> my_inventory = cript.Inventory(
         ...     name="my inventory", material=[my_material_1, my_material_2]

src/cript/nodes/exceptions.py

@@ -54,6 +54,19 @@ def __str__(self) -> str:
         return error_message
 
 
+class CRIPTMaterialIdentifierError(CRIPTException):
+    """Every material node needs to have at least one identifier set."""
+
+    def __init__(self, material_node):
+        self.material_node = material_node
+
+    def __str__(self) -> str:
+        error_message = "Every Material node needs at least one identifier from "
+        error_message += " [ 'amino_acid', 'bigsmiles', 'chem_formula', 'chem_repeat', 'chemical_id', 'inchi', 'lot_number', 'names', 'pubchem_cid', 'smiles','vendor'] set."
+        error_message += f" This node {self.material_node} has none set."
+        return error_message
+
+
 class CRIPTJsonDeserializationError(CRIPTException):
     """
     ## Definition

src/cript/nodes/primary_nodes/collection.py

@@ -175,11 +175,11 @@ def inventory(self) -> List[Any]:
         >>> my_collection = cript.Collection(name="my collection name")
         >>> material_1 = cript.Material(
         ...     name="material 1",
-        ...     identifier=[{"bigsmiles": "material 1 bigsmiles"}],
+        ...     bigsmiles = "material 1 bigsmiles",
         ... )
         >>> material_2 = cript.Material(
         ...     name="material 2",
-        ...     identifier=[{"bigsmiles": "material 2 bigsmiles"}],
+        ...     bigsmiles = "material 2 bigsmiles",
         ... )
         >>> my_inventory = cript.Inventory(
         ...     name="my inventory name", material=[material_1, material_2]

src/cript/nodes/primary_nodes/computation_process.py

@@ -154,7 +154,7 @@ def __init__(
         >>> input_data = cript.Data(name="my data name", type="afm_amp", file=[data_files])
         >>> my_material = cript.Material(
         ...     name="my material",
-        ...     identifier=[{"names": ["my material alternative name"]}]
+        ...     names = ["my material alternative name"]
         ... )
         >>> my_quantity = cript.Quantity(key="mass", value=1.23, unit="kg")
         >>> ingredient = cript.Ingredient(
@@ -368,7 +368,7 @@ def ingredient(self) -> List[Any]:
         Examples
         --------
         >>> import cript
-        >>> my_material = cript.Material(name="my material", identifier=[{"bigsmiles": "123456"}])
+        >>> my_material = cript.Material(name="my material", bigsmiles = "my bigsmiles")
         >>> my_quantity = cript.Quantity(
         ...     key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"
         ... )

src/cript/nodes/primary_nodes/data.py

@@ -401,7 +401,7 @@ def computation_process(self) -> Union[Any, None]:
         ... )
         >>> my_material = cript.Material(
         ...     name="my material name",
-        ...     identifier=[{"bigsmiles": "123456"}]
+        ...     bigsmiles = "123456"
         ... )
         >>> my_quantity = cript.Quantity(
         ...     key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"
@@ -459,7 +459,7 @@ def material(self) -> List[Any]:
         ...    data_dictionary="my file's data dictionary"
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
-        >>> my_material = cript.Material(name="my material name", identifier=[{"bigsmiles": "123456"}])
+        >>> my_material = cript.Material(name="my material name", bigsmiles = "123456")
         >>> my_data.material = [my_material]
 
         Returns

src/cript/nodes/primary_nodes/experiment.py

@@ -244,7 +244,7 @@ def computation_process(self) -> List[Any]:
         ... )
         >>> my_data = cript.Data(name="my data name", type="afm_amp", file=[my_file])
         >>> my_material = cript.Material(
-        ...     name="my material name", identifier=[{"bigsmiles": "123456"}]
+        ...     name="my material name", bigsmiles = "123456"
         ... )
         >>> my_quantity = cript.Quantity(
         ... key="mass", value=11.2, unit="kg", uncertainty=0.2, uncertainty_type="stdev"

src/cript/nodes/primary_nodes/inventory.py

@@ -73,11 +73,11 @@ def __init__(self, name: str, material: List[Material], notes: str = "", **kwarg
         >>> import cript
         >>> material_1 = cript.Material(
         ...    name="material 1",
-        ...    identifier=[{"bigsmiles": "material 1 bigsmiles"}],
+        ...    bigsmiles = "material 1 bigsmiles",
         ... )
         >>> material_2 = cript.Material(
         ...    name="material 2",
-        ...    identifier=[{"bigsmiles": "material 2 bigsmiles"}],
+        ...    bigsmiles = "material 2 bigsmiles",
         ... )
         >>> my_inventory = cript.Inventory(
         ...    name="my inventory name", material=[material_1, material_2]
@@ -113,12 +113,12 @@ def material(self) -> List[Material]:
         >>> import cript
         >>> my_material = cript.Material(
         ...    name="my material",
-        ...    identifier=[{"bigsmiles": "my bigsmiles"}],
+        ...    bigsmiles = "my bigsmiles",
         ... )
         >>> my_inventory = cript.Inventory(name="my inventory", material=[my_material])
         >>> new_material = cript.Material(
         ...    name="new material",
-        ...    identifier=[{"bigsmiles": "my bigsmiles"}],
+        ...    bigsmiles = "my bigsmiles",
         ... )
         >>> my_inventory.material = [new_material]