Merge branch 'develop' into advanced-pagination

docs/examples/synthesis.md

@@ -132,7 +132,7 @@ These materials are simple, notice how we use the SMILES notation here as an ide
 Similarly, we can create more initial materials.
 
 ```python
-toluene = cript.Material(name="toluene", identifier=[{"smiles": "Cc1ccccc1"}, {"pubchem_id": 1140}])
+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"]}])

src/cript/api/data_schema.py

@@ -211,11 +211,21 @@ def is_node_schema_valid(self, node_json: str, is_patch: bool = False, force_val
 
         # logging out info to the terminal for the user feedback
         # (improve UX because the program is currently slow)
-        log_message = f"Validating {node_type} graph..."
+        log_message = f"Validating {node_type} graph"
+        try:
+            log_message += " '" + str(node_dict["name"]) + "'"
+        except KeyError:
+            try:
+                log_message += " '" + str(node_dict["uid"]) + "'"
+            except KeyError:
+                pass
+
+        log_message += " ... "
+
         if force_validation:
-            log_message = "Forced: " + log_message + " if error occur, try setting `cript.API.skip_validation = False` for debugging."
+            log_message = "Forced: " + log_message + " if error occur, try setting `cript_api.schema.skip_validation = False` for debugging."
         else:
-            log_message += " (Can be disabled by setting `cript.API.skip_validation = True`.)"
+            log_message += " (Can be disabled by setting `cript_api.schema.skip_validation = True`.)"
 
         self._api.logger.info(log_message)
 

src/cript/nodes/primary_nodes/collection.py

@@ -105,16 +105,15 @@ def __init__(self, name: str, experiment: Optional[List[Any]] = None, inventory:
         if citation is None:
             citation = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             name=name,
             experiment=experiment,
             inventory=inventory,
             doi=doi,
             citation=citation,
         )
-
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/primary_nodes/computation.py

@@ -141,7 +141,7 @@ def __init__(
         if citation is None:
             citation = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             type=type,
             input_data=input_data,
@@ -151,8 +151,7 @@ def __init__(
             prerequisite_computation=prerequisite_computation,
             citation=citation,
         )
-
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     # ------------------ Properties ------------------
 

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=[{"alternative_names": "my material alternative name"}]
+        ...     identifier=[{"names": ["my material alternative name"]}]
         ... )
         >>> my_quantity = cript.Quantity(key="mass", value=1.23, unit="kg")
         >>> ingredient = cript.Ingredient(
@@ -220,7 +220,7 @@ def __init__(
         if citation is None:
             citation = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             type=type,
             input_data=input_data,
@@ -231,8 +231,7 @@ def __init__(
             property=property,
             citation=citation,
         )
-
-        # self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/primary_nodes/data.py

@@ -167,7 +167,7 @@ def __init__(
         if citation is None:
             citation = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             type=type,
             file=file,
@@ -178,8 +178,7 @@ def __init__(
             process=process,
             citation=citation,
         )
-
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/primary_nodes/experiment.py

@@ -135,7 +135,7 @@ def __init__(
 
         super().__init__(name=name, notes=notes, **kwargs)
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             name=name,
             process=process,
@@ -147,8 +147,7 @@ def __init__(
             notes=notes,
         )
 
-        # check if the code is still valid
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/primary_nodes/inventory.py

@@ -99,7 +99,8 @@ def __init__(self, name: str, material: List[Material], notes: str = "", **kwarg
 
         super().__init__(name=name, notes=notes, **kwargs)
 
-        self._json_attrs = replace(self._json_attrs, material=material)
+        new_json_attrs = replace(self._json_attrs, material=material)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/primary_nodes/material.py

@@ -126,7 +126,7 @@ def __init__(
         if keyword is None:
             keyword = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             name=name,
             identifier=identifier,
@@ -137,6 +137,7 @@ def __init__(
             computational_forcefield=computational_forcefield,
             keyword=keyword,
         )
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/primary_nodes/project.py

@@ -101,8 +101,8 @@ def __init__(self, name: str, collection: Optional[List[Collection]] = None, mat
         if material is None:
             material = []
 
-        self._json_attrs = replace(self._json_attrs, name=name, collection=collection, material=material)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, name=name, collection=collection, material=material)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     def validate(self, api=None, is_patch=False, force_validation: bool = False):
         from cript.nodes.exceptions import (

src/cript/nodes/primary_nodes/reference.py

@@ -168,7 +168,6 @@ def __init__(
         new_attrs = replace(self._json_attrs, type=type, title=title, author=author, journal=journal, publisher=publisher, year=year, volume=volume, issue=issue, pages=pages, doi=doi, issn=issn, arxiv_id=arxiv_id, pmid=pmid, website=website)
 
         self._update_json_attrs_if_valid(new_attrs)
-        self.validate()
 
     @property
     @beartype

src/cript/nodes/subobjects/algorithm.py

@@ -106,8 +106,8 @@ def __init__(self, key: str, type: str, parameter: Optional[List[Parameter]] = N
         if citation is None:
             citation = []
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, key=key, type=type, parameter=parameter)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, key=key, type=type, parameter=parameter)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     def key(self) -> str:

src/cript/nodes/subobjects/citation.py

@@ -104,8 +104,8 @@ def __init__(self, type: str, reference: Reference, **kwargs):
             Instantiate citation subobject
         """
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, type=type, reference=reference)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, type=type, reference=reference)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/subobjects/computational_forcefield.py

@@ -140,7 +140,7 @@ def __init__(self, key: str, building_block: str, coarse_grained_mapping: str =
         if data is None:
             data = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             key=key,
             building_block=building_block,
@@ -151,7 +151,7 @@ def __init__(self, key: str, building_block: str, coarse_grained_mapping: str =
             data=data,
             citation=citation,
         )
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/subobjects/condition.py

@@ -151,7 +151,7 @@ def __init__(
         if data is None:
             data = []
 
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             key=key,
             type=type,
@@ -164,7 +164,7 @@ def __init__(
             measurement_id=measurement_id,
             data=data,
         )
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/subobjects/equipment.py

@@ -94,8 +94,8 @@ def __init__(self, key: str, description: str = "", condition: Union[List[Condit
         if citation is None:
             citation = []
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, key=key, description=description, condition=condition, file=file, citation=citation)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, key=key, description=description, condition=condition, file=file, citation=citation)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/subobjects/ingredient.py

@@ -106,8 +106,8 @@ def __init__(self, material: Material, quantity: List[Quantity], keyword: Option
         super().__init__(**kwargs)
         if keyword is None:
             keyword = []
-        self._json_attrs = replace(self._json_attrs, material=material, quantity=quantity, keyword=keyword)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, material=material, quantity=quantity, keyword=keyword)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @classmethod
     def _from_json(cls, json_dict: dict):

src/cript/nodes/subobjects/parameter.py

@@ -92,8 +92,8 @@ def __init__(self, key: str, value: Number, unit: Optional[str] = None, **kwargs
             create Parameter sub-object
         """
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, key=key, value=value, unit=unit)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, key=key, value=value, unit=unit)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @classmethod
     def _from_json(cls, json_dict: dict):

src/cript/nodes/subobjects/property.py

@@ -167,7 +167,7 @@ def __init__(
             citation = []
 
         super().__init__(**kwargs)
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             key=key,
             type=type,
@@ -185,7 +185,7 @@ def __init__(
             citation=citation,
             notes=notes,
         )
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/subobjects/quantity.py

@@ -94,8 +94,8 @@ def __init__(self, key: str, value: Number, unit: str, uncertainty: Optional[Num
             create Quantity sub-object
         """
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, key=key, value=value, unit=unit, uncertainty=uncertainty, uncertainty_type=uncertainty_type)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, key=key, value=value, unit=unit, uncertainty=uncertainty, uncertainty_type=uncertainty_type)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @classmethod
     def _from_json(cls, json_dict: dict):

src/cript/nodes/subobjects/software.py

@@ -82,8 +82,8 @@ def __init__(self, name: str, version: str, source: str = "", **kwargs):
         """
         super().__init__(**kwargs)
 
-        self._json_attrs = replace(self._json_attrs, name=name, version=version, source=source)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, name=name, version=version, source=source)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/subobjects/software_configuration.py

@@ -97,8 +97,8 @@ def __init__(self, software: Software, algorithm: Optional[List[Algorithm]] = No
         if citation is None:
             citation = []
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, software=software, algorithm=algorithm, notes=notes, citation=citation)
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, software=software, algorithm=algorithm, notes=notes, citation=citation)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

src/cript/nodes/supporting_nodes/file.py

@@ -178,16 +178,15 @@ def __init__(self, name: str, source: str, type: str, extension: str, data_dicti
         super().__init__(name=name, notes=notes, **kwargs)
 
         # setting every attribute except for source, which will be handled via setter
-        self._json_attrs = replace(
+        new_json_attrs = replace(
             self._json_attrs,
             type=type,
             # always giving the function the required str regardless if the input `Path` or `str`
             source=str(source),
             extension=extension,
             data_dictionary=data_dictionary,
         )
-
-        self.validate()
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     def ensure_uploaded(self, api=None):
         """

src/cript/nodes/supporting_nodes/user.py

@@ -74,9 +74,8 @@ def __init__(self, username: str, email: Optional[str] = "", orcid: Optional[str
             user ORCID
         """
         super().__init__(**kwargs)
-        self._json_attrs = replace(self._json_attrs, username=username, email=email, orcid=orcid)
-
-        self.validate()
+        new_json_attrs = replace(self._json_attrs, username=username, email=email, orcid=orcid)
+        self._update_json_attrs_if_valid(new_json_attrs)
 
     @property
     @beartype

tests/nodes/primary_nodes/test_material.py

@@ -9,7 +9,7 @@
 from tests.utils.util import strip_uid_from_dict
 
 
-def test_create_complex_material(simple_material_node, simple_computational_forcefield_node, simple_process_node) -> None:
+def test_create_complex_material(cript_api, simple_material_node, simple_computational_forcefield_node, simple_process_node) -> None:
     """
     tests that a simple material can be created with only the required arguments
     """
@@ -20,7 +20,7 @@ def test_create_complex_material(simple_material_node, simple_computational_forc
     material_notes = "my material notes"
 
     component = [simple_material_node]
-    forcefield = [simple_computational_forcefield_node]
+    forcefield = simple_computational_forcefield_node
 
     my_property = [cript.Property(key="modulus_shear", type="min", value=1.23, unit="gram")]