Merge pull request #65 from quantori/fix-restore

Merge fix_restore branch into main

Author: SamDima

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pesn-sdk
-version = 1.1.0
+version = 1.2.0
 author = Quantori
 author_email = [email protected]
 description = Quantori Python SDK for PerkinElmer Signals Notebook
@@ -22,11 +22,11 @@ python_requires = >=3.9
 install_requires =
     Jinja2~=3.1.1
     requests~=2.27
-    pydantic==1.9.1
+    pydantic==1.10.4
     pandas~=1.4
 
 [options.extras_require]
-dev = pytest==6.2.5;pytest-mock==3.7.0;arrow==1.2.2;factory-boy==3.2.1;pytest-factoryboy==2.1.0;pytest-cov==3.0.0;mypy==0.931
+dev = pytest==6.2.5;pytest-mock==3.7.0;arrow==1.2.2;factory-boy==3.2.1;pytest-factoryboy==2.1.0;pytest-cov==3.0.0;mypy==1.0.0
 
 [options.packages.find]
 where = src

src/signals_notebook/api.py

@@ -92,10 +92,10 @@ def call(
         self,
         method: str,
         path: Union[str, Sequence[str]],
-        params: Dict[str, Any] = None,
+        params: Optional[Dict[str, Any]] = None,
         data: _Data = None,
-        json: Union[list, Dict[str, Any]] = None,
-        headers: Dict[str, str] = None,
+        json: Optional[Union[list, Dict[str, Any]]] = None,
+        headers: Optional[Dict[str, str]] = None,
     ) -> requests.Response:
         """Makes an API call
 
@@ -148,6 +148,7 @@ def call(
                 params=params,
                 headers=headers,
             )
+
         if not response.ok:
             log.error(
                 'Error has been occurred while getting response, status code: %s',

src/signals_notebook/attributes/attribute.py

@@ -117,7 +117,7 @@ def create(
         cls,
         name: str,
         description: str,
-        options: list[str] = None,
+        options: Optional[list[str]] = None,
     ) -> 'Attribute':
         """Create new Attribute
 

src/signals_notebook/common_types.py

@@ -297,7 +297,7 @@ class ResponseData(GenericModel, Generic[EntityClass]):
     relationships: Optional[dict[str, Any]] = Field(default=None)
     meta: Optional[dict[str, Any]] = Field(default=None)
 
-    def __init__(self, _context: dict[str, Any] = None, **kwargs):
+    def __init__(self, _context: Optional[dict[str, Any]] = None, **kwargs):
         attributes = kwargs.get('attributes', {})
 
         if _context:
@@ -310,7 +310,7 @@ class Response(GenericModel, Generic[EntityClass]):
     links: Optional[Links] = None
     data: Union[ResponseData[EntityClass], List[ResponseData[EntityClass]]]
 
-    def __init__(self, _context: dict[str, Any] = None, **kwargs):
+    def __init__(self, _context: Optional[dict[str, Any]] = None, **kwargs):
         data = kwargs.get('data', {})
 
         if _context:

src/signals_notebook/entities/admin_defined_object.py

@@ -1,7 +1,7 @@
 import json
 import logging
 from functools import cached_property
-from typing import Any, ClassVar, List, Literal, Optional
+from typing import Any, cast, ClassVar, List, Literal, Optional
 
 from pydantic import BaseModel, Field
 
@@ -56,7 +56,7 @@ class Config:
 
 class AdminDefinedObject(Container):
     type: Literal[EntityType.ADO] = Field(allow_mutation=False)
-    ado: AdoType = Field(default=CUSTOM_SYSTEM_OBJECT)
+    ado: AdoType
     _template_name: ClassVar = 'ado.html'
 
     class Config:
@@ -111,11 +111,7 @@ def create(
         )
 
         log.debug('Creating AdminDefinedObject for: %s', cls.__name__)
-        return super()._create(
-            digest=digest,
-            force=force,
-            request=request,
-        )
+        return cast('AdminDefinedObject', super()._create(digest=digest, force=force, request=request))
 
     def get_html(self) -> str:
         """Get in HTML format

src/signals_notebook/entities/chemical_drawing.py

@@ -116,7 +116,7 @@ def add_structures(
         self,
         structure: Structure,
         positions: ChemicalDrawingPosition,
-        digest: str = None,
+        digest: Optional[str] = None,
         force: bool = True,
     ) -> Structure:
         """Add reagent, reactant or product to ChemicalDrawing

src/signals_notebook/entities/container.py

@@ -120,13 +120,10 @@ def dump_templates(cls, base_path: str, fs_handler: FSHandler) -> None:
         templates = EntityStore.get_list(
             include_types=[entity_type], include_options=[EntityStore.IncludeOptions.TEMPLATE]
         )
-        try:
-            for template in templates:
-                template.dump(
-                    fs_handler.join_path(base_path, 'templates', entity_type),
-                    fs_handler,
-                    ['Templates', entity_type.value],
-                )
-
-        except TypeError:
-            pass
+
+        for template in templates:
+            template.dump(
+                fs_handler.join_path(base_path, 'templates', entity_type),
+                fs_handler,
+                ['Templates', entity_type.value],
+            )

src/signals_notebook/entities/entity.py

@@ -10,7 +10,6 @@
 from signals_notebook.api import SignalsNotebookApi
 from signals_notebook.common_types import (
     EID,
-    EntityClass,
     EntityCreationRequestPayload,
     EntityShortDescription,
     EntityType,
@@ -209,7 +208,9 @@ def delete(self) -> None:
         log.debug('Entity: %s was deleted from EntityStore', self.eid)
 
     @classmethod
-    def _create(cls, *, digest: str = None, force: bool = True, request: EntityCreationRequestPayload) -> EntityClass:
+    def _create(
+        cls, *, digest: Optional[str] = None, force: bool = True, request: EntityCreationRequestPayload,
+    ) -> 'Entity':
         api = SignalsNotebookApi.get_default_api()
         log.debug('Create Entity: %s...', cls.__name__)
 

src/signals_notebook/entities/entity_store.py

@@ -2,7 +2,7 @@
 import logging
 from datetime import datetime
 from enum import Enum
-from typing import cast, Generator, List, Union
+from typing import cast, Generator, List, Optional, Union
 
 from signals_notebook.api import SignalsNotebookApi
 from signals_notebook.common_types import EID, EntityType, Response, ResponseData
@@ -59,11 +59,11 @@ def get(cls, eid: EID) -> Entity:
     @classmethod
     def get_list(
         cls,
-        include_types: List[EntityType] = None,
-        exclude_types: List[EntityType] = None,
-        include_options: List[IncludeOptions] = None,
-        modified_after: datetime = None,
-        modified_before: datetime = None,
+        include_types: Optional[List[EntityType]] = None,
+        exclude_types: Optional[List[EntityType]] = None,
+        include_options: Optional[List[IncludeOptions]] = None,
+        modified_after: Optional[datetime] = None,
+        modified_before: Optional[datetime] = None,
     ) -> Generator[Entity, None, None]:
         """Get all entities
 
@@ -133,7 +133,7 @@ def refresh(cls, entity: Entity) -> None:
                 setattr(entity, field.name, new_value)
 
     @classmethod
-    def delete(cls, eid: EID, digest: str = None, force: bool = True) -> None:
+    def delete(cls, eid: EID, digest: Optional[str] = None, force: bool = True) -> None:
         """Delete Entity by ID
 
         Args:

src/signals_notebook/entities/experiment.py

@@ -2,7 +2,7 @@
 import logging
 from enum import Enum
 from functools import cached_property
-from typing import Any, ClassVar, Generator, Literal, Optional, Union
+from typing import Any, cast, ClassVar, Dict, Generator, List, Literal, Optional, Union
 
 from pydantic import BaseModel, Field
 
@@ -18,8 +18,12 @@
 
 
 class _Attributes(BaseModel):
-    name: str
+    name: Optional[str] = None
     description: Optional[str] = None
+    organization: Optional[str] = None
+    department: Optional[str] = None
+    project: Optional[str] = None
+    modality: Optional[str] = None
 
 
 class _Relationships(BaseModel):
@@ -58,12 +62,13 @@ def _get_entity_type(cls) -> EntityType:
     def create(
         cls,
         *,
-        name: str,
+        name: Optional[str] = None,
         description: Optional[str] = None,
         template: Optional['Experiment'] = None,
         notebook: Optional[Notebook] = None,
-        digest: str = None,
+        digest: Optional[str] = None,
         force: bool = True,
+        attributes: Optional[Dict[str, Any]] = None,
     ) -> 'Experiment':
         """Create new Experiment in Signals Notebook
 
@@ -74,6 +79,7 @@ def create(
             notebook: notebook where create experiment
             digest: Indicate digest
             force: Force to create without doing digest check
+            attributes:
 
         Returns:
             Experiment
@@ -89,20 +95,13 @@ def create(
         request = _RequestPayload(
             data=_RequestBody(
                 type=cls._get_entity_type(),
-                attributes=_Attributes(
-                    name=name,
-                    description=description,
-                ),
+                attributes=_Attributes(name=name, description=description, **(attributes or {})),
                 relationships=relationships,
             )
         )
 
         log.debug('Creating Notebook for: %s', cls.__name__)
-        return super()._create(
-            digest=digest,
-            force=force,
-            request=request,
-        )
+        return cast('Experiment', super()._create(digest=digest, force=force, request=request))
 
     @cached_property
     def stoichiometry(self) -> Union[Stoichiometry, list[Stoichiometry]]:
@@ -160,12 +159,62 @@ def _load(cls, path: str, fs_handler: FSHandler, parent: Any) -> None:
         from signals_notebook.item_mapper import ItemMapper
 
         metadata = json.loads(fs_handler.read(fs_handler.join_path(path, 'metadata.json')))
-        experiment = cls.create(
-            notebook=parent, name=metadata['name'], description=metadata['description'], force=True
-        )
+        try:
+            experiment = cls.create(
+                notebook=parent,
+                name=metadata['name'],
+                description=metadata['description'],
+                force=True,
+                attributes=dict(
+                    organization=metadata['Organization'],
+                    project=metadata['Project'],
+                    modality=metadata['Modality'],
+                    department=metadata['Department'],
+                ),
+            )
+        except Exception as e:
+            log.error(str(e))
+            if 'According to template, name is auto generated, can not be specified' in str(e):
+                log.error('Retrying create')
+                experiment = cls.create(
+                    notebook=parent,
+                    description=metadata['description'],
+                    force=True,
+                    attributes=dict(
+                        organization=metadata['Organization'],
+                        project=metadata['Project'],
+                        modality=metadata['Modality'],
+                        department=metadata['Department'],
+                    ),
+                )
+            else:
+                raise e
         child_entities_folders = fs_handler.list_subfolders(path)
         for child_entity in child_entities_folders:
             child_entity_type = child_entity.split(':')[0]
-            ItemMapper.get_item_class(child_entity_type)._load(
-                fs_handler.join_path(path, child_entity), fs_handler, experiment
-            )
+            try:
+                ItemMapper.get_item_class(child_entity_type)._load(
+                    fs_handler.join_path(path, child_entity), fs_handler, experiment
+                )
+            except NotImplementedError:
+                log.error('Failed to load entity %s. Not supported' % child_entity_type)
+
+    def dump(self, base_path: str, fs_handler: FSHandler, alias: Optional[List[str]] = None) -> None:
+        metadata = {k: v for k, v in self.dict().items() if k in ('name', 'description', 'eid')}
+        self._reload_properties()
+        for prop in self._properties:
+            if prop.name in ('Department', 'Project', 'Modality', 'Organization'):
+                metadata[prop.name] = prop.value
+
+        fs_handler.write(
+            fs_handler.join_path(base_path, self.eid, 'metadata.json'),
+            json.dumps(metadata),
+            alias + [self.name, '__Metadata'] if alias else None,
+        )
+        for child in self.get_children():
+            try:
+                child.dump(
+                    fs_handler.join_path(base_path, self.eid), fs_handler, alias + [self.name] if alias else None
+                )
+            except Exception as e:
+                log.error(str(e))