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pulling in changes for schema update
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| # CRIPT Python SDK Changelog | ||
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| ## Version 2.3.0 | ||
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| **New Features:** | ||
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| - `cript.API` objects now have a `DataSchema` attribute called `schema`, representing the JSON schema for node validation. | ||
| - This includes the ability to enable and disable node validation. | ||
| - `cript.API` objects now have `logger` attributes from the Python `logging` module to control logging flows. | ||
| - Refactor of Paginator: | ||
| - New Paginator objects for accessing data from the CRIPT data bank via search. | ||
| - Paginator are now Python iterators. You can use `for node in paginator: ...` directly. | ||
| - Paginator now return `cript.Node` objects natively. | ||
| - JSON response can be requested from Paginator alternatively. This is helpful for internal work and debugging. | ||
| - Additional information is added to the logging message when nodes are validated. For primary nodes, `name` is displayed; for others, the `UUID` is displayed. | ||
| - HTTP requests are now optimized, leaving connections open and grouping requests for better performance. | ||
| - A native iterator for nodes is now offered. It iterates in depth-first order over all child nodes of the root node. Cycles are automatically broken, and every node is visited exactly once. | ||
| - Materials with no identifier issue a warning to users. | ||
| - Debugging messages show full API requests and responses for debugging. | ||
| - Automated UUID caching for nodes can now be explicitly circumvented when using `cript.load_nodes_from_json`. Mostly useful for development. | ||
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| **Known Issues and Bugs:** | ||
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| - Saving projects is not supported. Temporarily, you can use `get_expanded_json` to store a JSON representation of projects, which can be uploaded into CRIPT at a later time. | ||
| - BigSMILES search patterns are not supported. | ||
| - Searching for more than 1000 pages (10000 entries) is not supported. | ||
| - Permission settings in CRIPT do not influence the behavior of the SDK objects. | ||
| - Tests that require valid tokens (like saving or searching) are not included in CI/CD tests. | ||
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| **Bugfixes:** | ||
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| - `cript.load_nodes_from_json` can now load JSON files that store different nodes in lists or dictionaries. | ||
| - Not all nodes were correctly validated at all times, especially if instantiated from JSON. All nodes are automatically validated now. | ||
| - The documentation has been updated to remove certain mistakes. | ||
| - Users can have only one Python object with the same UUID to avoid mis-updates. This did not work in all cases, but it works in all cases now. | ||
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| **Breaking Changes:** | ||
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| - `cript.API()` objects no longer have functions related to JSON schema validation. Please use the new `DataSchema` class instead. The `DataSchema` class can be accessed via the `schema` property of the API class. | ||
| - Indirect logging control via the API is defunct. Please use the direct access to the `logger` attribute of API classes to control logging output. | ||
| - The SDK used to use `identifier` dictionaries for material identifiers. This is updated to use individual attributes of the material node. This is consistent with the JSON schema and front-end but is a breaking change to older SDK versions and the original CRIPT publication. | ||
| - Projects were checked to ensure the presence of material and computation in Experiments. These errors were converted into warnings. | ||
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| ### Health Report | ||
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| ```shell | ||
| =============================================================================================== test session starts =============================================================================================== | ||
| platform linux -- Python 3.11.2, pytest-7.4.3 | ||
| plugins: cov-4.1.0 | ||
| collected 124 items | ||
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| tests/test_node_util.py ........... [ 8%] | ||
| tests/api/test_api.py ..... [ 12%] | ||
| tests/api/test_db_schema.py ..... [ 16%] | ||
| tests/api/test_search.py .....F [ 21%] | ||
| tests/nodes/test_utils.py .. [ 23%] | ||
| tests/nodes/primary_nodes/test_collection.py .....F [ 28%] | ||
| tests/nodes/primary_nodes/test_computation.py .....F [ 33%] | ||
| tests/nodes/primary_nodes/test_computational_process.py ....F [ 37%] | ||
| tests/nodes/primary_nodes/test_data.py ....F [ 41%] | ||
| tests/nodes/primary_nodes/test_experiment.py ....F [ 45%] | ||
| tests/nodes/primary_nodes/test_inventory.py ..F [ 47%] | ||
| tests/nodes/primary_nodes/test_material.py ...F [ 50%] | ||
| tests/nodes/primary_nodes/test_process.py .....F [ 55%] | ||
| tests/nodes/primary_nodes/test_project.py ...F [ 58%] | ||
| tests/nodes/primary_nodes/test_reference.py ......F [ 64%] | ||
| tests/nodes/subobjects/test_algorithm.py ..F [ 66%] | ||
| tests/nodes/subobjects/test_citation.py ..F [ 69%] | ||
| tests/nodes/subobjects/test_computational_forcefield.py ..F [ 71%] | ||
| tests/nodes/subobjects/test_condition.py ..F [ 74%] | ||
| tests/nodes/subobjects/test_equipment.py ..F [ 76%] | ||
| tests/nodes/subobjects/test_ingredient.py ..F [ 79%] | ||
| tests/nodes/subobjects/test_parameter.py ..F [ 81%] | ||
| tests/nodes/subobjects/test_property.py ..F [ 83%] | ||
| tests/nodes/subobjects/test_quantity.py ..F [ 86%] | ||
| tests/nodes/subobjects/test_software.py ...F [ 89%] | ||
| tests/nodes/subobjects/test_software_configuration.py ..F [ 91%] | ||
| tests/nodes/supporting_nodes/test_file.py ..s....F [ 98%] | ||
| tests/nodes/supporting_nodes/test_user.py .. [100%] | ||
| ============================================================================================= short test summary info ============================================================================================= | ||
| FAILED tests/api/test_search.py::test_api_search_bigsmiles - cript.nodes.exceptions.CRIPTJsonDeserializationError: JSON deserialization failed for node type Material with JSON str: Material | ||
| FAILED tests/nodes/primary_nodes/test_collection.py::test_integration_collection - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_computation.py::test_integration_computation - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_computational_process.py::test_integration_computational_process - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_data.py::test_integration_data - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_experiment.py::test_integration_experiment - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_inventory.py::test_integration_inventory - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_material.py::test_integration_material - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_process.py::test_integration_complex_process - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_project.py::test_integration_project - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/primary_nodes/test_reference.py::test_integration_reference - IndexError: list index out of range | ||
| FAILED tests/nodes/subobjects/test_algorithm.py::test_integration_algorithm - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_citation.py::test_integration_citation - IndexError: list index out of range | ||
| FAILED tests/nodes/subobjects/test_computational_forcefield.py::test_integration_computational_forcefield - AttributeError: 'NoneType' object has no attribute 'description' | ||
| FAILED tests/nodes/subobjects/test_condition.py::test_integration_process_condition - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_equipment.py::test_integration_equipment - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_ingredient.py::test_integration_ingredient - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_parameter.py::test_integration_parameter - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_property.py::test_integration_material_property - IndexError: list index out of range | ||
| FAILED tests/nodes/subobjects/test_quantity.py::test_integration_quantity - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_software.py::test_integration_software - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/subobjects/test_software_configuration.py::test_integration_software_configuration - AttributeError: 'list' object has no attribute 'starts with' | ||
| FAILED tests/nodes/supporting_nodes/test_file.py::test_integration_file - AttributeError: 'list' object has no attribute 'starts with' | ||
| ======================================================================== 23 failed, 100 passed, 1 skipped, 1 warning in 905.51s (0:15:05) ========================================================================= | ||
| ``` |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -25,9 +25,15 @@ def simple_project_node(simple_collection_node) -> cript.Project: | |
| def complex_project_dict(complex_collection_node, simple_material_node, complex_user_node) -> dict: | ||
| project_dict = {"node": ["Project"]} | ||
| project_dict["locked"] = True | ||
| project_dict["model_version"] = "1.0.0" | ||
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| # project_dict["model_version"] = "1.0.0" | ||
| # project_dict["updated_by"] = json.loads(copy.deepcopy(complex_user_node).get_expanded_json()) | ||
| # project_dict["created_by"] = json.loads(complex_user_node.get_expanded_json()) | ||
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| project_dict["model_version"] = "1.0.1" | ||
| # project_dict["updated_by"] = json.loads(copy.deepcopy(complex_user_node).get_expanded_json()) | ||
| # project_dict["created_by"] = json.loads(complex_user_node.get_expanded_json()) | ||
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| project_dict["public"] = True | ||
| project_dict["name"] = "my project name" | ||
| project_dict["notes"] = "my project notes" | ||
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@@ -60,7 +66,7 @@ def fixed_cyclic_project_node() -> cript.Project: | |
| project_json_string += '"created_at": "2024-03-12 15:58:12.486673",\n' | ||
| project_json_string += '"updated_at": "2024-03-12 15:58:12.486681",\n' | ||
| project_json_string += '"email": "[email protected]",\n' | ||
| project_json_string += '"model_version": "1.0.0",\n' | ||
| project_json_string += '"model_version": "1.0.1",\n' | ||
| project_json_string += '"orcid": "0000-0002-0000-0000",\n' | ||
| project_json_string += '"picture": "/my/picture/path",\n' | ||
| project_json_string += '"username": "testuser"\n' | ||
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@@ -72,13 +78,13 @@ def fixed_cyclic_project_node() -> cript.Project: | |
| project_json_string += '"created_at": "2024-03-12 15:58:12.486673",\n' | ||
| project_json_string += '"updated_at": "2024-03-12 15:58:12.486681",\n' | ||
| project_json_string += '"email": "[email protected]",\n' | ||
| project_json_string += '"model_version": "1.0.0",\n' | ||
| project_json_string += '"model_version": "1.0.1",\n' | ||
| project_json_string += '"orcid": "0000-0002-0000-0000",\n' | ||
| project_json_string += '"picture": "/my/picture/path",\n' | ||
| project_json_string += '"username": "testuser"\n' | ||
| project_json_string += "},\n" | ||
| project_json_string += '"locked": true,\n' | ||
| project_json_string += '"model_version": "1.0.0",\n' | ||
| project_json_string += '"model_version": "1.0.1",\n' | ||
| project_json_string += '"public": true,\n' | ||
| project_json_string += '"name": "my project name",\n' | ||
| project_json_string += '"notes": "my project notes",\n' | ||
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@@ -126,7 +132,7 @@ def fixed_cyclic_project_node() -> cript.Project: | |
| project_json_string += '"node": ["Property"],\n' | ||
| project_json_string += '"uid": "_:fc504202-6fdd-43c7-830d-40c7d3f0cb8c",\n' | ||
| project_json_string += '"uuid": "fc504202-6fdd-43c7-830d-40c7d3f0cb8c",\n' | ||
| project_json_string += '"key": "modulus_shear",\n' | ||
| project_json_string += '"key": "enthalpy",\n' | ||
| project_json_string += '"type": "value",\n' | ||
| project_json_string += '"value": 5.0,\n' | ||
| project_json_string += '"unit": "GPa",\n' | ||
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@@ -213,7 +219,7 @@ def fixed_cyclic_project_node() -> cript.Project: | |
| project_json_string += '"node": ["Property"],\n' | ||
| project_json_string += '"uid": "_:fde629f5-8d3a-4546-8cd3-9de63b990187",\n' | ||
| project_json_string += '"uuid": "fde629f5-8d3a-4546-8cd3-9de63b990187",\n' | ||
| project_json_string += '"key": "modulus_shear",\n' | ||
| project_json_string += '"key": "enthalpy",\n' | ||
| project_json_string += '"type": "value",\n' | ||
| project_json_string += '"value": 5.0,\n' | ||
| project_json_string += '"unit": "GPa",\n' | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -66,6 +66,16 @@ def complex_user_dict(cript_api) -> dict: | |
| user_dict = json.loads(user_node.get_json().json) | ||
| print("8888888--------") | ||
| print(user_dict) | ||
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| # def complex_user_dict() -> dict: #old code | ||
| # user_dict = {"node": ["User"]} | ||
| # user_dict["created_at"] = str(datetime.datetime.now()) | ||
| # user_dict["model_version"] = "1.0.1" | ||
| # user_dict["picture"] = "/my/picture/path" | ||
| # user_dict["updated_at"] = str(datetime.datetime.now()) | ||
| # user_dict["username"] = "testuser" | ||
| # user_dict["email"] = "[email protected]" | ||
| # user_dict["orcid"] = "0000-0002-0000-0000" | ||
| return user_dict | ||
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