CRIPT Python SDK 2.0 First Release

[nh916]

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[bearmit]

I'm following the instructions from https://c-accel-cript.github.io/Python-SDK/tutorial/cript_installation_guide/

Installing the package like that:
pip install git+https://github.com/C-Accel-CRIPT/Python-SDK@develop

Win11, Python 3.10.6

Install went well.

Now following https://c-accel-cript.github.io/Python-SDK/tutorial/how_to_get_api_token/

Not clear where I should paste my tokens, but I assume I need to create a *.py script file.

Now following https://c-accel-cript.github.io/Python-SDK/examples/synthesis/

I successfully setup my script to create a new project

(venv) PS C:\Users\berenger\sdktest> python synthesis.py
INFO: Validating Project graph...
(venv) PS C:\Users\berenger\sdktest>

I copy/pasted all the instructions, the project was generated but rejected by the server because of duplicates. My project name was changed, but I assume there are duplicates in the materials (maybe on experiments too).

Not easy to guess which node has a duplicate name, I assume this will happend to every user trying this.

The log looks like:

INFO: Validating Project graph...
Traceback (most recent call last):
  File "C:\Users\berenger\sdktest\synthesis.py", line 115, in <module>
    api.save(project)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 625, in save
    raise exc from exc
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 619, in save
    self._internal_save(project)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 706, in _internal_save
    raise CRIPTAPISaveError(api_host_domain=self._host, http_code=response["code"], api_response=response["error"], patch_request=patch_request, pre_saved_nodes=save_values.saved_uuid, json_data=json_data)  # type: ignore
cript.api.exceptions.CRIPTAPISaveError: API responded to POST with 'http:400 Duplicate names                          ['Anionic Polymerization of Styrene with SecBuLi'] in Experiment' data: {"node": ["Project"], "uid": "_:e0f40836-c32c-4ef3-b197-31204285cd05", "uuid": "e0f40836-c32c-4ef3-b197-31204285cd05", "name": "My first project created with the WebSDK develop", "collection": [{"node": ["Collection"], "uid": "_:2022575c-6275-49ab-bf01-0a1b381d82b0", "uuid": "2022575c-6275-49ab-bf01-0a1b381d82b0", "name": "Initial screening", "experiment": [{"node": ["Experiment"], "uid": "_:1d9a45a5-9996-487b-a007-998703454ec6", "uuid": "1d9a45a5-9996-487b-a007-998703454ec6", "name": "Anionic Polymerization of Styrene with SecBuLi"}, {"node": ["Experiment"], "uid": "_:5f53560e-1eb2-494c-b67e-b1d271a78625", "uuid": "5f53560e-1eb2-494c-b67e-b1d271a78625", "name": "Anionic Polymerization of Styrene with SecBuLi", "process": [{"node": ["Process"], "uid": "_:4ef58d70-815a-4780-8751-6c6587ae32ff", "uuid": "4ef58d70-815a-4780-8751-6c6587ae32ff", "name": "Anionic of Synthesis Poly-Styrene", "type": "multistep", "ingredient": [{"node": ["Ingredient"], "uid": "_:ecad3b35-26d3-4118-b490-bca7a396d5a8", "uuid": "ecad3b35-26d3-4118-b490-bca7a396d5a8", "material": {"uuid": "e52d861c-ccc2-42c6-a9c4-054847769e05"}, "quantity": [{"node": ["Quantity"], "uid": "_:4ed7c6b4-11cc-4f50-9efa-c27c7ed0a7f3", "uuid": "4ed7c6b4-11cc-4f50-9efa-c27c7ed0a7f3", "key": "volume", "value": 1.7e-08, "unit": "m**3"}], "keyword": ["initiator"]}, {"node": ["Ingredient"], "uid": "_:3283e47c-72f2-428a-a3db-8477e7754198", "uuid": "3283e47c-72f2-428a-a3db-8477e7754198", "material": {"uuid": "9ac2bb9d-3b24-42e6-833b-16d05f235273"}, "quantity": [{"node": ["Quantity"], "uid": "_:23b1f6e8-e295-4932-94c6-45effb2d68e2", "uuid": "23b1f6e8-e295-4932-94c6-45effb2d68e2", "key": "volume", "value": 0.0001, "unit": "m**3"}], "keyword": ["solvent"]}, {"node": ["Ingredient"], "uid": "_:d70ac8bb-c61f-4f30-815e-2ede3df98881", "uuid": "d70ac8bb-c61f-4f30-815e-2ede3df98881", "material": {"uuid": "a58cec1f-94b6-45f9-aca0-79e5893ba12d"}, "quantity": [{"node": ["Quantity"], "uid": "_:4a1ce7ed-b532-444f-939f-7547ae67b99a", "uuid": "4a1ce7ed-b532-444f-939f-7547ae67b99a", "key": "mass", "value": 0.000455, "unit": "kg"}], "keyword": ["monomer"]}, {"node": ["Ingredient"], "uid": "_:c71bf34b-c49d-4532-8b68-8ff19058c7fe", "uuid": "c71bf34b-c49d-4532-8b68-8ff19058c7fe", "material": {"uuid": "4ec8e732-5dec-440b-a752-d5096e5224bb"}, "quantity": [{"node": ["Quantity"], "uid": "_:f6f8d8a6-b3f8-40ab-be81-e3563e1d6256", "uuid": "f6f8d8a6-b3f8-40ab-be81-e3563e1d6256", "key": "volume", "value": 0.005, "unit": "m**3"}], "keyword": ["quench"]}, {"node": ["Ingredient"], "uid": "_:bea6caa7-0a1b-4588-96ff-751852bdd09b", "uuid": "bea6caa7-0a1b-4588-96ff-751852bdd09b", "material": {"uuid": "56ab0d1a-fcb7-44a2-a61c-b52a341236c4"}, "quantity": [{"node": ["Quantity"], "uid": "_:08423765-085f-4fba-9b85-f05688a86502", "uuid": "08423765-085f-4fba-9b85-f05688a86502", "key": "volume", "value": 0.1, "unit": "m**3"}], "keyword": ["workup"]}], "description": "In an argon filled glove box, a round bottom flask was filled with 216 ml of dried toluene. The solution of secBuLi (3 ml, 3.9 mmol) was added next, followed by styrene (22.3 g, 176 mmol) to initiate the polymerization. The reaction mixture immediately turned orange. After 30 min, the reaction was quenched with the addition of 3 ml of methanol. The polymer was isolated by precipitation in methanol 3 times and dried under vacuum.", "condition": [{"node": ["Condition"], "uid": "_:5b5f69de-12eb-4fda-85aa-32216b690f6d", "uuid": "5b5f69de-12eb-4fda-85aa-32216b690f6d", "key": "temperature", "type": "value", "value": 25, "unit": "celsius"}, {"node": ["Condition"], "uid": "_:e446ae2a-3b51-42a6-9512-b0dec166d617", "uuid": "e446ae2a-3b51-42a6-9512-b0dec166d617", "key": "time_duration", "type": "value", "value": 60, "unit": "min"}], "property": [{"node": ["Property"], "uid": "_:778e5096-e98d-4bd5-b4cf-f55405378e63", "uuid": "778e5096-e98d-4bd5-b4cf-f55405378e63", "key": "yield_mass", "type": "number", "value": 0.00047, "unit": "kilogram", "method": "scale"}]}]}], "inventory": [{"node": ["Inventory"], "uid": "_:7e4c4ee3-4dfe-4a6a-ace2-028180b95f22", "uuid": "7e4c4ee3-4dfe-4a6a-ace2-028180b95f22", "name": "Common chemicals for poly-styrene synthesis", "material": [{"uuid": "e52d861c-ccc2-42c6-a9c4-054847769e05"}, {"uuid": "9ac2bb9d-3b24-42e6-833b-16d05f235273"}, {"uuid": "a58cec1f-94b6-45f9-aca0-79e5893ba12d"}, {"uuid": "4ec8e732-5dec-440b-a752-d5096e5224bb"}, {"uuid": "56ab0d1a-fcb7-44a2-a61c-b52a341236c4"}]}]}], "material": [{"node": ["Material"], "uid": "_:ac8f953c-6d85-4544-9a4e-d10f87a4f28d", "uuid": "ac8f953c-6d85-4544-9a4e-d10f87a4f28d", "name": "polystyrene", "property": [{"node": ["Property"], "uid": "_:838158e7-b66f-4672-aa59-fa67bbf6d82c", "uuid": "838158e7-b66f-4672-aa59-fa67bbf6d82c", "key": "phase", "type": "none", "value": "solid", "unit": null}, {"node": ["Property"], "uid": "_:f752eceb-d7fc-46db-8f75-b91692f215f9", "uuid": "f752eceb-d7fc-46db-8f75-b91692f215f9", "key": "color", "type": "none", "value": "white", "unit": null}], "names": ["poly(styrene)", "poly(vinylbenzene)"], "bigsmiles": "[H]{[>][<]C(C[>])c1ccccc1[<]}C(C)CC", "chem_repeat": ["C8H8"]}]}
(venv) PS C:\Users\berenger\sdktest>

I suggest to define a global a prefix (or suffix) by doing let's say:
api.set_global_(suffix|prefix)("mySuperTest - ")

...or to display the list of duplicates.

My bad, I added two identical Experiments, I figured it out when adding a prefix manually replacing name=" by "name="SDKTestBerenger -

FName are fixed, but I got now an error regarding MaterialPost additionalProperties:

Traceback (most recent call last):
  File "C:\Users\berenger\sdktest\synthesis.py", line 112, in <module>
    api.save(project)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 619, in save
    self._internal_save(project)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 684, in _internal_save
    returned_save_values = _fix_node_save(self, node, response, save_values)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\utils\save_helper.py", line 77, in _fix_node_save
    returned_save_values = api._internal_save(missing_node, save_values)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 645, in _internal_save
    node.validate()
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\nodes\core.py", line 157, in validate
    api._is_node_schema_valid(self.get_json(is_patch=is_patch).json, is_patch=is_patch)
  File "<@beartype(cript.api.api.API._is_node_schema_valid) at 0x25e3b1fb010>", line 50, in _is_node_schema_valid
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 591, in _is_node_schema_valid
    raise CRIPTNodeSchemaError(node_type=node_dict["node"], json_schema_validation_error=str(error)) from error
cript.nodes.exceptions.CRIPTNodeSchemaError: JSON database schema validation for node ['Material'] failed.Error: Additional properties are not allowed ('pubchem_id' was unexpected)

Failed validating 'additionalProperties' in schema:
    {'$id': 'MaterialPost',
     'additionalProperties': False,
     'properties': {'amino_acid': {'type': 'string'},
                    'bigsmiles': {'type': 'string'},
                    'chem_formula': {'type': 'string'},
                    'chem_repeat': {'items': {'type': 'string'},
                                    'type': 'array'},
                    'chemical_id': {'type': 'string'},
                    'component': {'items': {'anyOf': [{'$ref': 'EdgeUUID'},
                                                      {'$ref': 'Edge'}]},
                                  'type': 'array'},
                    'computational_forcefield': {'anyOf': [{'$ref': 'EdgeUUID'},
                                                           {'$ref': 'ComputationalForcefieldPost'},
                                                           {'$ref': 'Edge'}]},
                    'created_at': {'$ref': 'Timestamp'},
                    'created_by': {'$ref': 'Creator'},
                    'inchi': {'type': 'string'},
                    'inchi_key': {'type': 'string'},
                    'keyword': {'$ref': 'MaterialKeyword'},
                    'locked': {'default': False, 'type': 'boolean'},
                    'lot_number': {'type': 'string'},
                    'model_version': {'$ref': 'ModelVersion'},
                    'mol_form': {'type': 'string'},
                    'name': {'$ref': 'NameField'},
                    'names': {'items': {'type': 'string'}, 'type': 'array'},
                    'node': {'items': {'enum': ['Material'],
                                       'type': 'string'},
                             'type': 'array'},
                    'notes': {'$ref': 'NotesField'},
                    'parent_material': {'anyOf': [{'$ref': 'EdgeUUID'},
                                                  {'$ref': 'Edge'}]},
                    'process': {'anyOf': [{'$ref': 'EdgeUUID'},
                                          {'$ref': 'ProcessPost'},
                                          {'$ref': 'Edge'}]},
                    'property': {'items': {'anyOf': [{'$ref': 'EdgeUUID'},
                                                     {'$ref': 'PropertyPost'}]},
                                 'type': 'array'},
                    'pubchem_cid': {'type': 'integer'},
                    'public': {'default': False, 'type': 'boolean'},
                    'smiles': {'type': 'string'},
                    'uid': {'$ref': 'TempUID'},
                    'updated_at': {'$ref': 'Timestamp'},
                    'updated_by': {'$ref': 'Creator'},
                    'uuid': {'default': 'uuid()',
                             'readOnly': True,
                             'type': 'string'},
                    'vendor': {'type': 'string'}},
     'required': ['node', 'name'],
     'type': 'object'}

On instance:
    {'name': 'SDKTestBerenger - toluene',
     'node': ['Material'],
     'pubchem_id': 1140,
     'smiles': 'Cc1ccccc1',
     'uid': '_:f982cc4c-4070-4e67-9121-26b9dd56f83d',
     'uuid': 'f982cc4c-4070-4e67-9121-26b9dd56f83d'}

I assume there is a typo in the documentation, and pubchem_cid should have been defined instead of pubchem_id.

Retrying... I assumed well, no more issue with pubchem_id.

But, I got another issue:

INFO: Validating Project graph...
INFO: Validating Material graph...
INFO: Validating Material graph...
Traceback (most recent call last):
  File "C:\Users\berenger\sdktest\synthesis.py", line 112, in <module>
    api.save(project)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 625, in save
    raise exc from exc
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 619, in save
    self._internal_save(project)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 684, in _internal_save
    returned_save_values = _fix_node_save(self, node, response, save_values)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\utils\save_helper.py", line 77, in _fix_node_save
    returned_save_values = api._internal_save(missing_node, save_values)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 684, in _internal_save
    returned_save_values = _fix_node_save(self, node, response, save_values)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\utils\save_helper.py", line 104, in _fix_node_save
    save_values += api._internal_save(duplicate_node, save_values)
  File "C:\Users\berenger\sdktest\venv\lib\site-packages\cript\api\api.py", line 706, in _internal_save
    raise CRIPTAPISaveError(api_host_domain=self._host, http_code=response["code"], api_response=response["error"], patch_request=patch_request, pre_saved_nodes=save_values.saved_uuid, json_data=json_data)  # type: ignore
cript.api.exceptions.CRIPTAPISaveError: API responded to POST with 'http:400 'name' is a required property at path: /' data: {"node": ["Material"], "uid": "_:061d7a40-1f1f-46c4-91f5-512a65a95895", "uuid": "061d7a40-1f1f-46c4-91f5-512a65a95895", "chemical_id": "598-30-1"}

Apparently the name is missing on the material.

After searching for cript.Material( I can confirm there is no unnammed material in the code. I am not sure what's the problem...

To be continued...

[bearmit]

I am not sure why, but I couldn't finish the walkthrough: https://c-accel-cript.github.io/Python-SDK/examples/synthesis/

The last error I got was not related to my data I think. It's like a node with a uuid was trying to be posted without a name. See my comments above this.

[InnocentBug]

I am not sure why, but I couldn't finish the walkthrough: https://c-accel-cript.github.io/Python-SDK/examples/synthesis/

The last error I got was not related to my data I think. It's like a node with a uuid was trying to be posted without a name. See my comments above this.

Yes, this is a confusing data error.
It is a duplicated name for the material.
We are aware that this is not a good error message for that.