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View Code? Open in Web Editor NEWMaterials for the Hackathon at the 2021 Crops in Silico Symposium & Workshop
License: BSD 3-Clause "New" or "Revised" License
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invalid syntax error with the co2.py model when attempting TYK#2 part 1
file: yamls/test2.yml
model:
name: co2
language: python
args: ../models/co2.py
function: calculate_concentration
file: yamls/connections_test2.yml
connections:
- input:
name: ../input/height.txt
filetype: table
output: co2:input
- input: co2:output
output:
name: ../output/co2.txt
filetype: table
field_names: [conc]
INFO:616:runner.startDrivers[497]:YggRunner(runner): Starting I/O drivers and models on system jupyter-cropsinsilico-2dcis2021-2dhackathon-2d1tlflgdz in namespace yggdrasil with rank 0
/srv/conda/envs/notebook/bin/python /home/jovyan/models/ygg_co2.py
File "/home/jovyan/models/ygg_co2.py", line 19
[doy, dist, height, offset=60.0] = temp_doy
^
SyntaxError: invalid syntax
ERROR:616:ModelDriver.kill_process[1451]:PythonModelDriver(co2): return code of 1 indicates model error. (sent messages: {'co2:output': 0})
ERROR:616:ConnectionDriver.run_loop[1026]:ConnectionDriver(co2:input): Could not send message.
ERROR:616:runner.waitModels[542]:YggRunner(runner): Error in model co2
ERROR:616:runner.waitModels[575]:YggRunner(runner): One or more models generated errors.
ConnectionDriver(co2:input): last action: after loop is_open(False, False), 7 received, 7 processed, 6 sent, 10 ready to recv 0 ready to send close state: output model exit
ConnectionDriver(co2:output): last action: after loop is_open(False, False), 0 received, 0 processed, 0 sent, 0 ready to recv 0 ready to send close state: input model exit
INFO:616:multitasking.printStatus[850]:PythonModelDriver(co2): yggdrasil.drivers.PythonModelDriver(co2): state: finished
INFO:616:runner.run[374]:YggRunner(runner): init 0.000010
INFO:616:runner.run[374]:YggRunner(runner): load drivers 0.011041
INFO:616:runner.run[374]:YggRunner(runner): start drivers 0.080985
INFO:616:runner.run[374]:YggRunner(runner): run models 0.206427
INFO:616:runner.run[374]:YggRunner(runner): at exit 0.001975
INFO:616:runner.run[376]:YggRunner(runner): ========================================
INFO:616:runner.run[377]:YggRunner(runner): Total 0.300437
file: output/co2.txt
====================
"Binder not found"
Context (Environment)
- MyBinder instance
- Local install
- Docker container
OS: Mac
Browser: Google Chrome
Type of Issue
- Jupyter notebook failed to open
- One or more of the cells failed
- Question
- Other (please describe below)
[OPTIONAL] Expected Behavior
When clicking on a notebook from the browser the notebook should open in a new tab.
[OPTIONAL] Current Behavior
The notebook does not open and this message is displayed in a new tab.
[OPTIONAL] Steps to Reproduce
- Open a MyBinder instance
- Wait
- Click on a notebook
Description
The 00-intro.ipynb notebook failed to open from the MyBinder browser page when I clicked on the file name.
Oops!
We can't seem to find the Binder page you are looking for.
404 error
Error for test 1: Both the input and output for this connection appear to be files
My yaml files are
yamls/test1.yaml
model:
name: light
language: python
args: ../models/weather.py
function: temp
yamls/connections_test1.yaml
connections:
- input:
name: ../input/intensity.txt
filetype: table
output: light:input
- input: temp:output
output:
name: ../output/temp.txt
filetype: table
field_names: [T]
Error message
---------------------------------------------------------------------------
ValidationError Traceback (most recent call last)
<ipython-input-15-5f295a9434fd> in <module>
1 tools.display_source('models/weather.py', number_lines=True)
2 tools.display_source('yamls/test1.yaml', number_lines=True)
----> 3 run(['yamls/test1.yaml', 'yamls/connections_test1.yaml'], production_run=True)
4 tools.display_source('output/temp.txt', number_lines=True)
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/runner.py in run(*args, **kwargs)
721
722 def run(*args, **kwargs):
--> 723 yggRunner = get_runner(*args, **kwargs)
724 try:
725 yggRunner.run()
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/runner.py in get_runner(models, **kwargs)
716 kwargs.update(rank=rank, host=host)
717 # Run
--> 718 yggRunner = YggRunner(models, **kwargs)
719 return yggRunner
720
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/runner.py in __init__(self, modelYmls, namespace, host, rank, ygg_debug_level, rmq_debug_level, ygg_debug_prefix, connection_task_method, as_function, production_run)
268 cfg_environment()
269 # Parse yamls
--> 270 self.drivers = yamlfile.parse_yaml(modelYmls, as_function=as_function)
271 self.connectiondrivers = self.drivers['connection']
272 self.modeldrivers = self.drivers['model']
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/yamlfile.py in parse_yaml(files, as_function)
184 # print('prepped')
185 # pprint.pprint(yml_prep)
--> 186 yml_norm = s.validate(yml_prep, normalize=True,
187 no_defaults=True, required_defaults=True)
188 # print('normalized')
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/schema.py in validate(self, obj, **kwargs)
1044 # kwargs.setdefault('no_defaults', True)
1045 kwargs.setdefault('schema_registry', self)
-> 1046 return metaschema.validate_instance(obj, self.schema, **kwargs)
1047
1048 def validate_component(self, comp_name, obj, **kwargs):
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/metaschema/__init__.py in validate_instance(obj, schema, **kwargs)
177 cls = get_validator()
178 cls.check_schema(schema)
--> 179 return cls(schema).validate(obj, **kwargs)
180
181
/srv/conda/envs/notebook/lib/python3.9/site-packages/yggdrasil/metaschema/normalizer.py in validate(self, instance, _schema, normalize, **kwargs)
338 if normalize:
339 with self.normalizing(**kwargs):
--> 340 super(Normalizer, self).validate(instance, _schema=_schema)
341 out = self._normalized
342 return out
/srv/conda/envs/notebook/lib/python3.9/site-packages/jsonschema/validators.py in validate(self, *args, **kwargs)
351 def validate(self, *args, **kwargs):
352 for error in self.iter_errors(*args, **kwargs):
--> 353 raise error
354
355 def is_type(self, instance, type):
ValidationError: Both the input and output for this connection appear to be files:
{'inputs': [{'filetype': 'binary',
'name': 'temp:output',
'serializer': {'seritype': 'direct'},
'working_dir': '/home/jovyan/yamls'}],
'outputs': [{'field_names': ['T'],
'filetype': 'table',
'name': '../output/temp.txt',
'working_dir': '/home/jovyan/yamls'}]}
Failed validating <function _normalize_connio_last at 0x7f02a1ebd940> in schema['properties']['connections']['items']['allOf']:
{'anyOf': [{'additionalProperties': True,
'description': 'Schema for connection component '
"['connection'] subtype.",
'properties': {'connection_type': {'description': 'Connection '
'between '
'one or '
'more '
'comms/files '
'and one '
'or more '
'comms/files.',
'enum': ['connection'],
'type': 'string'}},
'title': 'ConnectionDriver',
'type': 'object'},
{'additionalProperties': True,
'description': 'Schema for connection component '
"['rpc_response'] subtype.",
'properties': {'connection_type': {'description': 'Connection '
'between '
'one or '
'more '
'comms/files '
'and one '
'or more '
'comms/files.',
'enum': ['rpc_response'],
'type': 'string'}},
'title': 'RPCResponseDriver',
'type': 'object'},
{'additionalProperties': True,
'description': 'Schema for connection component '
"['rpc_request'] subtype.",
'properties': {'connection_type': {'description': 'Connection '
'between '
'one or '
'more '
'comms/files '
'and one '
'or more '
'comms/files.',
'enum': ['rpc_request'],
'type': 'string'}},
'title': 'RPCRequestDriver',
'type': 'object'},
{'additionalProperties': True,
'description': "Schema for connection component ['output'] "
'subtype.',
'properties': {'connection_type': {'description': 'Connection '
'between '
'a model '
'and one '
'or more '
'comms/files.',
'enum': ['output'],
'type': 'string'}},
'title': 'OutputDriver',
'type': 'object'},
{'additionalProperties': True,
'description': 'Schema for connection component '
"['file_output'] subtype.",
'properties': {'connection_type': {'description': 'Connection '
'between '
'a model '
'and a '
'file.',
'enum': ['file_output'],
'type': 'string'}},
'title': 'FileOutputDriver',
'type': 'object'},
{'additionalProperties': True,
'description': "Schema for connection component ['input'] "
'subtype.',
'properties': {'connection_type': {'description': 'Connection '
'between '
'one or '
'more '
'comms/files '
'and a '
'model.',
'enum': ['input'],
'type': 'string'}},
'title': 'InputDriver',
'type': 'object'},
{'additionalProperties': True,
'description': 'Schema for connection component '
"['file_input'] subtype.",
'properties': {'connection_type': {'description': 'Connection '
'between '
'a file '
'and a '
'model.',
'enum': ['file_input'],
'type': 'string'}},
'title': 'FileInputDriver',
'type': 'object'}]}
On instance['connections'][1]:
{'inputs': [{'filetype': 'binary',
'name': 'temp:output',
'serializer': {'seritype': 'direct'},
'working_dir': '/home/jovyan/yamls'}],
'outputs': [{'field_names': ['T'],
'filetype': 'table',
'name': '../output/temp.txt',
'working_dir': '/home/jovyan/yamls'}]}
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