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- builtins.object
-
- Artifact
- ClarityExceptions
- ClarityTools
- Process
- Sample
- StepTools
- builtins.tuple(builtins.object)
-
- PreviousStepArtifact
class Artifact(builtins.object) |
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Artifact(name: str = None, uri: str = None, art_type: str = None, sample_uri: str = None, container_uri: str = None, container_name: str = None, container_type: str = None, location: str = None, parent_process: str = None, reagent_label: str = None, udf: dict = <factory>) -> None
Stores the fields of an Artifact.
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Methods defined here:
- __eq__(self, other)
- __init__(self, name: str = None, uri: str = None, art_type: str = None, sample_uri: str = None, container_uri: str = None, container_name: str = None, container_type: str = None, location: str = None, parent_process: str = None, reagent_label: str = None, udf: dict = <factory>) -> None
- __repr__(self)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- __annotations__ = {'art_type': <class 'str'>, 'container_name': <class 'str'>, 'container_type': <class 'str'>, 'container_uri': <class 'str'>, 'location': <class 'str'>, 'name': <class 'str'>, 'parent_process': <class 'str'>, 'reagent_label': <class 'str'>, 'sample_uri': <class 'str'>, 'udf': <class 'dict'>, ...}
- __dataclass_fields__ = {'art_type': Field(name='art_type',type=<class 'str'>,default...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'container_name': Field(name='container_name',type=<class 'str'>,d...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'container_type': Field(name='container_type',type=<class 'str'>,d...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'container_uri': Field(name='container_uri',type=<class 'str'>,de...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'location': Field(name='location',type=<class 'str'>,default...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'name': Field(name='name',type=<class 'str'>,default=Non...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'parent_process': Field(name='parent_process',type=<class 'str'>,d...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'reagent_label': Field(name='reagent_label',type=<class 'str'>,de...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'sample_uri': Field(name='sample_uri',type=<class 'str'>,defau...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'udf': Field(name='udf',type=<class 'dict'>,default=<da...rue,metadata=mappingproxy({}),_field_type=_FIELD), ...}
- __dataclass_params__ = _DataclassParams(init=True,repr=True,eq=True,order=False,unsafe_hash=False,frozen=False)
- __hash__ = None
- art_type = None
- container_name = None
- container_type = None
- container_uri = None
- location = None
- name = None
- parent_process = None
- reagent_label = None
- sample_uri = None
- uri = None
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class ClarityExceptions(builtins.object) |
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Holds custom Clarity Exceptions.
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Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- CallError = <class 'ua_clarity_tools.ClarityExceptions.CallError'>
- This method call wasn't well-formed.
- EPPError = <class 'ua_clarity_tools.ClarityExceptions.EPPError'>
- The EPP script provided is not correct.
- TechnicianError = <class 'ua_clarity_tools.ClarityExceptions.TechnicianError'>
- A Clarity user technician has made a mistake.
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class ClarityTools(builtins.object) |
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ClarityTools(host, username, password)
Tools that interact with Clarity without a step. These tools are general
use functions for when caller is not attached to a step and knows the
endpoints they want to perform work on. These methods are not limited by
the requirement to have a step uri.
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Methods defined here:
- __init__(self, host, username, password)
- Initializes a ClarityAPI object for use within method calls.
username and password should be strings representing your creds in the
clarity environment.
host should be a string representing the url of your clarity api
endpoint.
- get_arts_from_samples(self, sample_uris)
- Map sample uris to their respective artifact uris from clarity.
Arguments:
sample_uris (list): A list of sample uris. All sample uris given
must have at least one artifact uri in clarity.
Returns:
smp_art_uris (dict): The sample uri mapped to the artifact uri.
- get_samples(self, uris)
- Returns a list of Sample data classes with data populated from the
get responses of given clarity sample URIs.
Arguments:
uris (list): List of Sample URIs harvested from the clarity env.
Returns:
samples (list): Returns a list of Sample data classes.
- get_udfs(self, target)
- Find all of the udfs with attach-to-name: target attributes.
Arguments:
target (str): A string representation of what attach-to-name
attributes to harvest.
Returns:
target_udfs (list): A list of all udf names for specified target.
Raises:
ClarityExceptions.CallError: If there are no target udfs found.
- set_reagent_label(self, limsid_label)
- Set reagent-label of all artifact limsid keys to their mapped value.
Arguments:
limsid_label (dict {str: str}): maps limsid's to
reagent-label information. If a value is Falsey, then all
labels will be removed.
Side Effects:
If successful, this method will add a reagent-label to each
artifact.
Overwrites the original reagent-label if it existed.
Raises:
RuntimeError: If there was an exception raised while POSTing.
- step_router(self, wf_name, dest_stage_name, art_uris, action='assign')
- Assign/unassign artifacts from current step to a destination step.
Assigning will move the artifacts to the given destination step.
Unassigning will remove the artifact from the step/queue, but does
not remove the artifact from the clarity environment
Arguments:
wf_name (string): The workflow name in which the destination
step is.
dest_stage_name (string): The step name that is the destination
for the artifacts.
art_uris (list): The list of artifact_uris to route to the
destination step.
action (string): Either 'assign' or 'unassign', determining which
action to perform.
Side Effects:
If successful, assigns or unassigns the artifacts to the
destination step in Clarity.
Raises:
ClarityExceptions.CallError: If that workflow or stage isn't found.
RuntimeError: If there was an exception raised while POSTing.
RuntimeError: If for some other, unknown reason the artifact was
not routed.
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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class PreviousStepArtifact(builtins.tuple) |
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PreviousStepArtifact(uri, art_type, generation_type)
PreviousStepArtifact(uri, art_type, generation_type)
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- Method resolution order:
- PreviousStepArtifact
- builtins.tuple
- builtins.object
Methods defined here:
- __getnewargs__(self)
- Return self as a plain tuple. Used by copy and pickle.
- __repr__(self)
- Return a nicely formatted representation string
- _asdict(self)
- Return a new OrderedDict which maps field names to their values.
- _replace(_self, **kwds)
- Return a new PreviousStepArtifact object replacing specified fields with new values
Class methods defined here:
- _make(iterable) from builtins.type
- Make a new PreviousStepArtifact object from a sequence or iterable
Static methods defined here:
- __new__(_cls, uri, art_type, generation_type)
- Create new instance of PreviousStepArtifact(uri, art_type, generation_type)
Data descriptors defined here:
- uri
- Alias for field number 0
- art_type
- Alias for field number 1
- generation_type
- Alias for field number 2
Data and other attributes defined here:
- _field_defaults = {}
- _fields = ('uri', 'art_type', 'generation_type')
- _fields_defaults = {}
Methods inherited from builtins.tuple:
- __add__(self, value, /)
- Return self+value.
- __contains__(self, key, /)
- Return key in self.
- __eq__(self, value, /)
- Return self==value.
- __ge__(self, value, /)
- Return self>=value.
- __getattribute__(self, name, /)
- Return getattr(self, name).
- __getitem__(self, key, /)
- Return self[key].
- __gt__(self, value, /)
- Return self>value.
- __hash__(self, /)
- Return hash(self).
- __iter__(self, /)
- Implement iter(self).
- __le__(self, value, /)
- Return self<=value.
- __len__(self, /)
- Return len(self).
- __lt__(self, value, /)
- Return self<value.
- __mul__(self, value, /)
- Return self*value.
- __ne__(self, value, /)
- Return self!=value.
- __rmul__(self, value, /)
- Return value*self.
- count(self, value, /)
- Return number of occurrences of value.
- index(self, value, start=0, stop=9223372036854775807, /)
- Return first index of value.
Raises ValueError if the value is not present.
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class Process(builtins.object) |
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Process(uri: str = None, technician: str = 'None', udf: dict = <factory>) -> None
Stores the fields of a Process.
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Methods defined here:
- __eq__(self, other)
- __init__(self, uri: str = None, technician: str = 'None', udf: dict = <factory>) -> None
- __repr__(self)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- __annotations__ = {'technician': <class 'str'>, 'udf': <class 'dict'>, 'uri': <class 'str'>}
- __dataclass_fields__ = {'technician': Field(name='technician',type=<class 'str'>,defau...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'udf': Field(name='udf',type=<class 'dict'>,default=<da...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'uri': Field(name='uri',type=<class 'str'>,default=None...rue,metadata=mappingproxy({}),_field_type=_FIELD)}
- __dataclass_params__ = _DataclassParams(init=True,repr=True,eq=True,order=False,unsafe_hash=False,frozen=False)
- __hash__ = None
- technician = 'None'
- uri = None
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class Sample(builtins.object) |
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Sample(name: str = '', uri: str = None, date_received: str = None, project_uri: str = None, project_name: str = None, artifact_uri: str = None, udf: dict = <factory>) -> None
Stores the fields of a Sample.
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Methods defined here:
- __eq__(self, other)
- __init__(self, name: str = '', uri: str = None, date_received: str = None, project_uri: str = None, project_name: str = None, artifact_uri: str = None, udf: dict = <factory>) -> None
- __repr__(self)
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
Data and other attributes defined here:
- __annotations__ = {'artifact_uri': <class 'str'>, 'date_received': <class 'str'>, 'name': <class 'str'>, 'project_name': <class 'str'>, 'project_uri': <class 'str'>, 'udf': <class 'dict'>, 'uri': <class 'str'>}
- __dataclass_fields__ = {'artifact_uri': Field(name='artifact_uri',type=<class 'str'>,def...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'date_received': Field(name='date_received',type=<class 'str'>,de...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'name': Field(name='name',type=<class 'str'>,default='',...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'project_name': Field(name='project_name',type=<class 'str'>,def...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'project_uri': Field(name='project_uri',type=<class 'str'>,defa...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'udf': Field(name='udf',type=<class 'dict'>,default=<da...rue,metadata=mappingproxy({}),_field_type=_FIELD), 'uri': Field(name='uri',type=<class 'str'>,default=None...rue,metadata=mappingproxy({}),_field_type=_FIELD)}
- __dataclass_params__ = _DataclassParams(init=True,repr=True,eq=True,order=False,unsafe_hash=False,frozen=False)
- __hash__ = None
- artifact_uri = None
- date_received = None
- name = ''
- project_name = None
- project_uri = None
- uri = None
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class StepTools(builtins.object) |
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StepTools(username=None, password=None, step_uri=None)
Defines step specific methods which act upon a given step uri in
Clarity. This class can be instantiated directly or from a Clarity EPP
script.
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Methods defined here:
- __init__(self, username=None, password=None, step_uri=None)
- Initialize LimsTools with information to access step details.
username and password should be strings representing your creds in the
clarity environment.
step_uri should be a string representing the step endpoint in your
clarity environment that you wish to perform work on.
- get_artifact_map(self, uri_only=False)
- Returns a map of input artifacts to output artifacts, either as uris
or as Artifact dataclasses. One input artifact can be mapped to a
list of their multiple output artifacts.
Arguments:
uri_only (boolean): This denotes whether to harvest this mapping as
uris or as namedtuples.
Returns:
artifact_map (dict {input artifact: [output_artifact]}):
Returns a dict of input artifact : all output artifacts.
- get_artifacts(self, stream, uri_only=False, container_info=False)
- Return the artifact information as a list of Artifact data classes.
Arguments:
stream (str): The source of the samples, either "input" or
"output".
Returns:
artifacts (list): Returns a list of Artifact data classes.
Notes:
Does not include 'PerAllInputs' shared output files.
- get_artifacts_previous_step(self, dest_step, stream, art_smp_uris, step_soup, results=None)
- Return artifact uris mapped to ancestor artifacts from a target
step.
Arguments:
dest_step (str): The name of the step where the ancestor
artifacts were created.
stream (str): The source of the samples, either "input" or
"output" in the dest_step.
art_smp_uris (dict {str: str}): A dict that maps smp_uris to
passed in art_uris.
step_soup: The step details soup for initial step.
results (dict): The empty dict that will eventually be returned
with the desired artifacts from the dest_step.
Returns:
results (dict {str: Artifact}): The dictionary that
maps the art_uri to the artifact namedtuple. All of the
'PerAllInputs' are stored in the results dict at
results['shared']. If the art_uri does not have ancestors at
that target, the art_uri will not be in the dictionary.
Exceptions:
RuntimeError: If that target_step is not in any of the provided
art_uri histories.
RuntimeError: If there are targets that ran through the step at
two or more different times. (The dest_step process id is not
the same for all of the passed-in samples.)
Requirements:
The targets to reroute must all have the same endpoint; if a sample
went through the step separately from its fellows, this
will not work.
- get_process_data(self)
- Retrieves Process data for the current step, including technician,
uri, and udfs.
Returns:
process: a Process dataclass representing the process of the
current step.
- set_artifact_udf(self, sample_values, stream)
- Set UDF values for analytes in the current step based on given
mapping.
Arguments:
sample_values (dict {str: [namedtuple]}): Maps sample limsid's to
a list of namedtuples called 'UDF' with the fields 'name',
'value'.
stream (str): The source of the samples, either "input" or
"output".
Side Effects:
Sets the samples' UDFs that were passed into the REST database.
Overwrites the value that was in that UDF if it existed.
Raises:
RuntimeError: If there was an exception raised while POSTing.
Requirements:
The UDF Value's type must be in line with Clarity's
initialization of that type.
- setup_arguments(self)
- Incorporate EPP arguments into your StepTools object.
Returns:
(arguments): The object that holds all of the arguments that
were parsed (at object.{dest}).
Data descriptors defined here:
- __dict__
- dictionary for instance variables (if defined)
- __weakref__
- list of weak references to the object (if defined)
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