galaxy-schema 23.2.1__tar.gz

galaxy-schema-23.2.1/HISTORY.rst

@@ -0,0 +1,10 @@
+History
+-------
+
+.. to_doc
+
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
+First release

galaxy-schema-23.2.1/LICENSE

@@ -0,0 +1,228 @@
+Copyright (c) 2005-2022 Galaxy Contributors (see CONTRIBUTORS.md)
+
+Work contributed from 2021-04-07 onwards is licensed under the MIT License.
+Work contributed before this date is licensed under the Academic Free License
+version 3.0.
+See https://github.com/galaxyproject/galaxy/ for the contribution history.
+See below for the full text of both licenses.
+
+
+Some icons found in Galaxy are from the Silk Icons set, available under
+the Creative Commons Attribution 2.5 License, from:
+
+http://www.famfamfam.com/lab/icons/silk/
+
+
+Other images and documentation are licensed under the Creative Commons
+Attribution 3.0 (CC BY 3.0) License. See:
+
+http://creativecommons.org/licenses/by/3.0/
+
+
+--------------------------------------------------------------------------------
+
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
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+
+The above copyright notice and this permission notice shall be included in all
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+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+
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galaxy-schema-23.2.1/MANIFEST.in

@@ -0,0 +1 @@
+include *.rst *.txt LICENSE */py.typed

galaxy-schema-23.2.1/PKG-INFO

@@ -0,0 +1,52 @@
+Metadata-Version: 2.1
+Name: galaxy-schema
+Version: 23.2.1
+Summary: Galaxy auth framework and implementations
+Home-page: https://github.com/galaxyproject/galaxy
+Author: Galaxy Project and Community
+Author-email: galaxy-committers@lists.galaxyproject.org
+License: AFL
+Keywords: Galaxy
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: Academic Free License (AFL)
+Classifier: Natural Language :: English
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Topic :: Software Development
+Classifier: Topic :: Software Development :: Code Generators
+Classifier: Topic :: Software Development :: Testing
+Requires-Python: >=3.7
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+
+
+.. image:: https://badge.fury.io/py/galaxy-schema.svg
+   :target: https://pypi.org/project/galaxy-schema/
+
+
+
+Overview
+--------
+
+The Galaxy_ API schema objects.
+
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/
+
+History
+-------
+
+.. to_doc
+
+-------------------
+23.2.1 (2024-02-21)
+-------------------
+
+First release

galaxy-schema-23.2.1/README.rst

@@ -0,0 +1,14 @@
+
+.. image:: https://badge.fury.io/py/galaxy-schema.svg
+   :target: https://pypi.org/project/galaxy-schema/
+
+
+
+Overview
+--------
+
+The Galaxy_ API schema objects.
+
+* Code: https://github.com/galaxyproject/galaxy
+
+.. _Galaxy: http://galaxyproject.org/

galaxy-schema-23.2.1/dev-requirements.txt

@@ -0,0 +1,10 @@
+# For testing
+-r test-requirements.txt
+
+# For dev
+sphinx
+mypy
+
+# For release
+build
+twine

galaxy-schema-23.2.1/galaxy/__init__.py

@@ -0,0 +1 @@
+__path__ = __import__("pkgutil").extend_path(__path__, __name__)  # type: ignore[has-type]

galaxy-schema-23.2.1/galaxy/schema/__init__.py

@@ -0,0 +1,115 @@
+from datetime import datetime
+from enum import Enum
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Union,
+)
+
+from pydantic import (
+    BaseModel,
+    Field,
+    Required,
+)
+
+
+class BootstrapAdminUser(BaseModel):
+    id = 0
+    email: Optional[str] = None
+    preferences: Dict[str, str] = {}
+    bootstrap_admin_user = True
+
+    def all_roles(*args) -> list:
+        return []
+
+
+class ValueFilterQueryParams(BaseModel):
+    """Allows filtering/querying elements by value like `q=<property>-<operator>&qv=<value>`
+
+    Multiple `q/qv` queries can be concatenated.
+    """
+
+    q: Optional[Union[List[str], str]] = Field(
+        default=None,
+        title="Filter Query",
+        description="Generally a property name to filter by followed by an (often optional) hyphen and operator string.",
+        example="create_time-gt",
+    )
+    qv: Optional[Union[List[str], str]] = Field(
+        default=None,
+        title="Filter Value",
+        description="The value to filter by.",
+        example="2015-01-29",
+    )
+
+
+class PaginationQueryParams(BaseModel):
+    """Used to paginate a the request results by limiting and offsetting."""
+
+    offset: Optional[int] = Field(
+        default=0,
+        ge=0,
+        title="Offset",
+        description="Starts at the beginning skip the first ( offset - 1 ) items and begin returning at the Nth item",
+    )
+    limit: Optional[int] = Field(
+        default=None,
+        ge=1,
+        title="Limit",
+        description="The maximum number of items to return.",
+    )
+
+
+class FilterQueryParams(ValueFilterQueryParams, PaginationQueryParams):
+    """Contains full filtering options to query elements, paginate and order them."""
+
+    order: Optional[str] = Field(
+        default=None,
+        title="Order",
+        description=(
+            "String containing one of the valid ordering attributes followed (optionally) "
+            "by '-asc' or '-dsc' for ascending and descending order respectively. "
+            "Orders can be stacked as a comma-separated list of values."
+        ),
+        example="name-dsc,create_time",
+    )
+
+
+class SerializationParams(BaseModel):
+    """Contains common parameters for customizing model serialization."""
+
+    view: Optional[str] = Field(
+        default=None,
+        title="View",
+        description=(
+            "The name of the view used to serialize this item. "
+            "This will return a predefined set of attributes of the item."
+        ),
+        example="summary",
+    )
+    keys: Optional[List[str]] = Field(
+        default=None,
+        title="Keys",
+        description=(
+            "List of keys (name of the attributes) that will be returned in addition "
+            "to the ones included in the `view`."
+        ),
+    )
+    default_view: Optional[str] = Field(
+        default=None,
+        title="Default View",
+        description="The item view that will be used in case none was specified.",
+    )
+
+
+class PdfDocumentType(str, Enum):
+    invocation_report = "invocation_report"
+    page = "page"
+
+
+class APIKeyModel(BaseModel):
+    key: str = Field(Required, title="Key", description="API key to interact with the Galaxy API")
+    create_time: datetime = Field(
+        Required, title="Create Time", description="The time and date this API key was created."
+    )

galaxy-schema-23.2.1/galaxy/schema/bco/__init__.py

@@ -0,0 +1,97 @@
+from typing import List
+
+from pydantic import BaseModel
+from typing_extensions import Literal
+
+from .description_domain import (
+    DescriptionDomain,
+    PipelineStep,
+    Uri as DescriptionDomainUri,
+    XrefItem,
+)
+from .error_domain import ErrorDomain
+from .execution_domain import (
+    ExecutionDomain,
+    ExternalDataEndpoint,
+    ScriptItem,
+    SoftwarePrerequisite,
+    Uri as ExecutionDomainUri,
+)
+from .io_domain import (
+    InputAndOutputDomain,
+    InputSubdomainItem,
+    OutputSubdomainItem,
+    Uri as InputAndOutputDomainUri,
+)
+from .parametric_domain import (
+    ParametricDomain,
+    ParametricDomainItem,
+)
+from .provenance_domain import (
+    ContributionEnum,
+    Contributor,
+    ProvenanceDomain,
+)
+from .usability_domain import UsabilityDomain
+
+SPEC_VERSION = "https://w3id.org/ieee/ieee-2791-schema/2791object.json"
+
+
+class GalaxyExtension(BaseModel):
+    galaxy_url: str
+    galaxy_version: str
+
+
+class GalaxyExtensionDomain(BaseModel):
+    extension_schema: Literal[
+        "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/galaxy/galaxy_extension.json"
+    ] = "https://raw.githubusercontent.com/biocompute-objects/extension_domain/1.2.0/galaxy/galaxy_extension.json"
+    galaxy_extension: GalaxyExtension
+
+
+class BioComputeObjectCore(BaseModel):
+    """BioComputeObject pre-hash, used to generate etag."""
+
+    description_domain: DescriptionDomain
+    error_domain: ErrorDomain
+    execution_domain: ExecutionDomain
+    extension_domain: List[GalaxyExtensionDomain]
+    io_domain: InputAndOutputDomain
+    parametric_domain: ParametricDomain
+    provenance_domain: ProvenanceDomain
+    usability_domain: UsabilityDomain
+
+
+class BioComputeObject(BioComputeObjectCore):
+    object_id: str
+    spec_version: str = SPEC_VERSION
+    etag: str
+
+
+__all__ = (
+    "BioComputeObjectCore",
+    "BioComputeObject",
+    "Contributor",
+    "ContributionEnum",
+    "DescriptionDomain",
+    "DescriptionDomainUri",
+    "ErrorDomain",
+    "ExecutionDomain",
+    "ExecutionDomainUri",
+    "ExternalDataEndpoint",
+    "GalaxyExtension",
+    "GalaxyExtensionDomain",
+    "InputAndOutputDomain",
+    "InputSubdomainItem",
+    "OutputSubdomainItem",
+    "InputAndOutputDomainUri",
+    "ParametricDomain",
+    "ParametricDomainItem",
+    "PipelineStep",
+    "ProvenanceDomain",
+    "ScriptItem",
+    "SoftwarePrerequisite",
+    "SPEC_VERSION",
+    "UsabilityDomain",
+    "XrefItem",
+)

galaxy-schema-23.2.1/galaxy/schema/bco/description_domain.py

@@ -0,0 +1,133 @@
+# generated by datamodel-codegen:
+#   filename:  https://opensource.ieee.org/2791-object/ieee-2791-schema/-/raw/master/description_domain.json
+#   timestamp: 2022-09-13T23:51:48+00:00
+
+from __future__ import annotations
+
+from datetime import datetime
+from enum import Enum
+from typing import (
+    List,
+    Optional,
+)
+
+from pydantic import (
+    AnyUrl,
+    BaseModel,
+    EmailStr,
+    Extra,
+    Field,
+)
+
+
+class XrefItem(BaseModel):
+    namespace: str = Field(..., description="External resource vendor prefix", example=["pubchem.compound"])
+    name: str = Field(..., description="Name of external reference", example=["PubChem-compound"])
+    ids: List[str] = Field(..., description="List of reference identifiers")
+    access_time: datetime = Field(..., description="Date and time the external reference was accessed")
+
+
+class Uri(BaseModel):
+    class Config:
+        extra = Extra.forbid
+
+    filename: Optional[str] = None
+    uri: AnyUrl
+    access_time: Optional[datetime] = Field(
+        None, description="Time stamp of when the request for this data was submitted"
+    )
+    sha1_checksum: Optional[str] = Field(
+        None, description="output of hash function that produces a message digest", regex="[A-Za-z0-9]+"
+    )
+
+
+class ObjectId(BaseModel):
+    __root__: str = Field(
+        ...,
+        description="A unique identifier that should be applied to each IEEE-2791 Object instance, generated and assigned by a IEEE-2791 database engine. IDs should never be reused",
+    )
+
+
+class ContributionEnum(Enum):
+    authoredBy = "authoredBy"
+    contributedBy = "contributedBy"
+    createdAt = "createdAt"
+    createdBy = "createdBy"
+    createdWith = "createdWith"
+    curatedBy = "curatedBy"
+    derivedFrom = "derivedFrom"
+    importedBy = "importedBy"
+    importedFrom = "importedFrom"
+    providedBy = "providedBy"
+    retrievedBy = "retrievedBy"
+    retrievedFrom = "retrievedFrom"
+    sourceAccessedBy = "sourceAccessedBy"
+
+
+class Contributor(BaseModel):
+    class Config:
+        extra = Extra.forbid
+
+    name: str = Field(..., description="Name of contributor", example=["Charles Darwin"])
+    affiliation: Optional[str] = Field(
+        None, description="Organization the particular contributor is affiliated with", example=["HMS Beagle"]
+    )
+    email: Optional[EmailStr] = Field(
+        None,
+        description="electronic means for identification and communication purposes",
+        example=["name@example.edu"],
+    )
+    contribution: List[ContributionEnum] = Field(
+        ..., description="type of contribution determined according to PAV ontology"
+    )
+    orcid: Optional[AnyUrl] = Field(
+        None,
+        description="Field to record author information. ORCID identifiers allow for the author to curate their information after submission. ORCID identifiers must be valid and must have the prefix ‘https://orcid.org/’",
+        example=["http://orcid.org/0000-0002-1825-0097"],
+    )
+
+
+class PrerequisiteItem(BaseModel):
+    name: str = Field(
+        ..., description="Public searchable name for reference or prereq.", example=["Hepatitis C virus genotype 1"]
+    )
+    uri: Uri
+
+
+class PipelineStep(BaseModel):
+    class Config:
+        extra = Extra.forbid
+
+    step_number: int = Field(
+        ...,
+        description="Non-negative integer value representing the position of the tool in a one-dimensional representation of the pipeline.",
+    )
+    name: str = Field(..., description="This is a recognized name of the software tool", example=["HIVE-hexagon"])
+    description: str = Field(
+        ..., description="Specific purpose of the tool.", example=["Alignment of reads to a set of references"]
+    )
+    version: Optional[str] = Field(
+        None,
+        description="Version assigned to the instance of the tool used corresponding to the upstream release.",
+        example=["1.3"],
+    )
+    prerequisite: Optional[List[PrerequisiteItem]] = Field(None, description="Reference or required prereqs")
+    input_list: List[Uri] = Field(..., description="URIs (expressed as a URN or URL) of the input files for each tool.")
+    output_list: List[Uri] = Field(
+        ..., description="URIs (expressed as a URN or URL) of the output files for each tool."
+    )
+
+
+class DescriptionDomain(BaseModel):
+    keywords: List[str] = Field(..., description="Keywords to aid in search-ability and description of the object.")
+    xref: Optional[List[XrefItem]] = Field(
+        None, description="List of the databases or ontology IDs that are cross-referenced in the IEEE-2791 Object."
+    )
+    platform: Optional[List[str]] = Field(
+        None,
+        description="reference to a particular deployment of an existing platform where this IEEE-2791 Object can be reproduced.",
+    )
+    pipeline_steps: List[PipelineStep] = Field(
+        ...,
+        description="Each individual tool (or a well defined and reusable script) is represented as a step. Parallel processes are given the same step number.",
+    )