feat(workflow_automation): add activities

We've encapsulated workflow activities within a component that aligns
with the schema and try to build a service that intuitively maps to
it. We've also namespaced this component so that it appears under
`nmdc_runtime/workflow_execution_activity` for easier importing around
the project as well as by external users.

components/nmdc_runtime/workflow/__init__.py

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+from .src.core import init_workflow_service
+from .src.spec import WorkflowCreate, WorkflowUpdate

components/nmdc_runtime/workflow/spec.py

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+from typing import Literal, Optional, Union
+
+from pydantic import BaseModel, Field
+
+
+class Sequencing(BaseModel):
+    Name: str = "Sequencing"
+    Enabled: bool = False
+    Git_repo: str = ""
+    Version: str = "v1.0.0"
+    Activity: Literal[
+        "metagenome_sequencing_activity_set"
+    ] = "metagenome_sequencing_activity_set"
+    Predecessor: str = ""
+    Input_prefix: str = ""
+    Inputs: list = []
+
+
+class ReadQcAnalysisInputs(BaseModel):
+    input_files: str = "Metagenome Raw Reads"
+    informed_by: str = ""
+    resource: str = "NERSC-Cori"
+    proj: str = ""
+
+
+class ReadQcAnalysis(BaseModel):
+    Name: str = "Read QC Analysis"
+    Enabled: bool = True
+    Git_repo: str = " https://github.com/microbiomedata/ReadsQC"
+    Version: str = "v1.0.6"
+    WDL: str = "rqcfilter.wdl"
+    Activity: Literal["read_qc_analysis_activity_set"] = "read_qc_analysis_activity_set"
+    Predecessor: str = "Sequencing"
+    Input_prefix: str = "nmdc_rqcfilter"
+    ID_type: str = "mgrc"
+    Inputs: ReadQcAnalysisInputs = ReadQcAnalysisInputs()
+
+
+class MetagenomeAnnotationInputs(BaseModel):
+    input_file: str = "Assembly Contigs"
+    imgap_project_id: str = "actid"
+    resource: str = "NERSC-Cori"
+    proj: str = ""
+    informed_by: str = ""
+    git_url: str = "https://github.com/microbiomedata/mg_annotation"
+
+
+class MetagenomeAnnotation(BaseModel):
+    Name: str = "Metagenome Annotation"
+    Enabled: bool = True
+    Git_repo: str = "https://github.com/microbiomedata/mg_annotation"
+    Version: str = "v1.0.0-beta"
+    WDL: str = "annotation_full.wdl"
+    Activity: Literal[
+        "metagenome_annotation_activity_set"
+    ] = "metagenome_annotation_activity_set"
+    Predecessor: str = "MetagenomeAssembly"
+    Input_prefix: str = "annotation"
+    ID_type: str = "mgann"
+    Inputs: MetagenomeAnnotationInputs = MetagenomeAnnotationInputs()
+
+
+class MetagenomeAssemblyInputs(BaseModel):
+    input_file: str = "Filtered Sequencing Reads"
+    rename_contig_prefix: str = "actid"
+    resource: str = "NERSC-Cori"
+    proj: str = ""
+    informed_by: str = ""
+    git_url: str = "https://github.com/microbiomedata/meta_assembly"
+
+
+class MetagenomeAssembly(BaseModel):
+    Name: str = "Metagenome Assembly"
+    Enabled: bool = True
+    Git_repo: str = "https://github.com/microbiomedata/metaAssembly"
+    Version: str = "v1.0.3-beta"
+    WDL: str = "jgi_assembly.wdl"
+    Activity: Literal[
+        "metagenome_assembly_activity_set"
+    ] = "metagenome_assembly_activity_set"
+    Predecessor: str = "Read QC Analysis"
+    Input_prefix: str = "jgi_metaASM"
+    ID_type: str = "mgasm"
+    Inputs: MetagenomeAssemblyInputs = MetagenomeAssemblyInputs()
+
+
+class MAGsInputs(BaseModel):
+    input_file: str = "Assembly Contigs"
+    contig_file: str = "Assembly Contigs"
+    gff_file: str = "Functional Annotation GFF"
+    cath_funfam_file: str = "CATH FunFams (Functional Families) Annotation GFF"
+    supfam_file: str = "SUPERFam Annotation GFF"
+    cog_file: str = "Clusters of Orthologous Groups (COG) Annotation GFF"
+    pfam_file: str = "Pfam Annotation GFF"
+    product_names_file: str = "Product names"
+    tigrfam_file: str = "TIGRFam Annotation GFF"
+    ec_file: str = "Annotation Enzyme Commission"
+    ko_file: str = "Annotation KEGG Orthology"
+    sam_file: str = "Assembly Coverage BAM"
+    smart_file: str = "SMART Annotation GFF"
+    proteins_file: str = "Annotation Amino Acid FASTA"
+    gene_phylogeny_file: str = "Gene Phylogeny"
+    resource: str = "NERSC-Cori"
+    proj: str = ""
+    informed_by: str = ""
+    git_url: str = "https://github.com/microbiomedata/metaMAGs"
+    url_root: str = "https://data.microbiomedata.org/data/"
+
+
+class MAGs(BaseModel):
+    Name: str = "MAGs"
+    Enabled: bool = True
+    Git_repo: str = "https://github.com/microbiomedata/metaMAGs"
+    Version: str = "v1.0.4-beta"
+    WDL: str = "mbin_nmdc.wdl"
+    Activity: Literal["mags_activity_set"] = "mags_activity_set"
+    Predecessor: str = "Metagenome Annotation"
+    Input_prefix: str = "nmdc_mags"
+    ID_type: str = "mgmag"
+    Inputs: MAGsInputs = MAGsInputs()
+
+
+class ReadBasedAnalysisInputs(BaseModel):
+    input_file: str = "Filtered Sequencing Reads"
+    prefix: str = "actid"
+    resource: str = "NERSC-Cori"
+    proj: str = ""
+    informed_by: str = ""
+    git_url: str = "https://github.com/microbiomedata/ReadbasedAnalysis"
+    url_root: str = "https://data.microbiomedata.org/data/"
+
+
+class ReadBasedAnalysis(BaseModel):
+    Name: str = "Readbased Analysis"
+    Enabled: bool = True
+    Git_repo: str = "https://github.com/microbiomedata/ReadbasedAnalysis"
+    Version: str = "v1.0.2-beta"
+    WDL: str = "ReadbasedAnalysis.wdl"
+    Activity: Literal[
+        "read_based_analysis_activity_set"
+    ] = "read_based_analysis_activity_set"
+    Predecessor: str = "Read QC Analysis"
+    Input_prefix: str = "nmdc_rba"
+    ID_type: str = "mgrba"
+    Inputs: ReadBasedAnalysisInputs = ReadBasedAnalysisInputs()
+
+
+class WorkflowModel(BaseModel):
+    workflow: Union[
+        ReadQcAnalysis,
+        MetagenomeAssembly,
+        MAGs,
+        ReadBasedAnalysis,
+        Sequencing,
+        MetagenomeAnnotation,
+    ] = Field(..., discriminator="Activity")
+
+
+def get_all_workflows():
+    return [
+        ReadQcAnalysis(Inputs=ReadQcAnalysisInputs()),
+        MetagenomeAssembly(Inputs=MetagenomeAssemblyInputs()),
+        MetagenomeAnnotation(Inputs=MetagenomeAnnotationInputs()),
+        MAGs(Inputs=MAGsInputs()),
+        ReadBasedAnalysis(Inputs=ReadBasedAnalysisInputs()),
+        Sequencing(),
+    ]

components/nmdc_runtime/workflow/src/__init__.py

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+from .core import init_workflow_service
+from .spec import WorkflowCreate, WorkflowUpdate

components/nmdc_runtime/workflow/src/core.py

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+from .spec import ResultWithErr, WorkflowQueriesABC, WorkflowUpdate
+from .store import WorkflowQueries
+
+
+class WorkflowService:
+    def __init__(
+        self, workflow_queries: WorkflowQueriesABC = WorkflowQueries()
+    ) -> None:
+        self.__queries = workflow_queries
+
+    async def update(self, workflow: WorkflowUpdate) -> ResultWithErr[dict]:
+        result = await self.__queries.workflow_update(workflow)
+        return {"data": result}, None
+
+
+def init_workflow_service() -> WorkflowService:
+    return WorkflowService()