small import and annotation fixes to make mypy happy

.gitignore

@@ -1,4 +1,4 @@
 doc/build
 __pycache__
 .ipynb_checkpoints
-
+.pytest_cache

mupifDB/api/client.py

@@ -3,7 +3,6 @@
 import datetime
 import sys
 import os
-import table_structures
 import tempfile
 import importlib
 import re
@@ -12,7 +11,8 @@
 import pydantic
 from typing import List,Optional,Literal
 
-from ..  import models
+from .. import models
+from .. import table_structures
 
 from rich import print_json
 from rich.pretty import pprint
@@ -115,7 +115,6 @@ def insertWorkflowHistory(wf: models.Workflow_Model):
 @if_granta(granta._getGrantaExecutionRecords)
 @pydantic.validate_call
 def getExecutionRecords(workflow_id: str|None=None, workflow_version: int|None=None, label: str|None=None, num_limit: int|None=None, status: str|None=None) -> List[models.WorkflowExecution_Model]: 
-    data = []
     query = "executions/?noparam"
     for n,a in [('num_limit',num_limit),('label',label),('workflow_id',workflow_id),('workflow_version',workflow_version),('status',status)]:
         if a is not None: query += f"&{n}={str(a)}"

mupifDB/api/main.py

@@ -34,7 +34,7 @@
 log=logging.getLogger('restApi')
 
 
-import table_structures
+from .. import table_structures
 
 client = MongoClient("mongodb://localhost:"+os.environ.get('MUPIFDB_MONGODB_PORT','27017'))
 db = client.MuPIF

mupifDB/models.py

@@ -9,7 +9,7 @@ class Parent_Model(pydantic.BaseModel):
     id: str
 
 class MongoObj_Model(pydantic.BaseModel):
-    dbID: Optional[str]=Field(None,alias=AliasChoices('_id','dbID'),serialization_alias='_id')
+    dbID: Optional[str]=Field(None,alias=AliasChoices('_id','dbID'),serialization_alias='_id') # type: ignore[arg-type]
     parent: Optional[Parent_Model]=None
 
 class UseCase_Model(MongoObj_Model):
@@ -66,10 +66,10 @@ class InputOutputBase_Model(pydantic.BaseModel):
             Name: str
             Description: Optional[str]=None
             Type: str
-            Type_ID: str = Field(...,alias=AliasChoices('Type_ID','TypeID'))
+            Type_ID: str = Field(...,alias=AliasChoices('Type_ID','TypeID'))                   # type: ignore[arg-type]
             ValueType: Literal['Vector','Scalar','Tensor','VectorArray']='Scalar'
             Units: str
-            ObjID: Optional[str|List[str]] = Field(None,alias=AliasChoices('ObjID','Obj_ID'))
+            ObjID: Optional[str|List[str]] = Field(None,alias=AliasChoices('ObjID','Obj_ID'))  # type: ignore[arg-type]
             @property
             def TypeID(self): return self.Type_ID
             # @property.setter(self,val): self.Type_ID=val
@@ -83,7 +83,7 @@ class Output_Model(InputOutputBase_Model):
         Outputs: List[Output_Model]
     wid: str
     Description: str
-    GridFSID: str = None
+    GridFSID: Optional[str] = None
     UseCase: str
     IOCard: IOCard_Model
     modulename: str

mupifDB/mupifdbRestApi.py

@@ -16,7 +16,7 @@
 sys.path.append(os.path.dirname(os.path.abspath(__file__))+"/.")
 import mupifDB
 from mongoflask import MongoJSONEncoder, ObjectIdConverter
-import table_structures
+from .. import table_structures
 import mupif as mp
 
 

mupifDB/mypy.ini

@@ -0,0 +1,22 @@
+[mypy]
+plugins = pydantic.mypy
+
+# https://docs.pydantic.dev/latest/integrations/mypy/#configuring-the-plugin
+[pydantic-mypy]
+init_forbid_extra = True
+init_typed = True
+# those are used in models.py aliases
+warn_required_dynamic_aliases = False
+
+[mypy-numpy]
+ignore_missing_imports = True
+[mypy-pidfile]
+ignore_missing_imports = True
+[mypy-jsonpickle]
+ignore_missing_imports = True
+[mypy-Pyro5]
+ignore_missing_imports = True
+[mypy-mupif]
+ignore_missing_imports = True
+[mypy-pygal]
+ignore_missing_imports = True

mupifDB/restLogger.py

@@ -30,7 +30,6 @@ def emit(self, record):
 
 
 if __name__ == '__main__':
-    import restApiControl
     logging.getLogger().setLevel(logging.DEBUG)
     log = logging.getLogger('test')
     log.setLevel(logging.DEBUG)

mupifDB/table_structures.py

@@ -1,3 +1,4 @@
+from typing import Any
 
 def extendRecord(record, structure):
     for def_key in structure.keys():
@@ -6,13 +7,13 @@ def extendRecord(record, structure):
     return record
 
 
-tableUseCase = {
+tableUseCase: dict[str,Any] = {
     'ucid': None,
     'Description': None,
 }
 
 
-tableWorkflow = {
+tableWorkflow: dict[str,Any] = {
     'wid': None,
     'Description': None,
     'UseCase': None,
@@ -26,7 +27,7 @@ def extendRecord(record, structure):
 }
 
 
-tableExecution = {
+tableExecution: dict[str,Any] = {
     'WorkflowID': None,
     'WorkflowVersion': None,
     'Status': "Created",
@@ -46,7 +47,7 @@ def extendRecord(record, structure):
 }
 
 
-tableUser = {
+tableUser: dict[str,Any] = {
     'IP': None,
     'Name': None,
     'Organization': None,

mupifDB/workflowmanager.py

@@ -16,7 +16,7 @@
 import pydantic
 from typing import Literal
 
-import table_structures
+from . import table_structures
 
 from mupifDB.api.client_util import api_type
 
@@ -43,7 +43,7 @@ def insertWorkflowDefinition(*, wid, description, source, useCase, workflowInput
     @param modulename
     @param classname
     """
-    insertWorkflowDefinition_real(
+    insertWorkflowDefinition_model(
         source=source,
         rec=models.Workflow_Model(
             wid=wid,
@@ -61,7 +61,7 @@ def insertWorkflowDefinition(*, wid, description, source, useCase, workflowInput
     )
 
 @pydantic.validate_call
-def insertWorkflowDefinition_real(source: pydantic.FilePath, rec: models.Workflow_Model):
+def insertWorkflowDefinition_model(source: pydantic.FilePath, rec: models.Workflow_Model):
     with open(source, 'rb') as f:
         rec.GridFSID=restApiControl.uploadBinaryFile(f)
         f.close()

mupifDB/workflowscheduler.py

@@ -43,7 +43,7 @@
 # try to import schedulerconfig.py
 authToken = None
 try:
-    import schedulerConfig
+    import schedulerConfig # type: ignore
     authKey = schedulerConfig.authToken
 except ImportError:
     log.info("schedulerConfig import failed")
@@ -126,7 +126,6 @@ def historyUpdateFailed(data, epoch):
 processedTasks = 0
 finishedTasks = 0 # with success
 failedTasks = 0
-lastJobs = {}  # dict, we-id key
 
 
 schedulerStatFile = "/var/lib/mupif/persistent/scheduler-stat.json"