Merge pull request #103 from pepkit/24_pop

Added pop column

Author: khoroshevskyi

docs/changelog.md

@@ -2,6 +2,11 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.7.0] -- 2023-XX-XX
+- Added pop to project table and annotation model
+- Switched to pydantic2
+- Updated requirements (psycopg2 -> psycopg3)
+
 ## [0.6.0] -- 2023-08-24
 - Added date filter to project annotation
 

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.6.0"
+__version__ = "0.7.0a1"

pepdbagent/db_utils.py

@@ -1,19 +1,17 @@
 import datetime
 import logging
-from typing import Any, Optional, List
+from typing import Optional, List
 
 from sqlalchemy import (
     BigInteger,
     FetchedValue,
-    PrimaryKeyConstraint,
     Result,
     Select,
     String,
     event,
     select,
     TIMESTAMP,
     ForeignKey,
-    ForeignKeyConstraint,
     UniqueConstraint,
 )
 from sqlalchemy.dialects.postgresql import JSON
@@ -92,6 +90,7 @@ class Projects(Base):
         onupdate=deliver_update_date, default=deliver_update_date
     )
     pep_schema: Mapped[Optional[str]]
+    pop: Mapped[Optional[bool]] = mapped_column(default=False)
     samples_mapping: Mapped[List["Samples"]] = relationship(
         back_populates="sample_mapping", cascade="all, delete-orphan"
     )

pepdbagent/models.py

@@ -1,9 +1,6 @@
 # file with pydantic models
-import datetime
 from typing import List, Optional, Union
-
-import peppy
-from pydantic import BaseModel, Extra, Field, validator
+from pydantic import BaseModel, Extra, Field, validator, ConfigDict, field_validator
 
 
 class AnnotationModel(BaseModel):
@@ -21,12 +18,14 @@ class AnnotationModel(BaseModel):
     submission_date: Optional[str]
     digest: Optional[str]
     pep_schema: Optional[str]
+    pop: Optional[bool] = False
 
-    class Config:
-        allow_population_by_field_name = True
-        validate_assignment = True
+    model_config = ConfigDict(
+        validate_assignment=True,
+        populate_by_name=True,
+    )
 
-    @validator("is_private")
+    @field_validator("is_private")
     def is_private_should_be_bool(cls, v):
         if not isinstance(v, bool):
             return False
@@ -71,20 +70,20 @@ class UpdateItems(BaseModel):
     Model used for updating individual items in db
     """
 
-    name: Optional[str]
-    description: Optional[str]
-    tag: Optional[str]
-    is_private: Optional[bool]
-    pep_schema: Optional[str]
-    digest: Optional[str]
-    config: Optional[dict]
-    samples: Optional[List[dict]]
-    subsamples: Optional[List[List[dict]]]
-    description: Optional[str]
-
-    class Config:
-        arbitrary_types_allowed = True
-        extra = Extra.forbid
+    name: Optional[str] = None
+    description: Optional[str] = None
+    tag: Optional[str] = None
+    is_private: Optional[bool] = None
+    pep_schema: Optional[str] = None
+    digest: Optional[str] = None
+    config: Optional[dict] = None
+    samples: Optional[List[dict]] = None
+    subsamples: Optional[List[List[dict]]] = None
+
+    model_config = ConfigDict(
+        arbitrary_types_allowed=True,
+        extra="forbid",
+    )
 
     @property
     def number_of_samples(self) -> Union[int, None]:
@@ -99,37 +98,35 @@ class UpdateModel(BaseModel):
     Model used for updating individual items and creating sql string in the code
     """
 
-    config: Optional[dict]
+    config: Optional[dict] = None
     name: Optional[str] = None
     tag: Optional[str] = None
-    private: Optional[bool] = Field(alias="is_private")
-    digest: Optional[str]
-    number_of_samples: Optional[int]
-    pep_schema: Optional[str]
+    private: Optional[bool] = Field(alias="is_private", default=None)
+    digest: Optional[str] = None
+    number_of_samples: Optional[int] = None
+    pep_schema: Optional[str] = None
     description: Optional[str] = ""
     # last_update_date: Optional[datetime.datetime] = datetime.datetime.now(datetime.timezone.utc)
 
-    @validator("tag", "name")
+    @field_validator("tag", "name")
     def value_must_not_be_empty(cls, v):
         if "" == v:
             return None
         return v
 
-    @validator("tag", "name")
+    @field_validator("tag", "name")
     def value_must_be_lowercase(cls, v):
         if v:
             return v.lower()
         return v
 
-    @validator("tag", "name")
+    @field_validator("tag", "name")
     def value_should_not_contain_question(cls, v):
         if "?" in v:
             return ValueError("Question mark (?) is prohibited in name and tag.")
         return v
 
-    class Config:
-        extra = Extra.forbid
-        allow_population_by_field_name = True
+    model_config = ConfigDict(populate_by_name=True, extra="forbid")
 
 
 class NamespaceInfo(BaseModel):

pepdbagent/modules/annotation.py

@@ -2,8 +2,7 @@
 from datetime import datetime
 from typing import List, Literal, Optional, Union
 
-from sqlalchemy import Engine, and_, func, or_, select
-from sqlalchemy.exc import IntegrityError
+from sqlalchemy import and_, func, or_, select
 from sqlalchemy.sql.selectable import Select
 
 from pepdbagent.const import (
@@ -189,6 +188,7 @@ def _get_single_annotation(
             Projects.last_update_date,
             Projects.digest,
             Projects.pep_schema,
+            Projects.pop,
         ).where(
             and_(
                 Projects.name == name,
@@ -214,6 +214,7 @@ def _get_single_annotation(
                 last_update_date=str(query_result.last_update_date),
                 digest=query_result.digest,
                 pep_schema=query_result.pep_schema,
+                pop=query_result.pop,
             )
             _LOGGER.info(f"Annotation of the project '{namespace}/{name}:{tag}' has been found!")
             return annot
@@ -307,6 +308,7 @@ def _get_projects(
             Projects.last_update_date,
             Projects.digest,
             Projects.pep_schema,
+            Projects.pop,
         ).select_from(Projects)
 
         statement = self._add_condition(
@@ -337,6 +339,7 @@ def _get_projects(
                     last_update_date=str(result.last_update_date),
                     digest=result.digest,
                     pep_schema=result.pep_schema,
+                    pop=result.pop,
                 )
             )
         return results_list
@@ -445,7 +448,7 @@ def _add_date_filter_if_provided(
             return statement
         else:
             if filter_by:
-                _LOGGER.warning(f"filter_start_date was not provided, skipping filter...")
+                _LOGGER.warning("filter_start_date was not provided, skipping filter...")
             return statement
 
     def get_project_number_in_namespace(