Merge pull request #135 from pepkit/133_update_improvements

133 update improvements

README.md

@@ -4,7 +4,7 @@
 ![Run pytests](https://github.com/pepkit/pepdbagent/workflows/Run%20pytests/badge.svg)
 [![pypi-badge](https://img.shields.io/pypi/v/pepdbagent?color=%2334D058)](https://pypi.org/project/pepdbagent)
 [![pypi-version](https://img.shields.io/pypi/pyversions/pepdbagent.svg?color=%2334D058)](https://pypi.org/project/pepdbagent)
-[![Downloads](https://static.pepy.tech/badge/pepdbagent)](https://pepy.tech/project/pepdbagent)
+[![Coverage](https://coverage-badge.samuelcolvin.workers.dev/pepkit/pepdbagent.svg)](https://coverage-badge.samuelcolvin.workers.dev/redirect/pepkit/pepdbagent)
 [![Github badge](https://img.shields.io/badge/source-github-354a75?logo=github)](https://github.com/pepkit/pepdbagent)
 
 
@@ -135,4 +135,4 @@ agent.namespace.get(query='search_pattern', admin=['databio', 'geo', 'ncbi'])
 For more information, developers should use `pepdbagent pytest` as documentation due to its natural language syntax and the 
 ability to write tests that serve as executable examples. 
 This approach not only provides detailed explanations but also ensures that code examples are kept 
-up-to-date with the latest changes in the codebase.
+up-to-date with the latest changes in the codebase.

docs/changelog.md

@@ -2,6 +2,12 @@
 
 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.
 
+## [0.9.0] -- 2024-06-25
+- Introduced new sample ordering with linked list [#133](https://github.com/pepkit/pepdbagent/issues/133)
+- Efficiency improvements of project update function 
+- Test restructuring 
+
+
 ## [0.8.0] -- 2024-02-26
 - Fixed forking schema
 - Improved forking efficiency [#129](https://github.com/pepkit/pepdbagent/issues/129)

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.8.0"
+__version__ = "0.9.0"

pepdbagent/const.py

@@ -18,3 +18,5 @@
 
 SUBMISSION_DATE_KEY = "submission_date"
 LAST_UPDATE_DATE_KEY = "last_update_date"
+
+PEPHUB_SAMPLE_ID_KEY = "ph_id"

pepdbagent/db_utils.py

@@ -1,32 +1,26 @@
 import datetime
 import logging
-from typing import Optional, List
+from typing import List, Optional
 
 from sqlalchemy import (
+    TIMESTAMP,
     BigInteger,
     FetchedValue,
+    ForeignKey,
     Result,
     Select,
     String,
+    UniqueConstraint,
     event,
     select,
-    TIMESTAMP,
-    ForeignKey,
-    UniqueConstraint,
 )
 from sqlalchemy.dialects.postgresql import JSON
 from sqlalchemy.engine import URL, create_engine
 from sqlalchemy.exc import ProgrammingError
 from sqlalchemy.ext.compiler import compiles
-from sqlalchemy.orm import (
-    DeclarativeBase,
-    Mapped,
-    Session,
-    mapped_column,
-    relationship,
-)
+from sqlalchemy.orm import DeclarativeBase, Mapped, Session, mapped_column, relationship
 
-from pepdbagent.const import POSTGRES_DIALECT, PKG_NAME
+from pepdbagent.const import PKG_NAME, POSTGRES_DIALECT
 from pepdbagent.exceptions import SchemaError
 
 _LOGGER = logging.getLogger(PKG_NAME)
@@ -93,7 +87,7 @@ class Projects(Base):
     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"
+        back_populates="project_mapping", cascade="all, delete-orphan"
     )
     subsamples_mapping: Mapped[List["Subsamples"]] = relationship(
         back_populates="subsample_mapping", cascade="all, delete-orphan"
@@ -133,10 +127,22 @@ class Samples(Base):
 
     id: Mapped[int] = mapped_column(primary_key=True)
     sample: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
-    row_number: Mapped[int]
+    row_number: Mapped[int]  # TODO: should be removed
     project_id = mapped_column(ForeignKey("projects.id", ondelete="CASCADE"))
+    project_mapping: Mapped["Projects"] = relationship(back_populates="samples_mapping")
     sample_name: Mapped[Optional[str]] = mapped_column()
-    sample_mapping: Mapped["Projects"] = relationship(back_populates="samples_mapping")
+    guid: Mapped[Optional[str]] = mapped_column(nullable=False, unique=True)
+
+    parent_guid: Mapped[Optional[str]] = mapped_column(
+        ForeignKey("samples.guid", ondelete="CASCADE"),
+        nullable=True,
+        doc="Parent sample id. Used to create a hierarchy of samples.",
+    )
+
+    parent_mapping: Mapped["Samples"] = relationship(
+        "Samples", remote_side=guid, back_populates="child_mapping"
+    )
+    child_mapping: Mapped["Samples"] = relationship("Samples", back_populates="parent_mapping")
 
     views: Mapped[Optional[List["ViewSampleAssociation"]]] = relationship(
         back_populates="sample", cascade="all, delete-orphan"
@@ -318,3 +324,15 @@ def check_db_connection(self):
             self.session_execute(select(Projects).limit(1))
         except ProgrammingError:
             raise SchemaError()
+
+    def delete_schema(self, engine=None) -> None:
+        """
+        Delete sql schema in the database.
+
+        :param engine: sqlalchemy engine [Default: None]
+        :return: None
+        """
+        if not engine:
+            engine = self._engine
+        Base.metadata.drop_all(engine)
+        return None

pepdbagent/exceptions.py

@@ -61,6 +61,16 @@ def __init__(self, msg=""):
         super().__init__(f"""Sample does not exist. {msg}""")
 
 
+class SampleTableUpdateError(PEPDatabaseAgentError):
+    def __init__(self, msg=""):
+        super().__init__(f"""Sample table update error. {msg}""")
+
+
+class ProjectDuplicatedSampleGUIDsError(SampleTableUpdateError):
+    def __init__(self, msg=""):
+        super().__init__(f"""Project has duplicated sample GUIDs. {msg}""")
+
+
 class SampleAlreadyExistsError(PEPDatabaseAgentError):
     def __init__(self, msg=""):
         super().__init__(f"""Sample already exists. {msg}""")

pepdbagent/models.py

@@ -1,7 +1,8 @@
 # file with pydantic models
-from typing import List, Optional, Union, Dict
-from pydantic import BaseModel, Field, ConfigDict, field_validator
-from peppy.const import CONFIG_KEY, SUBSAMPLE_RAW_LIST_KEY, SAMPLE_RAW_DICT_KEY
+from typing import Dict, List, Optional, Union
+
+from peppy.const import CONFIG_KEY, SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_LIST_KEY
+from pydantic import BaseModel, ConfigDict, Field, field_validator
 
 from pepdbagent.const import DEFAULT_TAG
 

pepdbagent/modules/annotation.py

@@ -3,16 +3,16 @@
 from typing import List, Literal, Optional, Union
 
 from sqlalchemy import and_, func, or_, select
-from sqlalchemy.sql.selectable import Select
 from sqlalchemy.orm import Session
+from sqlalchemy.sql.selectable import Select
 
 from pepdbagent.const import (
     DEFAULT_LIMIT,
     DEFAULT_OFFSET,
     DEFAULT_TAG,
+    LAST_UPDATE_DATE_KEY,
     PKG_NAME,
     SUBMISSION_DATE_KEY,
-    LAST_UPDATE_DATE_KEY,
 )
 from pepdbagent.db_utils import BaseEngine, Projects
 from pepdbagent.exceptions import FilterError, ProjectNotFoundError, RegistryPathError

pepdbagent/modules/namespace.py

@@ -1,20 +1,20 @@
 import logging
-from typing import List, Union, Tuple
 from collections import Counter
 from datetime import datetime, timedelta
+from typing import List, Tuple, Union
 
 from sqlalchemy import distinct, func, or_, select, text
-from sqlalchemy.sql.selectable import Select
 from sqlalchemy.orm import Session
+from sqlalchemy.sql.selectable import Select
 
-from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_OFFSET, PKG_NAME, DEFAULT_LIMIT_INFO
+from pepdbagent.const import DEFAULT_LIMIT, DEFAULT_LIMIT_INFO, DEFAULT_OFFSET, PKG_NAME
+from pepdbagent.db_utils import BaseEngine, Projects
 from pepdbagent.exceptions import NamespaceNotFoundError
-from pepdbagent.db_utils import Projects, BaseEngine
 from pepdbagent.models import (
+    ListOfNamespaceInfo,
     Namespace,
-    NamespaceList,
     NamespaceInfo,
-    ListOfNamespaceInfo,
+    NamespaceList,
     NamespaceStats,
 )
 from pepdbagent.utils import tuple_converter