Skip to content

Commit

Permalink
Merge pull request #139 from pepkit/history
Browse files Browse the repository at this point in the history
Project history
  • Loading branch information
khoroshevskyi authored Jul 8, 2024
2 parents 5a37bf8 + 92a9ac6 commit d2bacb6
Show file tree
Hide file tree
Showing 14 changed files with 850 additions and 20 deletions.
2 changes: 2 additions & 0 deletions pepdbagent/const.py
Original file line number Diff line number Diff line change
Expand Up @@ -20,3 +20,5 @@
LAST_UPDATE_DATE_KEY = "last_update_date"

PEPHUB_SAMPLE_ID_KEY = "ph_id"

MAX_HISTORY_SAMPLES_NUMBER = 2000
53 changes: 52 additions & 1 deletion pepdbagent/db_utils.py
Original file line number Diff line number Diff line change
@@ -1,10 +1,12 @@
import datetime
import enum
import logging
from typing import List, Optional

from sqlalchemy import (
TIMESTAMP,
BigInteger,
Enum,
FetchedValue,
ForeignKey,
Result,
Expand Down Expand Up @@ -119,6 +121,10 @@ class Projects(Base):

namespace_mapping: Mapped["User"] = relationship("User", back_populates="projects_mapping")

history_mapping: Mapped[List["HistoryProjects"]] = relationship(
back_populates="project_mapping", cascade="all, delete-orphan"
) # TODO: check if cascade is correct

__table_args__ = (UniqueConstraint("namespace", "name", "tag"),)


Expand All @@ -131,7 +137,6 @@ class Samples(Base):

id: Mapped[int] = mapped_column(primary_key=True)
sample: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
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()
Expand Down Expand Up @@ -245,6 +250,52 @@ class ViewSampleAssociation(Base):
view: Mapped["Views"] = relationship(back_populates="samples")


class HistoryProjects(Base):

__tablename__ = "project_history"

id: Mapped[int] = mapped_column(primary_key=True)
project_id: Mapped[int] = mapped_column(ForeignKey("projects.id", ondelete="CASCADE"))
user: Mapped[str] = mapped_column(ForeignKey("users.namespace", ondelete="SET NULL"))
update_time: Mapped[datetime.datetime] = mapped_column(
TIMESTAMP(timezone=True), default=deliver_update_date
)
project_yaml: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())

project_mapping: Mapped["Projects"] = relationship(
"Projects", back_populates="history_mapping"
)
sample_changes_mapping: Mapped[List["HistorySamples"]] = relationship(
back_populates="history_project_mapping", cascade="all, delete-orphan"
)


class UpdateTypes(enum.Enum):
"""
Enum for the type of update
"""

UPDATE = "update"
INSERT = "insert"
DELETE = "delete"


class HistorySamples(Base):

__tablename__ = "sample_history"

id: Mapped[int] = mapped_column(primary_key=True)
history_id: Mapped[int] = mapped_column(ForeignKey("project_history.id", ondelete="CASCADE"))
guid: Mapped[str] = mapped_column(nullable=False)
parent_guid: Mapped[Optional[str]] = mapped_column(nullable=True)
sample_json: Mapped[dict] = mapped_column(JSON, server_default=FetchedValue())
change_type: Mapped[UpdateTypes] = mapped_column(Enum(UpdateTypes), nullable=False)

history_project_mapping: Mapped["HistoryProjects"] = relationship(
"HistoryProjects", back_populates="sample_changes_mapping"
)


class BaseEngine:
"""
A class with base methods, that are used in several classes. e.g. fetch_one or fetch_all
Expand Down
10 changes: 10 additions & 0 deletions pepdbagent/exceptions.py
Original file line number Diff line number Diff line change
Expand Up @@ -107,3 +107,13 @@ def __init__(self, msg=""):
class NamespaceNotFoundError(PEPDatabaseAgentError):
def __init__(self, msg=""):
super().__init__(f"""Project does not exist. {msg}""")


class HistoryNotFoundError(PEPDatabaseAgentError):
def __init__(self, msg=""):
super().__init__(f"""History does not exist. {msg}""")


class UserNotFoundError(PEPDatabaseAgentError):
def __init__(self, msg=""):
super().__init__(f"""User does not exist. {msg}""")
22 changes: 22 additions & 0 deletions pepdbagent/models.py
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
# file with pydantic models
import datetime
from typing import Dict, List, Optional, Union

from peppy.const import CONFIG_KEY, SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_LIST_KEY
Expand Down Expand Up @@ -224,3 +225,24 @@ class NamespaceStats(BaseModel):
namespace: Union[str, None] = None
projects_updated: Dict[str, int] = None
projects_created: Dict[str, int] = None


class HistoryChangeModel(BaseModel):
"""
Model for history change
"""

change_id: int
change_date: datetime.datetime
user: str


class HistoryAnnotationModel(BaseModel):
"""
History annotation model
"""

namespace: str
name: str
tag: str = DEFAULT_TAG
history: List[HistoryChangeModel]
Loading

0 comments on commit d2bacb6

Please sign in to comment.