From 7e3b041bb87ec1065060088c98b94629a7fc0e65 Mon Sep 17 00:00:00 2001
From: Khoroshevskyi <sasha99250@gmail.com>
Date: Fri, 21 Jun 2024 14:00:37 -0400
Subject: [PATCH] sample add fix
---
pepdbagent/db_utils.py | 2 +-
pepdbagent/modules/project.py | 11 ++++----
pepdbagent/modules/sample.py | 51 +++++++++++++++++++----------------
pepdbagent/utils.py | 5 ++++
tests/test_pepagent.py | 8 +++---
5 files changed, 43 insertions(+), 34 deletions(-)
diff --git a/pepdbagent/db_utils.py b/pepdbagent/db_utils.py
index 7dc7a3a..fd5c7cd 100644
--- a/pepdbagent/db_utils.py
+++ b/pepdbagent/db_utils.py
@@ -139,7 +139,7 @@ class Samples(Base):
sample_name: Mapped[Optional[str]] = mapped_column()
guid: Mapped[Optional[str]] = mapped_column(nullable=False, unique=True)
- parent_guid: Mapped[Optional[int]] = mapped_column(
+ 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.",
diff --git a/pepdbagent/modules/project.py b/pepdbagent/modules/project.py
index 1675068..c9697f8 100644
--- a/pepdbagent/modules/project.py
+++ b/pepdbagent/modules/project.py
@@ -2,7 +2,6 @@
import json
import logging
from typing import Union, List, NoReturn, Dict
-import uuid
import peppy
from sqlalchemy import and_, delete, select
@@ -36,7 +35,7 @@
SampleTableUpdateError,
)
from pepdbagent.models import UpdateItems, UpdateModel, ProjectDict
-from pepdbagent.utils import create_digest, registry_path_converter, order_samples
+from pepdbagent.utils import create_digest, registry_path_converter, order_samples, generate_guid
_LOGGER = logging.getLogger(PKG_NAME)
@@ -547,7 +546,7 @@ def update(
f"Please provide it to update samples, or use overwrite method."
)
- self._update_samples_with_ids(
+ self._update_samples(
project_id=found_prj.id,
samples_list=update_dict["samples"],
sample_name_key=update_dict["config"].get(
@@ -574,7 +573,7 @@ def update(
else:
raise ProjectNotFoundError("No items will be updated!")
- def _update_samples_with_ids(
+ def _update_samples(
self,
project_id: int,
samples_list: List[Dict[str, str]],
@@ -600,7 +599,7 @@ def _update_samples_with_ids(
new_sample[PEPHUB_SAMPLE_ID_KEY] for new_sample in samples_list
}
new_samples_dict: dict = {
- new_sample[PEPHUB_SAMPLE_ID_KEY] or str(uuid.uuid4()): new_sample
+ new_sample[PEPHUB_SAMPLE_ID_KEY] or generate_guid(): new_sample
for new_sample in samples_list
}
@@ -887,7 +886,7 @@ def _add_samples_to_project(
row_number=row_number,
sample_name=sample.get(sample_table_index),
parent_guid=previous_sample_guid,
- guid=str(uuid.uuid4()),
+ guid=generate_guid(),
)
projects_sa.samples_mapping.append(sample)
previous_sample_guid = sample.guid
diff --git a/pepdbagent/modules/sample.py b/pepdbagent/modules/sample.py
index 5106fed..e2677cc 100644
--- a/pepdbagent/modules/sample.py
+++ b/pepdbagent/modules/sample.py
@@ -4,11 +4,10 @@
import peppy
from peppy.const import SAMPLE_TABLE_INDEX_KEY
-from sqlalchemy import select, and_, func
+from sqlalchemy import select, and_
from sqlalchemy.orm import Session
from sqlalchemy.orm.attributes import flag_modified
-
from pepdbagent.const import (
DEFAULT_TAG,
PKG_NAME,
@@ -16,6 +15,7 @@
from pepdbagent.exceptions import SampleNotFoundError, SampleAlreadyExistsError
from pepdbagent.db_utils import BaseEngine, Samples, Projects
+from pepdbagent.utils import generate_guid, order_samples
_LOGGER = logging.getLogger(PKG_NAME)
@@ -216,29 +216,10 @@ def add(
raise KeyError(
f"Sample index key {project_mapping.config.get(SAMPLE_TABLE_INDEX_KEY, 'sample_name')} not found in sample dict"
)
- project_where_statement = (
- Samples.project_id
- == select(Projects.id)
- .where(
- and_(
- Projects.namespace == namespace,
- Projects.name == name,
- Projects.tag == tag,
- ),
- )
- .scalar_subquery()
- )
statement = select(Samples).where(
- and_(project_where_statement, Samples.sample_name == sample_name)
+ and_(Samples.project_id == project_mapping.id, Samples.sample_name == sample_name)
)
-
sample_mapping = session.scalar(statement)
- row_number = (
- session.execute(
- select(func.max(Samples.row_number)).where(project_where_statement)
- ).one()[0]
- or 0
- )
if sample_mapping and not overwrite:
raise SampleAlreadyExistsError(
@@ -257,9 +238,11 @@ def add(
else:
sample_mapping = Samples(
sample=sample_dict,
- row_number=row_number + 1,
+ row_number=0,
project_id=project_mapping.id,
sample_name=sample_name,
+ guid=generate_guid(),
+ parent_guid=self._get_last_sample_guid(project_mapping.id),
)
project_mapping.number_of_samples += 1
project_mapping.last_update_date = datetime.datetime.now(datetime.timezone.utc)
@@ -267,6 +250,28 @@ def add(
session.add(sample_mapping)
session.commit()
+ def _get_last_sample_guid(self, project_id: int) -> str:
+ """
+ Get last sample guid from the project
+
+ :param project_id: project_id of the project
+ :return: guid of the last sample
+ """
+ statement = select(Samples).where(Samples.project_id == project_id)
+ with Session(self._sa_engine) as session:
+ samples_results = session.scalars(statement)
+
+ result_dict = {}
+ for sample in samples_results:
+ sample_dict = sample.sample
+
+ result_dict[sample.guid] = {
+ "sample": sample_dict,
+ "guid": sample.guid,
+ "parent_guid": sample.parent_guid,
+ }
+ return order_samples(result_dict)[-1]["guid"]
+
def delete(
self,
namespace: str,
diff --git a/pepdbagent/utils.py b/pepdbagent/utils.py
index 7c1d32b..4bb7103 100644
--- a/pepdbagent/utils.py
+++ b/pepdbagent/utils.py
@@ -3,6 +3,7 @@
from collections.abc import Iterable
from hashlib import md5
from typing import Tuple, Union, List
+import uuid
import ubiquerg
from peppy.const import SAMPLE_RAW_DICT_KEY
@@ -150,3 +151,7 @@ def order_samples(results: dict) -> List[dict]:
else:
current = None
return ordered_sequence
+
+
+def generate_guid() -> str:
+ return str(uuid.uuid4())
diff --git a/tests/test_pepagent.py b/tests/test_pepagent.py
index 4d4b0b3..f1f9967 100644
--- a/tests/test_pepagent.py
+++ b/tests/test_pepagent.py
@@ -1103,7 +1103,7 @@ def test_update(self, initiate_pepdb_con, namespace, name, sample_name):
sample_name=sample_name,
update_dict={"organism": "butterfly"},
)
- one_sample = initiate_pepdb_con.sample.get(namespace, name, sample_name)
+ one_sample = initiate_pepdb_con.sample.get(namespace, name, sample_name, raw=False)
assert one_sample.organism == "butterfly"
@pytest.mark.parametrize(
@@ -1120,7 +1120,7 @@ def test_update_sample_name(self, initiate_pepdb_con, namespace, name, sample_na
sample_name=sample_name,
update_dict={"sample_name": "butterfly"},
)
- one_sample = initiate_pepdb_con.sample.get(namespace, name, "butterfly")
+ one_sample = initiate_pepdb_con.sample.get(namespace, name, "butterfly", raw=False)
assert one_sample.sample_name == "butterfly"
@pytest.mark.parametrize(
@@ -1212,10 +1212,10 @@ def test_delete_sample(self, initiate_pepdb_con, namespace, name, sample_name):
],
)
def test_add_sample(self, initiate_pepdb_con, namespace, name, tag, sample_dict):
- prj = initiate_pepdb_con.project.get(namespace, name)
+ prj = initiate_pepdb_con.project.get(namespace, name, raw=False)
initiate_pepdb_con.sample.add(namespace, name, tag, sample_dict)
- prj2 = initiate_pepdb_con.project.get(namespace, name)
+ prj2 = initiate_pepdb_con.project.get(namespace, name, raw=False)
assert len(prj.samples) + 1 == len(prj2.samples)
assert prj2.samples[-1].sample_name == sample_dict["sample_name"]