diff --git a/geomagio/api/db/MetadataDatabaseFactory.py b/geomagio/api/db/MetadataDatabaseFactory.py
index bb494b0c6e58bb8959a8bd1e2f02bbd355627874..d221c4de48cb9bca4bdeb825739b658393e7cc7c 100644
--- a/geomagio/api/db/MetadataDatabaseFactory.py
+++ b/geomagio/api/db/MetadataDatabaseFactory.py
@@ -1,8 +1,6 @@
from datetime import datetime
-from enum import Enum
-from typing import List, Union
+from typing import List
-from fastapi import Response
from obspy import UTCDateTime
from sqlalchemy import or_, Table
@@ -12,11 +10,6 @@ from .metadata_history_table import metadata_history
from .metadata_table import metadata
-class TableType(str, Enum):
- METADATA = "metadata"
- HISTORY = "history"
-
-
class MetadataDatabaseFactory(object):
def __init__(
self, table: Table = metadata, history_table: Table = metadata_history
@@ -24,38 +17,20 @@ class MetadataDatabaseFactory(object):
self.table = table
self.history_table = history_table
- async def create_metadata(
- self, meta: Metadata, table: TableType = TableType.METADATA
- ) -> Metadata:
- exclude = {"id"}
- if table is TableType.HISTORY:
- query = self.history_table.insert()
- meta.metadata_id = meta.id
- else:
- query = self.table.insert()
- exclude.add("metadata_id")
- values = meta.datetime_dict(exclude=exclude, exclude_none=True)
+ async def create_metadata(self, meta: Metadata) -> Metadata:
+ query = metadata.insert()
+ values = meta.datetime_dict(exclude={"id", "metadata_id"}, exclude_none=True)
query = query.values(**values)
meta.id = await database.execute(query)
return meta
- async def delete_metadata(self, id: int) -> None:
- query = self.table.delete().where(self.table.c.id == id)
- await database.execute(query)
-
- async def get_metadata_by_id(
- self, id: int, table: TableType = TableType.METADATA
- ) -> Union[Metadata, List[Metadata]]:
- if table == TableType.HISTORY:
- query = self.history_table.select()
- query = query.where(self.history_table.c.metadata_id == id)
- rows = await database.fetch_all(query)
- return [Metadata(**row) for row in rows]
- meta = await self.get_metadata(id=id)
- if len(meta) != 1:
- return Response(status_code=404)
- else:
- return meta[0]
+ async def create_metadata_history(self, meta: Metadata) -> Metadata:
+ query = self.history_table.insert()
+ meta.metadata_id = meta.id
+ values = meta.datetime_dict(exclude={"id"}, exclude_none=True)
+ query = query.values(**values)
+ meta.id = await database.execute(query)
+ return meta
async def get_metadata(
self,
@@ -73,7 +48,8 @@ class MetadataDatabaseFactory(object):
data_valid: bool = None,
metadata_valid: bool = None,
reviewed: bool = None,
- ) -> List[Metadata]:
+ status: str = None,
+ ):
table = self.table
query = table.select()
if id:
@@ -90,11 +66,17 @@ class MetadataDatabaseFactory(object):
query = query.where(table.c.location.like(location))
if starttime:
query = query.where(
- or_(table.c.endtime == None, table.c.endtime > starttime)
+ or_(
+ table.c.endtime == None,
+ table.c.endtime > starttime,
+ )
)
if endtime:
query = query.where(
- or_(table.c.starttime == None, table.c.starttime < endtime)
+ or_(
+ table.c.starttime == None,
+ table.c.starttime < endtime,
+ )
)
if created_after:
query = query.where(table.c.created_time > created_after)
@@ -106,21 +88,39 @@ class MetadataDatabaseFactory(object):
query = query.where(table.c.metadata_valid == metadata_valid)
if reviewed is not None:
query = query.where(table.c.reviewed == reviewed)
+ if status is not None:
+ query = query.where(table.c.status == status)
rows = await database.fetch_all(query)
return [Metadata(**row) for row in rows]
+ async def get_metadata_by_id(self, id: int):
+ meta = await self.get_metadata(id=id)
+ if len(meta) != 1:
+ raise ValueError(f"{len(meta)} records found")
+ return meta[0]
+
+ async def get_metadata_history(self, metadata_id: int) -> List[Metadata]:
+ query = self.history_table.select()
+ query = query.where(self.history_table.c.metadata_id == metadata_id)
+ rows = await database.fetch_all(query)
+ metadata = [Metadata(**row) for row in rows]
+ current_metadata = await self.get_metadata_by_id(id=metadata_id)
+ metadata.append(current_metadata)
+ # return records in order of age
+ metadata.reverse()
+ return metadata
+
async def update_metadata(
- self,
- meta: Metadata,
- username: str,
+ self, meta: Metadata, username: str, status: str = None
) -> Metadata:
- original_metadata = await self.get_metadata_by_id(id=meta.id)
- await self.create_metadata(meta=original_metadata, table=TableType.HISTORY)
- meta.updated_by = username
- meta.updated_time = UTCDateTime()
- query = self.table.update().where(self.table.c.id == meta.id)
- values = meta.datetime_dict(exclude={"id", "metadata_id"})
- query = query.values(**values)
- await database.execute(query)
- updated_metadata = await self.get_metadata_by_id(id=meta.id)
- return updated_metadata
+ async with database.transaction() as transaction:
+ original_metadata = await self.get_metadata_by_id(id=meta.id)
+ await self.create_metadata_history(meta=original_metadata)
+ meta.updated_by = username
+ meta.updated_time = UTCDateTime()
+ meta.status = status or meta.status
+ query = self.table.update().where(self.table.c.id == meta.id)
+ values = meta.datetime_dict(exclude={"id", "metadata_id"})
+ query = query.values(**values)
+ await database.execute(query)
+ return await self.get_metadata_by_id(id=meta.id)
diff --git a/geomagio/api/db/metadata_table.py b/geomagio/api/db/metadata_table.py
index a99def5c74c3d6450432fd4830bc8f673f6e1130..c80567828aac49c19ac310f2bf894eb22a7aa4a5 100644
--- a/geomagio/api/db/metadata_table.py
+++ b/geomagio/api/db/metadata_table.py
@@ -42,6 +42,8 @@ metadata = Table(
Column("metadata_valid", Boolean, default=True, index=True),
# whether metadata has been reviewed
Column("reviewed", Boolean, default=True, index=True),
+ # deletion status indicator
+ Column("status", String(length=255), nullable=True),
# metadata json blob
Column("metadata", JSON, nullable=True),
# general comment
@@ -65,6 +67,7 @@ metadata = Table(
"metadata_valid",
"data_valid",
"reviewed",
+ "status",
),
Index(
"index_category_time",
diff --git a/geomagio/api/secure/metadata.py b/geomagio/api/secure/metadata.py
index 07f7a65427e8e309fa3015451caa026852e10d06..baf4094a0f4227c3cc225c2a406a731ef218ec70 100644
--- a/geomagio/api/secure/metadata.py
+++ b/geomagio/api/secure/metadata.py
@@ -34,7 +34,7 @@ async def create_metadata(
metadata: Metadata,
user: User = Depends(require_user()),
):
- metadata = await MetadataDatabaseFactory().create_metadata(metadata)
+ metadata = await MetadataDatabaseFactory().create_metadata(meta=metadata)
return Response(metadata.json(), status_code=201, media_type="application/json")
@@ -42,14 +42,11 @@ async def create_metadata(
async def delete_metadata(
id: int, user: User = Depends(require_user([os.getenv("ADMIN_GROUP", "admin")]))
):
- await MetadataDatabaseFactory().delete_metadata(id)
-
-
-@router.get("/metadata/{id}/history", response_model=List[Metadata])
-async def get_metadata_history(
- id: int,
-):
- return await MetadataDatabaseFactory().get_metadata_by_id(id=id, table="history")
+ database_factory = MetadataDatabaseFactory()
+ metadata = await database_factory.get_metadata_by_id(id=id)
+ await database_factory.update_metadata(
+ meta=metadata, username=user.nickname, status="deleted"
+ )
@router.get("/metadata", response_model=List[Metadata])
@@ -66,6 +63,7 @@ async def get_metadata(
data_valid: bool = None,
metadata_valid: bool = True,
reviewed: bool = None,
+ status: str = None,
):
query = MetadataQuery(
category=category,
@@ -80,9 +78,10 @@ async def get_metadata(
data_valid=data_valid,
metadata_valid=metadata_valid,
reviewed=reviewed,
+ status=status,
)
metas = await MetadataDatabaseFactory().get_metadata(
- **query.datetime_dict(exclude={"id"})
+ **query.datetime_dict(exclude={"id", "metadata_id"})
)
return metas
@@ -92,6 +91,15 @@ async def get_metadata_by_id(id: int):
return await MetadataDatabaseFactory().get_metadata_by_id(id=id)
+@router.get("/metadata/{metadata_id}/history", response_model=List[Metadata])
+async def get_metadata_history(
+ metadata_id: int,
+):
+ return await MetadataDatabaseFactory().get_metadata_history(
+ metadata_id=metadata_id,
+ )
+
+
@router.put("/metadata/{id}", response_model=Metadata)
async def update_metadata(
id: int,
@@ -99,6 +107,5 @@ async def update_metadata(
user: User = Depends(require_user([os.getenv("REVIEWER_GROUP", "reviewer")])),
):
return await MetadataDatabaseFactory().update_metadata(
- meta=metadata,
- username=user.nickname,
+ meta=metadata, username=user.nickname
)
diff --git a/geomagio/api/ws/metadata.py b/geomagio/api/ws/metadata.py
index 827fdcaf6208a77a1b06a2c240e93caa29f24ed4..57b89cb3049bf4f2b1ae3f72aaf33e90c7d6113c 100644
--- a/geomagio/api/ws/metadata.py
+++ b/geomagio/api/ws/metadata.py
@@ -21,6 +21,7 @@ async def get_metadata(
data_valid: bool = None,
metadata_valid: bool = True,
reviewed: bool = None,
+ status: str = None,
):
query = MetadataQuery(
category=category,
@@ -33,6 +34,7 @@ async def get_metadata(
data_valid=data_valid,
metadata_valid=metadata_valid,
reviewed=reviewed,
+ status=status,
)
metas = await MetadataDatabaseFactory().get_metadata(
**query.datetime_dict(exclude={"id"})
diff --git a/geomagio/metadata/Metadata.py b/geomagio/metadata/Metadata.py
index 4dede4eeec2778f67a03b740bc465c7fb0325aad..b6bcb6ba04f9da7692010636ba2a76cbb3272e60 100644
--- a/geomagio/metadata/Metadata.py
+++ b/geomagio/metadata/Metadata.py
@@ -80,6 +80,8 @@ class Metadata(BaseModel):
comment: str = None
# review specific comment
review_comment: str = None
+ # deletion status indicator
+ status: str = None
def datetime_dict(self, **kwargs):
values = self.dict(**kwargs)
diff --git a/geomagio/metadata/MetadataQuery.py b/geomagio/metadata/MetadataQuery.py
index dd80ae06729915a6a04a2531bd7eb3d548180fd0..025c000b720511bbd4238f029241d583710b587e 100644
--- a/geomagio/metadata/MetadataQuery.py
+++ b/geomagio/metadata/MetadataQuery.py
@@ -22,6 +22,7 @@ class MetadataQuery(BaseModel):
data_valid: Optional[bool] = None
metadata_valid: Optional[bool] = None
reviewed: Optional[bool] = None
+ status: Optional[str] = None
def datetime_dict(self, **kwargs):
values = self.dict(**kwargs)
diff --git a/geomagio/metadata/main.py b/geomagio/metadata/main.py
index 863052286d5a04bfcc69a533d3f6f102eb1a975a..1b7c8da81289523cab910e66f07088d91d089a1d 100644
--- a/geomagio/metadata/main.py
+++ b/geomagio/metadata/main.py
@@ -148,6 +148,7 @@ def get(
metadata_valid: Optional[bool] = None,
network: Optional[str] = None,
reviewed: Optional[bool] = None,
+ status: Optional[str] = None,
starttime: Optional[str] = None,
station: Optional[str] = None,
url: str = GEOMAG_API_URL,
@@ -166,6 +167,7 @@ def get(
reviewed=reviewed,
starttime=UTCDateTime(starttime) if starttime else None,
station=station,
+ status=status,
)
metadata = MetadataFactory(url=url).get_metadata(query=query)
if getone: