diff --git a/geomagio/api/secure/login.py b/geomagio/api/secure/login.py
index c3407d9317c5f6d4fad6f6a0f62c0b2b23d1df40..b687dec3bd562b92b6b30ac4657db62936e5d279 100644
--- a/geomagio/api/secure/login.py
+++ b/geomagio/api/secure/login.py
@@ -35,6 +35,7 @@ Usage:
"""
import logging
import os
+import requests
from typing import Callable, List, Optional
from authlib.integrations.starlette_client import OAuth
@@ -56,7 +57,8 @@ class User(BaseModel):
async def current_user(request: Request) -> Optional[User]:
- """Get logged in user, or None if not logged in.
+ """Get user information from gitlab access token or session(if currently logged in).
+ Returns none if access token is not vald or user is not logged in.
Usage example:
user: Optional[User] = Depends(current_user)
@@ -64,9 +66,45 @@ async def current_user(request: Request) -> Optional[User]:
"""
if "user" in request.session:
return User(**request.session["user"])
+ if "apiuser" in request.session:
+ return User(**request.session["apiuser"])
+ if "Authorization" in request.headers:
+ user = get_api_user(token=request.headers["Authorization"])
+ if user is not None:
+ request.session["apiuser"] = user.dict()
+ return user
return None
+def get_api_user(token: str) -> Optional[User]:
+ url = os.getenv("GITLAB_API_URL")
+ header = {"PRIVATE-TOKEN": token}
+ # request user information from gitlab api with access token
+ userinfo_response = requests.get(
+ f"{url}/user",
+ headers=header,
+ )
+ userinfo = userinfo_response.json()
+ try:
+ user = User(
+ email=userinfo["email"],
+ sub=userinfo["id"],
+ name=userinfo["name"],
+ nickname=userinfo["username"],
+ picture=userinfo["avatar_url"],
+ )
+ except KeyError:
+ logging.info(f"Invalid token: {userinfo_response.status_code}")
+ return None
+ # use valid token to retrieve user's groups
+ groups_response = requests.get(
+ f"{url}/groups",
+ headers=header,
+ )
+ user.groups = [g["full_path"] for g in groups_response.json()]
+ return user
+
+
def require_user(
allowed_groups: List[str] = None,
) -> Callable[[Request, User], User]:
diff --git a/geomagio/api/secure/metadata.py b/geomagio/api/secure/metadata.py
index 710128d1af33bd856d08c0b2d48b9b1cabff5029..e619c66362b8b4e960dd92cba5b5d88ff493b6b2 100644
--- a/geomagio/api/secure/metadata.py
+++ b/geomagio/api/secure/metadata.py
@@ -19,11 +19,10 @@ from typing import List
from fastapi import APIRouter, Body, Depends, Request, Response
from obspy import UTCDateTime
-from ...metadata import Metadata, MetadataCategory
+from ...metadata import Metadata, MetadataCategory, MetadataQuery
+from ... import pydantic_utcdatetime
from ..db import metadata_table
from .login import require_user, User
-from .MetadataQuery import MetadataQuery
-from ... import pydantic_utcdatetime
# routes for login/logout
router = APIRouter()
@@ -41,7 +40,7 @@ async def create_metadata(
@router.delete("/metadata/{id}")
async def delete_metadata(
- id: int, user: User = Depends(require_user(os.getenv("ADMIN_GROUP", "admin")))
+ id: int, user: User = Depends(require_user([os.getenv("ADMIN_GROUP", "admin")]))
):
await metadata_table.delete_metadata(id)
diff --git a/geomagio/api/ws/metadata.py b/geomagio/api/ws/metadata.py
index 9f4febeb93bc0a3b89541697df2bc405a5f9881d..655c33e59f0ec84b4329e5e3c6642c6dbe24882c 100644
--- a/geomagio/api/ws/metadata.py
+++ b/geomagio/api/ws/metadata.py
@@ -3,8 +3,7 @@ from typing import List
from fastapi import APIRouter
from obspy import UTCDateTime
-from ...metadata import Metadata, MetadataCategory
-from ..secure.MetadataQuery import MetadataQuery
+from ...metadata import Metadata, MetadataCategory, MetadataQuery
from ..db import metadata_table
router = APIRouter()
diff --git a/geomagio/apiclient/MetadataFactory.py b/geomagio/apiclient/MetadataFactory.py
new file mode 100644
index 0000000000000000000000000000000000000000..288901c6856ce2a2a90ec8054555283b301d4d2e
--- /dev/null
+++ b/geomagio/apiclient/MetadataFactory.py
@@ -0,0 +1,71 @@
+import os
+import requests
+from typing import List, Union
+
+from obspy import UTCDateTime
+from pydantic import parse_obj_as
+
+from ..metadata import Metadata, MetadataQuery
+
+
+class MetadataFactory(object):
+ def __init__(
+ self,
+ url: str = "http://{}/ws/secure/metadata".format(
+ os.getenv("GEOMAG_API_HOST", "127.0.0.1:8000")
+ ),
+ token: str = os.getenv("GITLAB_API_TOKEN"),
+ ):
+ self.url = url
+ self.token = token
+ self.header = self._get_headers()
+
+ def _get_headers(self):
+ return {"Authorization": self.token} if self.token else None
+
+ def delete_metadata(self, metadata: Metadata) -> bool:
+ response = requests.delete(url=f"{self.url}/{metadata.id}", headers=self.header)
+ if response.status_code == 200:
+ return True
+ return False
+
+ def get_metadata(self, query: MetadataQuery) -> List[Metadata]:
+ if query.id:
+ response = self.get_metadata_by_id(id=query.id)
+ else:
+ args = parse_params(query=query)
+ response = requests.get(url=self.url, params=args, headers=self.header)
+ metadata = parse_obj_as(Union[List[Metadata], Metadata], response.json())
+ if isinstance(metadata, Metadata):
+ metadata = [metadata]
+ return metadata
+
+ def get_metadata_by_id(self, id: int) -> requests.Response:
+ return requests.get(f"{self.url}/{id}", headers=self.header)
+
+ def create_metadata(self, metadata: Metadata) -> Metadata:
+ response = requests.post(
+ url=self.url, data=metadata.json(), headers=self.header
+ )
+ return Metadata(**response.json())
+
+ def update_metadata(self, metadata: Metadata) -> Metadata:
+ response = requests.put(
+ url=f"{self.url}/{metadata.id}", data=metadata.json(), headers=self.header
+ )
+ return Metadata(**response.json())
+
+
+def parse_params(query: MetadataQuery) -> str:
+ query = query.dict(exclude_none=True)
+ args = {}
+ for key in query.keys():
+ element = query[key]
+ # convert times to strings
+ if isinstance(element, UTCDateTime):
+ element = element.isoformat()
+ # get string value of metadata category
+ if key == "category":
+ element = element.value
+ args[key] = element
+ return args
diff --git a/geomagio/apiclient/__init__.py b/geomagio/apiclient/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..53bb45e4c2ebd258886d2bcf0d41522b7a519bdb
--- /dev/null
+++ b/geomagio/apiclient/__init__.py
@@ -0,0 +1,4 @@
+from .metadata import app
+from .MetadataFactory import MetadataFactory
+
+__all__ = ["app", "MetadataFactory"]
diff --git a/geomagio/apiclient/metadata.py b/geomagio/apiclient/metadata.py
new file mode 100644
index 0000000000000000000000000000000000000000..afb3ea63e3c64354553c11c0b8b8cc4773bdb7f3
--- /dev/null
+++ b/geomagio/apiclient/metadata.py
@@ -0,0 +1,144 @@
+import sys
+import json
+import os
+from typing import Dict, Optional
+
+from obspy import UTCDateTime
+import typer
+
+from ..metadata import Metadata, MetadataCategory, MetadataQuery
+from .MetadataFactory import MetadataFactory
+
+
+def load_metadata(input_file: str) -> Optional[Dict]:
+ if input_file is None:
+ return None
+ if input_file == "-":
+ data = json.loads(sys.stdin.read())
+ return data
+ with open(input_file, "r") as file:
+ data = json.load(file)
+ return data
+
+
+app = typer.Typer()
+
+
+@app.command()
+def create(
+ url: str = "http://{}/ws/secure/metadata".format(
+ os.getenv("GEOMAG_API_HOST", "127.0.0.1:8000")
+ ),
+ category: MetadataCategory = None,
+ channel: str = None,
+ created_after: str = None,
+ created_before: str = None,
+ data_valid: bool = True,
+ endtime: str = None,
+ id: int = None,
+ input_file: str = None,
+ location: str = None,
+ metadata_valid: bool = True,
+ network: str = None,
+ starttime: str = None,
+ station: str = None,
+ wrap: bool = True,
+):
+ input_metadata = load_metadata(input_file=input_file)
+ if not wrap:
+ metadata = Metadata(**input_metadata)
+ else:
+ metadata = Metadata(
+ category=category,
+ channel=channel,
+ created_after=UTCDateTime(created_after) if created_after else None,
+ created_before=UTCDateTime(created_before) if created_before else None,
+ data_valid=data_valid,
+ endtime=UTCDateTime(endtime) if endtime else None,
+ id=id,
+ location=location,
+ metadata=input_metadata,
+ metadata_valid=metadata_valid,
+ network=network,
+ starttime=UTCDateTime(starttime) if starttime else None,
+ station=station,
+ )
+ metadata = MetadataFactory(url=url).create_metadata(metadata=metadata)
+ print(metadata.json())
+
+
+@app.command()
+def delete(
+ input_file: str,
+ url: str = "http://{}/ws/secure/metadata".format(
+ os.getenv("GEOMAG_API_HOST", "127.0.0.1:8000")
+ ),
+):
+ metadata_dict = load_metadata(input_file=input_file)
+ metadata = Metadata(**metadata_dict)
+ deleted = MetadataFactory(url=url).delete_metadata(metadata=metadata)
+ if not deleted:
+ sys.exit(1)
+
+
+@app.command()
+def get(
+ url: str = "http://{}/ws/secure/metadata".format(
+ os.getenv("GEOMAG_API_HOST", "127.0.0.1:8000")
+ ),
+ category: Optional[MetadataCategory] = None,
+ channel: Optional[str] = None,
+ created_after: Optional[str] = None,
+ created_before: Optional[str] = None,
+ data_valid: Optional[bool] = True,
+ endtime: Optional[str] = None,
+ id: Optional[int] = None,
+ location: Optional[str] = None,
+ metadata_valid: Optional[bool] = True,
+ network: Optional[str] = None,
+ starttime: Optional[str] = None,
+ station: Optional[str] = None,
+ getone: bool = False,
+):
+ query = MetadataQuery(
+ category=category,
+ channel=channel,
+ created_after=UTCDateTime(created_after) if created_after else None,
+ created_before=UTCDateTime(created_before) if created_before else None,
+ data_valid=data_valid,
+ endtime=UTCDateTime(endtime) if endtime else None,
+ id=id,
+ location=location,
+ metadata_valid=metadata_valid,
+ network=network,
+ starttime=UTCDateTime(starttime) if starttime else None,
+ station=station,
+ )
+ metadata = MetadataFactory(url=url).get_metadata(query=query)
+ if not metadata:
+ print([])
+ return
+
+ if getone:
+ if len(metadata) > 1:
+ raise ValueError("More than one matching record")
+ print(metadata[0].json())
+ return
+ print("[" + ",".join([m.json() for m in metadata]) + "]")
+
+
+@app.command()
+def update(
+ input_file: str,
+ url: str = "http://{}/ws/secure/metadata".format(
+ os.getenv("GEOMAG_API_HOST", "127.0.0.1:8000")
+ ),
+):
+ metadata_dict = load_metadata(input_file=input_file)
+ metadata = Metadata(**metadata_dict)
+ response = MetadataFactory(url=url).update_metadata(metadata=metadata)
+ print(response.json())
+
+
+def main():
+ app()
diff --git a/geomagio/api/secure/MetadataQuery.py b/geomagio/metadata/MetadataQuery.py
similarity index 79%
rename from geomagio/api/secure/MetadataQuery.py
rename to geomagio/metadata/MetadataQuery.py
index 6b30699d9ef1371019a6b89aaa0244b5b0c30111..36e6c3ebe3cd20d880c25ff0d683757c84a2d833 100644
--- a/geomagio/api/secure/MetadataQuery.py
+++ b/geomagio/metadata/MetadataQuery.py
@@ -2,9 +2,10 @@ from datetime import timezone
from obspy import UTCDateTime
from pydantic import BaseModel
+from typing import Optional
-from ...metadata import MetadataCategory
-from ... import pydantic_utcdatetime
+from .. import pydantic_utcdatetime
+from .MetadataCategory import MetadataCategory
class MetadataQuery(BaseModel):
@@ -18,8 +19,8 @@ class MetadataQuery(BaseModel):
station: str = None
channel: str = None
location: str = None
- data_valid: bool = None
- metadata_valid: bool = True
+ data_valid: Optional[bool] = None
+ metadata_valid: Optional[bool] = None
def datetime_dict(self, **kwargs):
values = self.dict(**kwargs)
diff --git a/geomagio/metadata/__init__.py b/geomagio/metadata/__init__.py
index 7502db0243cac6af13d38c8386c3dd292ae386c2..37b2adc332b5f6a90f02c75ac9166cf19de48089 100644
--- a/geomagio/metadata/__init__.py
+++ b/geomagio/metadata/__init__.py
@@ -1,5 +1,6 @@
from .Metadata import Metadata
from .MetadataCategory import MetadataCategory
+from .MetadataQuery import MetadataQuery
-__all__ = ["Metadata", "MetadataCategory"]
+__all__ = ["Metadata", "MetadataCategory", "MetadataQuery"]
diff --git a/geomagio/processing/__init__.py b/geomagio/processing/__init__.py
index b17686a9ee5a9b5cda1a2960f69c27c9d8305d95..be97cfbd5e32485df54fc814fd646c595685fed7 100644
--- a/geomagio/processing/__init__.py
+++ b/geomagio/processing/__init__.py
@@ -17,7 +17,7 @@ __all__ = [
"obsrio_minute",
"obsrio_second",
"obsrio_temperatures",
- "obsrid_tenhertz",
+ "obsrio_tenhertz",
"rotate",
"sqdist_minute",
]
diff --git a/setup.py b/setup.py
index 6216d647e18bb973c54c54a4011d9db32115d710..a73fd11e7b6ce8880a573af13857d342c6348f12 100644
--- a/setup.py
+++ b/setup.py
@@ -25,8 +25,9 @@ setuptools.setup(
use_pipfile=True,
entry_points={
"console_scripts": [
- "magproc-prepfiles=geomagio.processing.magproc:main",
"generate-matrix=geomagio.processing.adjusted:main",
+ "geomag-apiclient=geomagio.apiclient.metadata:main",
+ "magproc-prepfiles=geomagio.processing.magproc:main",
"obsrio-filter=geomagio.processing.obsrio:main",
],
},