Merge branch 'main' into albireox/issue33

CHANGELOG.rst

@@ -14,6 +14,7 @@ Change Log
 * Adds ``db_reset`` option to avoid closing and resetting the database connection
 * Updates main, cone, and carton/program search to use new ``has_been_observed`` column; default is True.
 * Updates the ``append_pipes`` query to return the new ``has_been_observed`` column
+* Include parent catalog associations in the ``/target/catalogs`` endpoint (#37).
 * Adds endpoint to get parent catalog data for a given target (#38).
 
 0.1.0 (10-24-2023)

python/valis/db/models.py

@@ -7,7 +7,7 @@
 import datetime
 import math
 from typing import Optional, Annotated, Any, TypeVar
-from pydantic import ConfigDict, BaseModel, Field, BeforeValidator, field_validator, FieldValidationInfo
+from pydantic import ConfigDict, BaseModel, Field, BeforeValidator, FieldSerializationInfo, field_serializer, field_validator, FieldValidationInfo
 from enum import Enum
 
 
@@ -204,7 +204,17 @@ class ParentCatalogModel(PeeweeBase):
 
 class CatalogResponse(CatalogModel, SDSSidFlatBase):
     """ Response model for source catalog and sdss_id information """
-    pass
+
+    parent_catalogs: dict[str, Any] = Field(..., description='The parent catalog associations for a given catalogid')
+
+    @field_serializer('parent_catalogs')
+    def serialize_parent_catalogs(v: dict[str, Any], info: FieldSerializationInfo) -> dict[str, Any]:
+        """ Serialize the parent catalogs, excluding None values and trimming strings."""
+
+        if info.exclude_none:
+            return {k: v.strip() if isinstance(v, str) else v for k, v in v.items() if v is not None}
+        else:
+            return v
 
 
 class CartonModel(PeeweeBase):

python/valis/db/queries.py

@@ -6,7 +6,7 @@
 
 import itertools
 import packaging
-from typing import Union, Generator
+from typing import Sequence, Union, Generator
 
 import astropy.units as u
 import deepmerge
@@ -113,8 +113,8 @@ def convert_coords(ra: Union[str, float], dec: Union[str, float]) -> tuple:
     """
     is_hms = set('hms: ') & set(str(ra))
     if is_hms:
-        ra = str(ra).replace(' ', ':')
-        dec = str(dec).replace(' ', ':')
+        ra = str(ra).strip().replace(' ', ':')
+        dec = str(dec).strip().replace(' ', ':')
         unit = ('hourangle', 'degree') if is_hms else ('degree', 'degree')
         coord = SkyCoord(f'{ra} {dec}', unit=unit)
         ra = round(coord.ra.value, 5)
@@ -182,7 +182,7 @@ def get_targets_by_sdss_id(sdss_id: Union[int, list[int]] = []) -> peewee.ModelS
     peewee.ModelSelect
         the ORM query
     """
-    if type(sdss_id) is int:
+    if type(sdss_id) in (int, str):
         sdss_id = [sdss_id]
 
     return vizdb.SDSSidStacked.select().where(vizdb.SDSSidStacked.sdss_id.in_(sdss_id))
@@ -690,8 +690,10 @@ def get_catalog_sources(sdss_id: int) -> peewee.ModelSelect:
     """
 
     s = vizdb.SDSSidFlat.select(vizdb.SDSSidFlat).where(vizdb.SDSSidFlat.sdss_id == sdss_id).alias('s')
-    return cat.Catalog.select(cat.Catalog, starfields(s)).\
-        join(s, on=(s.c.catalogid == cat.Catalog.catalogid)).order_by(cat.Catalog.version.desc())
+    return cat.Catalog.select(cat.Catalog, cat.SDSS_ID_To_Catalog, starfields(s)).\
+        join(s, on=(s.c.catalogid == cat.Catalog.catalogid)).\
+        join(cat.SDSS_ID_To_Catalog, on=(s.c.catalogid == cat.SDSS_ID_To_Catalog.catalogid)).\
+        order_by(cat.Catalog.version.desc())
 
 
 def get_parent_catalog_data(sdss_id: int, catalog: str) -> peewee.ModelSelect:

python/valis/routes/query.py

@@ -82,6 +82,7 @@ async def main_search(self, body: SearchModel):
         """ Main query for UI and for combining queries together """
 
         print('form data', body)
+        query = None
 
         # build the coordinate query
         if body.ra and body.dec:
@@ -97,9 +98,13 @@ async def main_search(self, body: SearchModel):
                                           'program' if body.program else 'carton',
                                           query=query)
         # append query to pipes
-        query = append_pipes(query, observed=body.observed)
+        if query:
+            query = append_pipes(query, observed=body.observed)
 
-        return {'status': 'success', 'data': query.dicts().iterator(), 'msg': 'data successfully retrieved'}
+        # query iterator
+        res = query.dicts().iterator() if query else []
+
+        return {'status': 'success', 'data': res, 'msg': 'data successfully retrieved'}
 
     @router.get('/cone', summary='Perform a cone search for SDSS targets with sdss_ids',
                 response_model=List[SDSSModel], dependencies=[Depends(get_pw_db)])

python/valis/routes/target.py

@@ -4,7 +4,7 @@
 import re
 import httpx
 import orjson
-from typing import Tuple, List, Union, Optional, Annotated
+from typing import Any, Tuple, List, Union, Optional, Annotated
 from pydantic import field_validator, model_validator, BaseModel, Field, model_serializer
 from fastapi import APIRouter, HTTPException, Query, Path, Depends
 from fastapi_restful.cbv import cbv
@@ -182,7 +182,19 @@ async def get_spectrum(self, sdss_id: Annotated[int, Path(title="The sdss_id of
                 response_model_exclude_unset=True, response_model_exclude_none=True)
     async def get_catalogs(self, sdss_id: int = Path(title="The sdss_id of the target to get", example=23326)):
         """ Return catalog information for a given sdss_id """
-        return get_catalog_sources(sdss_id).dicts().iterator()
+
+        sdss_id_data = get_catalog_sources(sdss_id).dicts()
+
+        # The response has the parent catalogs at the same level as the other
+        # columns. For the response we want to nest them under a parent_catalogs key.
+        # This takes advantage that all the parent catalog columns have '__' in the name.
+        response_data: list[dict[str, Any]] = []
+        for row in sdss_id_data:
+            s_data = {k: v for k, v in row.items() if '__' not in k}
+            cat_data = {k.split('__')[0]: v for k, v in row.items() if '__' in k}
+            response_data.append({**s_data, 'parent_catalogs': cat_data})
+
+        return response_data
 
     @router.get('/parents/{parent_catalog}/{sdss_id}',
                 dependencies=[Depends(get_pw_db)],