from kf_utils.dataservice.delete import delete_entities

# Delete all studies in Dataservice (raises Exception on deletion of non-local resources)
delete_entities(kf_api_url, study_ids=None)

# Delete a study in Dataservice (raises Exception on deletion of non-local resources)
delete_entities(kf_api_url, study_ids=["SD_12345678"])

# Delete a study in Dataservice (allows deletion of non-local resources)
delete_entities(kf_api_url, study_ids=["SD_12345678"], safety_check=False)

from kf_utils.dataservice.scrape import *

# Yield all entities from the given endpoint matching the given filter query
for e in yield_entities_from_filter(
    kf_api_url, "participants", {"study_id": "SD_12345678"}, show_progress=True
):
  ...

# Yield all entities matching the given kfids
for e in yield_entities_from_kfids(
    kf_api_url, ["PT_12345678", "BS_99999999"], show_progress=True
):
  ...

# Compatibility wrapper for yielding entities from kfid or a filter query
for e in yield_entities(
    kf_api_url, "participants", {"study_id": "SD_12345678"}, show_progress=True
):
  ...

for e in yield_entities(
    kf_api_url, None, ["PT_12345678", "BS_99999999"], show_progress=True
):
  ...

# Like yield_entities_from_filter but just yields the kfids
for kfid in yield_kfids(
    kf_api_url, "participants", {"study_id": "SD_12345678"}, show_progress=True
):
  ...

from kf_utils.dataservice.descendants import *

api_url = "https://kf-api-dataservice.kidsfirstdrc.org"
db_url = f"postgres://{USER_NAME}:{PASSWORD}@kf-dataservice-api-prd-2019-9-11.c3siovbugjym.us-east-1.rds.amazonaws.com:5432/kfpostgresprd"

# Get descendant entities for these families, including any genomic files that
# are only partially composed of these families' biospecimens
d1 = find_descendants_by_kfids(
    db_url or api_url, "families", ["FM_11111111", "FM_22222222", "FM_33333333"],
    ignore_gfs_with_hidden_external_contribs=False, kfids_only=False
)

# Get descendant kfids for hidden families in SD_DYPMEHHF, but only include
# genomic files with other contributing biospecimens if those specimens are visible
d2 = find_descendants_by_filter(
    api_url, "families", {"study_id": "SD_DYPMEHHF", "visible": False},
    ignore_gfs_with_hidden_external_contribs=True, kfids_only=True, db_url=db_url
)

# List genomic files with contributions from these biospecimens that also have
# contributions from biospecimens that aren't these
promiscuous_gs = find_gfs_with_extra_contributors(
    db_url or api_url, ["BS_11111111", "BS_22222222", "BS_33333333"]
)

# Hide all visible families in study SD_DYPMEHHF and all of their descendants.
# Genomic files receive the specified acl.
# This and unhide_descendants_by_filter are not symmetrical.
hide_descendants_by_filter(
    api_url, "families", {"study_id": "SD_DYPMEHHF", "visible": True}, gf_acl=["SD_DYPMEHHF", "phs001436.c999"], db_url=db_url, dry_run=False
)

# Unhide all hidden families in study SD_DYPMEHHF and all of their descendants except for
# genomic files with additional contributing specimens if those specimens will remain
# hidden.
# This and hide_descendants_by_filter are not symmetrical.
unhide_descendants_by_filter(
    api_url, "families", {"study_id": "SD_DYPMEHHF", "visible": False}, db_url=db_url, dry_run=False
)

# Hide these families and all of their descendants. Genomic files receive the
# specified acl.
# This and unhide_descendants_by_kfids are not symmetrical.
hide_descendants_by_kfids(
    api_url, "families", ["FM_12345678", "FM_87654321"], gf_acl=["SD_DYPMEHHF", "phs001436.c999"], db_url=db_url, dry_run=False
)

# Unhide these families and all of their descendants except for genomic files with
# additional contributing specimens if those specimens will remain hidden.
# This and hide_descendants_by_kfids are not symmetrical.
unhide_descendants_by_kfids(
    api_url, "families", ["FM_12345678", "FM_87654321"], db_url=db_url, dry_run=False
)

from kf_utils.dataservice.patch import *

host = "http://localhost:5000"

# Patch the given KFIDs with the given changes
patches = {
    "PT_12345678": {"visible": True},
    "BS_99999999": {"participant_id": "PT_12345678", "visible": False}
}
send_patches(host, patches)

things = [
    {"kf_id": "PT_11223344", "visible": True},
    {"kf_id": "PT_22334455", "visible": False}
]

def my_patch_func(thing):
    return {"external_id": "VISIBLE" if thing["visible"] else "HIDDEN"}

# Patch the given KFIDs or entities according to the result of the function
patch_things_with_func(host, things, my_patch_func)

# Hide the given KFIDs and assign an empty acl to the hidden genomic file
hide_kfids(host, ["PT_12345678", "GF_99999999"], gf_acl=[])

# Unhide the given KFIDs
unhide_kfids(host, ["PT_12345678", "BS_99999999"])

from kf_utils.dataservice.reporting import *

# Generate a report on which S3 files have been loaded into the data service
# and which loaded files no longer exist on S3 by merging the details together.

ds_url = "https://kf-api-dataservice.kidsfirstdrc.org"
study_kfid = "SD_12345678"
study_bucket = "kf-study-us-east-1-prd-sd-12345678"
exclude_s3_keypaths = ("path/with_files/I_don't_care_about", "another/one")

# This can take a while to run because of API limitations.
output = merge_s3_and_kf_gfs(
    ds_url, study_kfid, study_bucket, exclude_s3_keypaths
)

from kf_utils.dbgap.release import get_latest_released_sample_status

# Get the sample status data for the latest "released" version of this study
versioned_accession, study_data = get_latest_released_sample_status("phs001138")