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More Data Models (#172)
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This PR does two major things:
- Allow object/model retrieval using `api_url` (was done with the direct
request, now forced through the APIs)
- Fix resulting deprecation warnings on key access (i.e. `object["pk"]`

It also makes the recurse_call wrapper more robust by outputting the
error (`raise from e`) and allowing for retries when `ObjectNotFound` is
thrown.
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@chrisvanrun
chrisvanrun authored Nov 12, 2024
1 parent 8da138a commit b063078
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Showing 5 changed files with 209 additions and 102 deletions.
30 changes: 21 additions & 9 deletions gcapi/apibase.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -143,14 +143,21 @@ def iterate_all(self, params=None) -> Iterator[T]:
yield from current_list
offset += req_count

def detail(self, pk=None, **params) -> Generator[T, dict[Any, Any], T]:
if all((pk, params)):
raise ValueError("Only one of pk or params must be specified")

if pk is not None:
def detail(
self, pk=None, api_url=None, **params
) -> Generator[T, dict[Any, Any], T]:
if sum(bool(arg) for arg in [pk, api_url, params]) != 1:
raise ValueError(
"Exactly one of pk, api_url, or params must be specified"
)
if pk is not None or api_url is not None:
if pk is not None:
request_kwargs = dict(path=urljoin(self.base_path, pk + "/"))
else:
request_kwargs = dict(url=api_url)
try:
result = yield self.yield_request(
method="GET", path=urljoin(self.base_path, pk + "/")
method="GET", **request_kwargs
)
return self.model(**result)
except HTTPStatusError as e:
Expand All @@ -170,6 +177,8 @@ def detail(self, pk=None, **params) -> Generator[T, dict[Any, Any], T]:


class ModifiableMixin(Common):
response_model: type

def _process_request_arguments(self, data):
if data is None:
data = {}
Expand All @@ -188,13 +197,16 @@ def perform_request(self, method, data=None, pk=False):
return (yield from self._execute_request(method, data, pk))

def create(self, **kwargs):
return (yield from self.perform_request("POST", data=kwargs))
result = yield from self.perform_request("POST", data=kwargs)
return self.response_model(**result)

def update(self, pk, **kwargs):
return (yield from self.perform_request("PUT", pk=pk, data=kwargs))
result = yield from self.perform_request("PUT", pk=pk, data=kwargs)
return self.rsponse_model(**result)

def partial_update(self, pk, **kwargs):
return (yield from self.perform_request("PATCH", pk=pk, data=kwargs))
result = yield from self.perform_request("PATCH", pk=pk, data=kwargs)
return result

def delete(self, pk):
return (yield from self.perform_request("DELETE", pk=pk))
61 changes: 33 additions & 28 deletions gcapi/client.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -57,11 +57,11 @@ def download(
if pk is not None:
image = yield from self.detail(pk=pk)
elif url is not None:
image = yield self.yield_request(method="GET", url=url)
image = yield from self.detail(api_url=url)
else:
image = yield from self.detail(**params)

files = image["files"]
files = image.files

# Make sure file destination exists
p = Path(filename).absolute()
Expand All @@ -72,16 +72,16 @@ def download(
# Download the files
downloaded_files = []
for file in files:
if image_type and file["image_type"] != image_type:
if image_type and file.image_type != image_type:
continue

data = (
yield self.yield_request(
method="GET", url=file["file"], follow_redirects=True
method="GET", url=file.file, follow_redirects=True
)
).content

suffix = file["file"].split(".")[-1]
suffix = file.file.split(".")[-1]
local_file = directory / f"{basename}.{suffix}"
with local_file.open("wb") as fp:
fp.write(data)
Expand All @@ -96,11 +96,13 @@ class UploadSessionsAPI(
):
base_path = "cases/upload-sessions/"
model = gcapi.models.RawImageUploadSession
response_model = gcapi.models.RawImageUploadSession


class WorkstationSessionsAPI(APIBase[gcapi.models.Session]):
base_path = "workstations/sessions/"
model = gcapi.models.Session
response_model = gcapi.models.RawImageUploadSession


class ReaderStudyQuestionsAPI(APIBase[gcapi.models.Question]):
Expand All @@ -113,11 +115,13 @@ class ReaderStudyMineAnswersAPI(
):
base_path = "reader-studies/answers/mine/"
model = gcapi.models.ReaderStudy
response_model = gcapi.models.Answer


class ReaderStudyAnswersAPI(ModifiableMixin, APIBase[gcapi.models.Answer]):
base_path = "reader-studies/answers/"
model = gcapi.models.Answer
response_model = gcapi.models.Answer

sub_apis = {"mine": ReaderStudyMineAnswersAPI}

Expand All @@ -142,6 +146,7 @@ class ReaderStudyDisplaySetsAPI(
):
base_path = "reader-studies/display-sets/"
model = gcapi.models.DisplaySet
response_model = gcapi.models.DisplaySetPost


class ReaderStudiesAPI(APIBase[gcapi.models.ReaderStudy]):
Expand Down Expand Up @@ -177,6 +182,7 @@ class AlgorithmsAPI(APIBase[gcapi.models.Algorithm]):
class AlgorithmJobsAPI(ModifiableMixin, APIBase[gcapi.models.HyperlinkedJob]):
base_path = "algorithms/jobs/"
model = gcapi.models.HyperlinkedJob
response_model = gcapi.models.JobPost

@mark_generator
def by_input_image(self, pk):
Expand All @@ -191,6 +197,7 @@ class ArchivesAPI(APIBase[gcapi.models.Archive]):
class ArchiveItemsAPI(ModifiableMixin, APIBase[gcapi.models.ArchiveItem]):
base_path = "archives/items/"
model = gcapi.models.ArchiveItem
response_model = gcapi.models.ArchiveItemPost


class ComponentInterfacesAPI(APIBase[gcapi.models.ComponentInterface]):
Expand All @@ -207,13 +214,12 @@ class UploadsAPI(APIBase[gcapi.models.UserUpload]):
max_retries = 10

def create(self, *, filename):
return (
yield self.yield_request(
method="POST",
path=self.base_path,
json={"filename": str(filename)},
)
result = yield self.yield_request(
method="POST",
path=self.base_path,
json={"filename": str(filename)},
)
return self.model(**result)

def generate_presigned_urls(self, *, pk, s3_upload_id, part_numbers):
url = urljoin(
Expand Down Expand Up @@ -248,8 +254,8 @@ def list_parts(self, *, pk, s3_upload_id):
def upload_fileobj(self, *, fileobj, filename):
user_upload = yield from self.create(filename=filename)

pk = user_upload["pk"]
s3_upload_id = user_upload["s3_upload_id"]
pk = user_upload.pk
s3_upload_id = user_upload.s3_upload_id

try:
parts = yield from self._put_fileobj(
Expand All @@ -261,11 +267,10 @@ def upload_fileobj(self, *, fileobj, filename):
)
raise

return ( # noqa: B901
yield from self.complete_multipart_upload(
pk=pk, s3_upload_id=s3_upload_id, parts=parts
)
result = yield from self.complete_multipart_upload(
pk=pk, s3_upload_id=s3_upload_id, parts=parts
)
return self.model(**result) # noqa: B901

def _put_fileobj(self, *, fileobj, pk, s3_upload_id):
part_number = 1 # s3 uses 1-indexed chunks
Expand Down Expand Up @@ -502,7 +507,7 @@ def _upload_image_files(self, *, files, **kwargs):

return (
yield from self.__org_api_meta.raw_image_upload_sessions.create(
uploads=[u["api_url"] for u in uploads], **kwargs
uploads=[u.api_url for u in uploads], **kwargs
)
)

Expand Down Expand Up @@ -677,7 +682,7 @@ def run_external_job(self, *, algorithm: str, inputs: dict[str, Any]):
raw_image_upload_session = (
yield from self._upload_image_files(files=value)
)
i["upload_session"] = raw_image_upload_session["api_url"]
i["upload_session"] = raw_image_upload_session.api_url
elif isinstance(value, str):
i["image"] = value
elif ci["super_kind"].lower() == "file": # type: ignore
Expand All @@ -686,7 +691,7 @@ def run_external_job(self, *, algorithm: str, inputs: dict[str, Any]):
f"Only a single file can be provided for {ci['title']}." # type: ignore
)
upload = yield from self._upload_file(value)
i["user_upload"] = upload["api_url"]
i["user_upload"] = upload.api_url
else:
i["value"] = value
job["inputs"].append(i) # type: ignore
Expand All @@ -703,13 +708,13 @@ def update_archive_item(
First, retrieve the archive items from your archive:
archive = next(client.archives.iterate_all(params={"slug": "..."}))
items = list(
client.archive_items.iterate_all(params={"archive": archive["pk"]})
client.archive_items.iterate_all(params={"archive": archive.pk})
)
To then add, for example, a PDF report and a lung volume
value to the first archive item , provide the interface slugs together
with the respective value or file path as follows:
client.update_archive_item(
archive_item_pk=items[0]['id'],
archive_item_pk=items[0].id,
values={
"report": [...],
"lung-volume": 1.9,
Expand Down Expand Up @@ -754,7 +759,7 @@ def update_archive_item(
raw_image_upload_session = (
yield from self._upload_image_files(files=value)
)
i["upload_session"] = raw_image_upload_session["api_url"]
i["upload_session"] = raw_image_upload_session.api_url
elif isinstance(value, str):
i["image"] = value
elif ci.super_kind.lower() == "file":
Expand All @@ -764,7 +769,7 @@ def update_archive_item(
f"to a {ci.slug} interface."
)
upload = yield from self._upload_file(value)
i["user_upload"] = upload["api_url"]
i["user_upload"] = upload.api_url
else:
i["value"] = value
civs["values"].append(i)
Expand Down Expand Up @@ -870,19 +875,19 @@ def add_cases_to_reader_study(
super_kind = interface.super_kind.casefold()
if super_kind == "image":
yield from self._upload_image_files(
display_set=ds["pk"], interface=slug, files=value
display_set=ds.pk, interface=slug, files=value
)
data = {}
elif super_kind == "file":
upload = yield from self._upload_file(value)
data["user_upload"] = upload["api_url"]
data["user_upload"] = upload.api_url
else:
data["value"] = value
if data:
values.append(data)
yield from self.__org_api_meta.reader_studies.display_sets.partial_update(
pk=ds["pk"], values=values
pk=ds.pk, values=values
)

res.append(ds["pk"])
res.append(ds.pk)
return res # noqa: B901
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