From 1c3ca4caeae1f847244f3660f57e1510dafd98cd Mon Sep 17 00:00:00 2001 From: Eleanor Lewis Date: Thu, 11 Jul 2024 16:45:51 -0700 Subject: [PATCH 1/3] check for presence of ident instead of state --- pori_python/ipr/connection.py | 87 +++++++++++++++++++---------------- 1 file changed, 47 insertions(+), 40 deletions(-) diff --git a/pori_python/ipr/connection.py b/pori_python/ipr/connection.py index b267f06..8ad5453 100644 --- a/pori_python/ipr/connection.py +++ b/pori_python/ipr/connection.py @@ -18,14 +18,14 @@ def __init__(self, username: str, password: str, url: str = DEFAULT_URL): self.username = username self.password = password self.headers = { - 'Accept': 'application/json', - 'Content-Type': 'application/json', - 'Content-Encoding': 'deflate', + "Accept": "application/json", + "Content-Type": "application/json", + "Content-Encoding": "deflate", } self.cache: Dict[str, List[Dict]] = {} self.request_count = 0 - def request(self, endpoint: str, method: str = 'GET', **kwargs) -> Dict: + def request(self, endpoint: str, method: str = "GET", **kwargs) -> Dict: """Request wrapper to handle adding common headers and logging Args: @@ -35,9 +35,9 @@ def request(self, endpoint: str, method: str = 'GET', **kwargs) -> Dict: Returns: dict: the json response as a python dict """ - url = f'{self.url}/{endpoint}' + url = f"{self.url}/{endpoint}" self.request_count += 1 - headers = kwargs.pop('headers', self.headers) + headers = kwargs.pop("headers", self.headers) resp = requests.request( method, url, headers=headers, auth=(self.username, self.password), **kwargs ) @@ -47,7 +47,7 @@ def request(self, endpoint: str, method: str = 'GET', **kwargs) -> Dict: # try to get more error details message = str(err) try: - message += ' ' + resp.json()['error']['message'] + message += " " + resp.json()["error"]["message"] except Exception: pass @@ -58,8 +58,8 @@ def post(self, uri: str, data: Dict = {}, **kwargs) -> Dict: """Convenience method for making post requests""" return self.request( uri, - method='POST', - data=zlib.compress(json.dumps(data, allow_nan=False).encode('utf-8')), + method="POST", + data=zlib.compress(json.dumps(data, allow_nan=False).encode("utf-8")), **kwargs, ) @@ -67,8 +67,8 @@ def get(self, uri: str, data: Dict = {}, **kwargs) -> Dict: """Convenience method for making get requests""" return self.request( uri, - method='GET', - data=zlib.compress(json.dumps(data, allow_nan=False).encode('utf-8')), + method="GET", + data=zlib.compress(json.dumps(data, allow_nan=False).encode("utf-8")), **kwargs, ) @@ -76,48 +76,51 @@ def upload_report( self, content: Dict, mins_to_wait: int = 5, async_upload: bool = False ) -> Dict: if async_upload: - initial_result = self.post('reports-async', content) + initial_result = self.post("reports-async", content) + report_id = initial_result["ident"] def check_status(interval: int = 5, num_attempts: int = 5): for i in range(num_attempts): - logger.info(f'checking report loading status in {interval} seconds') + logger.info(f"checking report loading status in {interval} seconds") time.sleep(interval) - current_status = self.get(f'reports-async/{report_id}') - if current_status['state'] not in [ - 'active', - 'ready', - 'waiting', - 'completed', - 'failed', + current_status = self.get(f"reports-async/{report_id}") + + if current_status.get("ident", False): + return current_status + + if current_status["state"] not in [ + "active", + "ready", + "waiting", + "completed", + "failed", ]: raise Exception( - f'async report upload in unexpected state: {current_status}' + f"async report upload in unexpected state: {current_status}" ) - if current_status['state'] == 'failed': + if current_status["state"] == "failed": raise Exception( f'report upload failed with reason: {current_status["failedReason"]}' ) - if current_status['state'] in ['ready', 'completed']: - return current_status return current_status current_status = check_status() - if current_status['state'] in ['active', 'waiting']: + if current_status["state"] in ["active", "waiting"]: current_status = check_status(interval=30) - if current_status['state'] in ['active', 'waiting']: + if current_status["state"] in ["active", "waiting"]: current_status = check_status(interval=60, num_attempts=mins_to_wait) - if current_status['state'] in ['active', 'waiting']: + if current_status["state"] in ["active", "waiting"]: raise Exception( - f'async report upload taking longer than expected: {current_status}' + f"async report upload taking longer than expected: {current_status}" ) return current_status else: - return self.post('reports', content) + return self.post("reports", content) def set_analyst_comments(self, report_id: str, data: Dict) -> Dict: """ @@ -128,12 +131,14 @@ def set_analyst_comments(self, report_id: str, data: Dict) -> Dict: Pending: https://www.bcgsc.ca/jira/browse/DEVSU-1177 """ return self.request( - f'/reports/{report_id}/summary/analyst-comments', - method='PUT', - data=zlib.compress(json.dumps(data, allow_nan=False).encode('utf-8')), + f"/reports/{report_id}/summary/analyst-comments", + method="PUT", + data=zlib.compress(json.dumps(data, allow_nan=False).encode("utf-8")), ) - def post_images(self, report_id: str, files: Dict[str, str], data: Dict[str, str] = {}) -> None: + def post_images( + self, report_id: str, files: Dict[str, str], data: Dict[str, str] = {} + ) -> None: """ Post images to the report """ @@ -147,27 +152,29 @@ def post_images(self, report_id: str, files: Dict[str, str], data: Dict[str, str if not os.path.exists(path): raise FileNotFoundError(path) current_files[key] = path - open_files = {k: open(f, 'rb') for (k, f) in current_files.items()} + open_files = {k: open(f, "rb") for (k, f) in current_files.items()} try: resp = self.request( - f'reports/{report_id}/image', - method='POST', + f"reports/{report_id}/image", + method="POST", data=data, files=open_files, headers={}, ) for status in resp: - if status.get('upload') != 'successful': - image_errors.add(status['key']) + if status.get("upload") != "successful": + image_errors.add(status["key"]) finally: for handler in open_files.values(): handler.close() start_index += IMAGE_MAX if image_errors: - raise ValueError(f'Error uploading images ({", ".join(sorted(list(image_errors)))})') + raise ValueError( + f'Error uploading images ({", ".join(sorted(list(image_errors)))})' + ) def get_spec(self) -> Dict: """ Get the current IPR spec, for the purposes of current report upload fields """ - return self.request('/spec.json', method='GET') + return self.request("/spec.json", method="GET") From d2181701281fe2745d0583627325e42beef8c298 Mon Sep 17 00:00:00 2001 From: Eleanor Lewis Date: Thu, 11 Jul 2024 16:48:04 -0700 Subject: [PATCH 2/3] minor cleanup --- pori_python/ipr/connection.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/pori_python/ipr/connection.py b/pori_python/ipr/connection.py index 8ad5453..dfb6e0f 100644 --- a/pori_python/ipr/connection.py +++ b/pori_python/ipr/connection.py @@ -89,20 +89,21 @@ def check_status(interval: int = 5, num_attempts: int = 5): if current_status.get("ident", False): return current_status + if current_status["state"] == "failed": + raise Exception( + f'async report upload failed with reason: {current_status["failedReason"]}' + ) + if current_status["state"] not in [ "active", "ready", "waiting", "completed", - "failed", ]: raise Exception( f"async report upload in unexpected state: {current_status}" ) - if current_status["state"] == "failed": - raise Exception( - f'report upload failed with reason: {current_status["failedReason"]}' - ) + return current_status current_status = check_status() From 70ded3c8b506c49726a075a622e511e11c92fac5 Mon Sep 17 00:00:00 2001 From: Eleanor Lewis Date: Thu, 11 Jul 2024 16:51:06 -0700 Subject: [PATCH 3/3] lint with black --- pori_python/ipr/connection.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/pori_python/ipr/connection.py b/pori_python/ipr/connection.py index dfb6e0f..5f4e846 100644 --- a/pori_python/ipr/connection.py +++ b/pori_python/ipr/connection.py @@ -137,9 +137,7 @@ def set_analyst_comments(self, report_id: str, data: Dict) -> Dict: data=zlib.compress(json.dumps(data, allow_nan=False).encode("utf-8")), ) - def post_images( - self, report_id: str, files: Dict[str, str], data: Dict[str, str] = {} - ) -> None: + def post_images(self, report_id: str, files: Dict[str, str], data: Dict[str, str] = {}) -> None: """ Post images to the report """ @@ -170,9 +168,7 @@ def post_images( handler.close() start_index += IMAGE_MAX if image_errors: - raise ValueError( - f'Error uploading images ({", ".join(sorted(list(image_errors)))})' - ) + raise ValueError(f'Error uploading images ({", ".join(sorted(list(image_errors)))})') def get_spec(self) -> Dict: """