geoseeq 0.5.6a11__py3-none-any.whl → 0.5.6a12__py3-none-any.whl

geoseeq/cli/main.py

@@ -53,7 +53,7 @@ def version():
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    click.echo('0.5.6a11')  # remember to update setup
+    click.echo('0.5.6a12')  # remember to update setup
 
 
 @main.group('advanced')

geoseeq/cli/upload/upload.py

@@ -36,8 +36,9 @@ hidden_option = click.option('--hidden/--no-hidden', default=False, help='Upload
 
 @click.command('files')
 @use_common_state
-@click.option('--cores', default=1, help='Number of uploads to run in parallel')
-@click.option('--threads-per-upload', default=4, help='Number of threads used to upload each file')
+@click.option('--cores', default=1, help='Number of uploads to run in parallel', show_default=True)
+@click.option('--threads-per-upload', default=4, help='Number of threads used to upload each file', show_default=True)
+@click.option('--num-retries', default=3, help='Number of times to retry a failed upload', show_default=True)
 @yes_option
 @private_option
 @link_option
@@ -45,10 +46,11 @@ hidden_option = click.option('--hidden/--no-hidden', default=False, help='Upload
 @hidden_option
 @no_new_versions_option
 @click.option('-n', '--geoseeq-file-name', default=None, multiple=True,
-              help='Specify a different name for the file on GeoSeeq than the local file name.')
+              help='Specify a different name for the file on GeoSeeq than the local file name.',
+              show_default=True)
 @folder_id_arg
 @click.argument('file_paths', type=click.Path(exists=True), nargs=-1)
-def cli_upload_file(state, cores, threads_per_upload, yes, private, link_type, recursive, hidden, no_new_versions, geoseeq_file_name, folder_id, file_paths):
+def cli_upload_file(state, cores, threads_per_upload, num_retries, yes, private, link_type, recursive, hidden, no_new_versions, geoseeq_file_name, folder_id, file_paths):
     """Upload files to GeoSeeq.
 
     This command uploads files to either a sample or project on GeoSeeq. It can be used to upload
@@ -93,6 +95,8 @@ def cli_upload_file(state, cores, threads_per_upload, yes, private, link_type, r
 
     ---
     """
+    if num_retries < 1:
+        raise click.UsageError('--num-retries must be at least 1')
     knex = state.get_knex()
     result_folder = handle_folder_id(knex, folder_id, yes=yes, private=private, create=True)
     if geoseeq_file_name:
@@ -113,6 +117,7 @@ def cli_upload_file(state, cores, threads_per_upload, yes, private, link_type, r
         log_level=state.log_level,
         no_new_versions=no_new_versions,
         use_cache=state.use_cache,
+        num_retries=num_retries,
     )
     for geoseeq_file_name, file_path in name_pairs:
         if isfile(file_path):

geoseeq/result/file_upload.py

@@ -188,9 +188,11 @@ class ResultFileUpload:
                     f"Upload for part {num + 1} failed. Attempt {attempts + 1} of {max_retries}."
                 )
                 attempts += 1
-                if attempts == max_retries:
+                if attempts >= max_retries:
                     raise e
-                time.sleep(10**attempts)  # exponential backoff, (10 ** 2)s default max
+
+                retry_time = min(8 ** attempts, 120)  # exponential backoff, max 120s
+                time.sleep(retry_time)
             
         etag = http_response.headers["ETag"].replace('"', "")
         blob = {"ETag": etag, "PartNumber": num + 1}

geoseeq/upload_download_manager.py

@@ -21,7 +21,8 @@ def _make_in_process_logger(log_level):
 def _upload_one_file(args):
     (result_file, filepath, session, progress_tracker,
      link_type, overwrite, log_level, parallel_uploads,
-     use_cache, no_new_versions, threads_per_upload) = args
+     use_cache, no_new_versions, threads_per_upload,
+     num_retries) = args
     if parallel_uploads:
         _make_in_process_logger(log_level)
     if link_type == 'upload':
@@ -30,7 +31,7 @@ def _upload_one_file(args):
             filepath,
             session=session, overwrite=overwrite, progress_tracker=progress_tracker,
             threads=threads_per_upload, use_cache=use_cache,
-            no_new_versions=no_new_versions
+            no_new_versions=no_new_versions, max_retries=num_retries,
         )
     else:
         result_file.link_file(link_type, filepath)
@@ -48,6 +49,7 @@ class GeoSeeqUploadManager:
                  log_level=logging.WARNING,
                  overwrite=True,
                  no_new_versions=False,
+                 num_retries=3,
                  use_cache=True):
         self.session = session
         self.n_parallel_uploads = n_parallel_uploads
@@ -59,6 +61,7 @@ class GeoSeeqUploadManager:
         self.no_new_versions = no_new_versions
         self.use_cache = use_cache
         self.threads_per_upload = threads_per_upload
+        self.num_retries = num_retries
 
     def add_result_file(self, result_file, local_path):
         self._result_files.append((result_file, local_path))
@@ -84,7 +87,7 @@ class GeoSeeqUploadManager:
                 self.session, self.progress_tracker_factory(local_path),
                 self.link_type, self.overwrite, self.log_level,
                 self.n_parallel_uploads > 1, self.use_cache, self.no_new_versions,
-                self.threads_per_upload
+                self.threads_per_upload, self.num_retries
             ) for result_file, local_path in self._result_files
         ]
         out = []

{geoseeq-0.5.6a11.dist-info → geoseeq-0.5.6a12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a11
+Version: 0.5.6a12
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a11.dist-info → geoseeq-0.5.6a12.dist-info}/RECORD

@@ -11,7 +11,7 @@ geoseeq/project.py,sha256=-9Y2ik0-BpT3iqh89v8VQBbdadhI58oaUP9oZK8oetc,13741
 geoseeq/remote_object.py,sha256=Es-JlAz8iLRmCpAzh1MOwUh2MqtbuQM-p8wHIBAqNlQ,7131
 geoseeq/sample.py,sha256=whgEVk6GnDJJLjn5uTOqFqRtVxZD3BgjTo7brAC5noU,7981
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
-geoseeq/upload_download_manager.py,sha256=aydSVTAjyupd4gkqmImtcSTXEPBAAqQ1HFgfAk83Scw,7605
+geoseeq/upload_download_manager.py,sha256=-s2Zdru_O2YWThAdmXRksIx2q8RwSOEZ2nLvm1VM4EM,7738
 geoseeq/user.py,sha256=tol8i1UGLRrbMw5jeJDnna1ikRgrCDd50Jxz0a1lSgg,690
 geoseeq/utils.py,sha256=PDRiEQIZYTcfEV9AYvloQVvfqs5JaebcFZodAa2SUW8,3577
 geoseeq/work_orders.py,sha256=5uLVVfdKE8qh4gGaHkdBpXJGRTujuSg59knWCqEET4A,8071
@@ -22,7 +22,7 @@ geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
 geoseeq/cli/download.py,sha256=_upzZo08K0fAPbEsyi1uN0HGNUaY1pl6OoGPcWmvSUY,17765
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=zsPFQY__lqMeG_l4GTjonmddbe8p1FHjksouuK2U07c,3260
+geoseeq/cli/main.py,sha256=lqRT8Y62SqLQs9J_P7TCZIZ9CGk6sMphKOALz9TSQ0o,3260
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/run.py,sha256=bx2AV6VIqOSTlxUda78xl0XxcZ8TXlQx02-e7iLQPwI,3838
@@ -37,7 +37,7 @@ geoseeq/cli/shared_params/id_handlers.py,sha256=501K9sCVkI0YGDQ62vXk_DM5lMMDrdB5
 geoseeq/cli/shared_params/obj_getters.py,sha256=ZSkt6LnDkVFlNVYKgLrjzg60-6BthZMr3eeD3HNqzac,2741
 geoseeq/cli/shared_params/opts_and_args.py,sha256=LrDkv9WtUryM4uUMXPRk04-EBcTQ7q5V6Yu-XRDUvvA,2083
 geoseeq/cli/upload/__init__.py,sha256=3C9_S9t7chmYU-2ot89NV03x-EtmsjibulErKaU9w1k,627
-geoseeq/cli/upload/upload.py,sha256=_ZR2tkugaB71rVTJFAwRCZLedqGO58sgTsHILebfvDs,9370
+geoseeq/cli/upload/upload.py,sha256=whhj-cX324_N_IQKuR3t-Zw4BFzDz7NHzMrmWg5aqiE,9688
 geoseeq/cli/upload/upload_advanced.py,sha256=Jq5eGe-wOdrzxGWVwaFPg0BAJcW0YSx_eHEmYjJeKuA,3434
 geoseeq/cli/upload/upload_reads.py,sha256=EMGqyZf11xwN4v2j8gNxMagTbE4kaOd-_hwupmg5I-8,10670
 geoseeq/contrib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -64,7 +64,7 @@ geoseeq/plotting/map/overlay.py,sha256=4VmxqOESTQra9tPr8b8OLEUhJSit9lNipabeSznEY
 geoseeq/result/__init__.py,sha256=IFHIyRV8ZzuKIfwfze1SXgcKwNMcSgMAknLHMkwjXIU,356
 geoseeq/result/bioinfo.py,sha256=QQtbyogrdro9avJSN0713sxLVnVeA24mFw3hWtKDKyw,1782
 geoseeq/result/file_download.py,sha256=vbYo2B4JshTIqLaklcgcBb7NY9cD5pMkas95GuQxW8s,5776
-geoseeq/result/file_upload.py,sha256=z3ImHlVhli6ZwOHP7GvJqxnVxKYpMyBojqrpdBSBJIs,13176
+geoseeq/result/file_upload.py,sha256=qQ2F28W6ieLoEsbqCWr61cQ8hYlNaKkhn4DBQ5xqR-I,13214
 geoseeq/result/result_file.py,sha256=1Yj9fkZhds3J-tay6eNH2-EHi00MovHGV1M80_ckHD8,8677
 geoseeq/result/result_folder.py,sha256=6porOXPh7Tpxw3oX5yMRPYQzNCGYqszqmFJd3SwQmTc,11122
 geoseeq/result/utils.py,sha256=C-CxGzB3WddlnRiqFSkrY78I_m0yFgNqsTBRzGU-y8Q,2772
@@ -80,9 +80,9 @@ geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_api_client.py,sha256=TS5njc5pcPP_Ycy-ljcfPVT1hQRBsFVdQ0lCqBmoesU,12810
 tests/test_plotting.py,sha256=TcTu-2ARr8sxZJ7wPQxmbs3-gHw7uRvsgrhhhg0qKik,784
-geoseeq-0.5.6a11.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.5.6a11.dist-info/METADATA,sha256=sVpz2que_a-pWGG7WNGLz2IFGoNOeofn27ZKxqZdsts,4806
-geoseeq-0.5.6a11.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-geoseeq-0.5.6a11.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.5.6a11.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.5.6a11.dist-info/RECORD,,
+geoseeq-0.5.6a12.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.5.6a12.dist-info/METADATA,sha256=DTEadRCMzytqJtg9vPNagyrMCY8l8gIslgIr7PaOA1o,4806
+geoseeq-0.5.6a12.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+geoseeq-0.5.6a12.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.5.6a12.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.5.6a12.dist-info/RECORD,,