geoseeq 0.6.12.dev2__py3-none-any.whl → 0.6.13__py3-none-any.whl

geoseeq/cli/main.py

@@ -54,7 +54,7 @@ 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('0.6.12dev2')  # remember to update pyproject.toml
+    click.echo('0.6.13')  # remember to update pyproject.toml
 
 
 @main.group('advanced')

geoseeq/id_constructors/from_ids.py

@@ -1,4 +1,5 @@
 from geoseeq import GeoseeqNotFoundError
+import logging
 from .from_uuids import (
     org_from_uuid,
     project_from_uuid,
@@ -24,9 +25,12 @@ from .from_names import (
 from .utils import is_grn_or_uuid, is_name
 from geoseeq.knex import with_knex
 
+logger = logging.getLogger("geoseeq_api")  # Same name as calling module
+
 
 def _generic_from_id(knex, id, from_uuid_func, from_name_func):
     """Return the object which the id points to."""
+    logger.debug(f'Getting object from id: {id}, knex: {knex}, from_uuid_func: {from_uuid_func}, from_name_func: {from_name_func}')
     if is_grn_or_uuid(id):
         id = id.split(':')[-1]  # if this is a GRN, get the UUID. Won't hurt if it's already a UUID.
         return from_uuid_func(knex, id)

geoseeq/knex.py

@@ -222,16 +222,20 @@ class Knex:
 def with_knex(func):
     def wrapper(*args, **kwargs):
         # check if any of the arguments are a knex instance
+        logger.debug(f"Checking for knex in args: {args}, kwargs: {kwargs}")
         any_knex = any([isinstance(arg, Knex) for arg in args])
         if any_knex:
+            logger.debug("knex found in args args: {args}, kwargs: {kwargs}")
             return func(*args, **kwargs)
         else:
+            logger.debug("knex not found in args args: {args}, kwargs: {kwargs}")
             varnames = [
                 varname for varname in func.__code__.co_varnames
                 if varname != "knex"
             ]
             kwargs.update(zip(varnames, args))
             if "knex" not in kwargs:
+                logger.debug("knex not found in kwargs args: {args}, kwargs: {kwargs}")
                 profile = kwargs.pop("profile", "")
                 kwargs['knex'] = Knex.load_profile(profile=profile)
             # reorder kwargs to match the function signature

geoseeq/upload_download_manager.py

@@ -127,17 +127,16 @@ class GeoSeeqUploadManager:
 
 
 def _download_one_file(args):
-    original_url, file_path, key, callback, pbar, ignore_errors, head, log_level, parallel_downloads = args
+    url, file_path, key, callback, pbar, ignore_errors, head, log_level, parallel_downloads = args
     if parallel_downloads:
         _make_in_process_logger(log_level)
-    if isinstance(original_url, ResultFile):
-        url = original_url.get_download_url()
+    if dirname(file_path):
+        makedirs(dirname(file_path), exist_ok=True)
+    if isinstance(url, ResultFile):
+        local_path = url.download(filename=file_path, progress_tracker=pbar, head=head)
     else:
-        url = original_url
-    try:
-        if dirname(file_path):
-            makedirs(dirname(file_path), exist_ok=True)
         local_path = download_url(url, filename=file_path, progress_tracker=pbar, head=head)
+    try:
         if callback is not None:
             callback_result = callback(local_path)
         else:

{geoseeq-0.6.12.dev2.dist-info → geoseeq-0.6.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.12.dev2
+Version: 0.6.13
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.6.12.dev2.dist-info → geoseeq-0.6.13.dist-info}/RECORD

@@ -4,14 +4,14 @@ geoseeq/blob_constructors.py,sha256=AkWpDQY0EdGMxF1p6eRspyHKubcUdiW4it-_Q7S2QWk,
 geoseeq/bulk_creators.py,sha256=pdn-Dv7yv5SFv-PfDuQbuOnw2W4-BfIfRJVRAhM8U6s,2115
 geoseeq/constants.py,sha256=z_ninEd7WsS5DaLntdR-sqAFib6Ie22jlhPKzLvLerw,449
 geoseeq/file_system_cache.py,sha256=HzVZWtwLD2fjWWSo_UfWmGeBltm9He4lP_OqzKwNGWg,4138
-geoseeq/knex.py,sha256=GXPsV65w1co1OvpB4pngH4f5I1p1AAxDWX7e2QkMXw0,7987
+geoseeq/knex.py,sha256=zcjafsmUn9SC3LlRnvvaXpr-pHYZ0IXk7LpzuUoE3MI,8312
 geoseeq/organization.py,sha256=bJkYL8_D-k6IYAaii2ZbxjwYnXy6lvu6iLXscxKlA3w,2542
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
 geoseeq/project.py,sha256=kN6m1N4Tlud7saU03Sbir-oIBnXet_Cwi2OVVdaeag0,13929
 geoseeq/remote_object.py,sha256=GYN6PKU7Zz3htIdpFjfZiFejzGqqJHbJyKlefM1Eixk,7151
 geoseeq/sample.py,sha256=nlvmSy2WmiOMamkulNRloFPX7E9jVs34m1vO1PSOrHU,8336
 geoseeq/search.py,sha256=gawad6Cx5FxJBPlYkXWb-UKAO-UC0_yhvyU9Ca1kaNI,3388
-geoseeq/upload_download_manager.py,sha256=n9gghhN6WAlV6kpKXhR8inyKilo3vexRVWJSiwlujtI,9372
+geoseeq/upload_download_manager.py,sha256=TCdTKtQTPIakVuvpXa0OHgOBy7mtV0gHBqHDJYc2UO0,9361
 geoseeq/user.py,sha256=tol8i1UGLRrbMw5jeJDnna1ikRgrCDd50Jxz0a1lSgg,690
 geoseeq/utils.py,sha256=ZXpWb2MetUIeLrExiXb7IaOXYrW1pvrdP3o0KWzbwCs,4035
 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=W3OswqpHg1thzW6CJ7IcSS0Te2LA2WfgYISQMSl4GQg,18921
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=Vf6c8exFrzRQfUggMvzNAdP98bDF1ekweoMGFsKzEs8,3922
+geoseeq/cli/main.py,sha256=3ocIYX6j1YMNFqxXoLCbcfFdUubBC06r1y-c6g0bIak,3918
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/project.py,sha256=V5SdXm2Hwo2lxrkpwRDedw-mAE4XnM2uwT-Gj1D90VQ,3030
@@ -50,7 +50,7 @@ geoseeq/contrib/ncbi/cli.py,sha256=j9zEcaZPTryK3a4xluRxigcJKDhRpRxbp3KZSx-Bfhk,2
 geoseeq/contrib/ncbi/setup_logging.py,sha256=Tp1bY1U0f-o739aHpvVYriG2qdd1lFvCYBXZeXQgt-w,175
 geoseeq/id_constructors/__init__.py,sha256=w5E0PNQ9UuAxBeZbDI7KBnUoERd85gGz3nScz45bd2o,126
 geoseeq/id_constructors/from_blobs.py,sha256=aj7M7NRpKGs3u3xUvuFJwmJdFeIcJPmaI2_bhwbFfEs,5702
-geoseeq/id_constructors/from_ids.py,sha256=bbAJX4LnuN70v9bny6N-jAwOudb2-ztHvlMBgRuSDz0,3151
+geoseeq/id_constructors/from_ids.py,sha256=vwv_R1uZ5hdeUvpKmNLOTz02PCvwfd6yQ7aAXqi0hZo,3372
 geoseeq/id_constructors/from_names.py,sha256=RqgFjDsAwQcidMkZwX7oB00OvBAKTiilHYetTPogJ40,4174
 geoseeq/id_constructors/from_uuids.py,sha256=5NrQoRBNBfiB48SIB6QFZvO0lxNrxAHbu1MDkNRSu_4,3305
 geoseeq/id_constructors/resolvers.py,sha256=8hp5xJSCoZrAXtMT54Hp4okt63l909XqJU3IQx-VCgc,2676
@@ -85,9 +85,9 @@ 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-0.6.12.dev2.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.6.12.dev2.dist-info/METADATA,sha256=lB84tEqqjrvgoJUV-DdiFSzFYxjKLtjr78vXQzRMUzg,4937
-geoseeq-0.6.12.dev2.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-geoseeq-0.6.12.dev2.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
-geoseeq-0.6.12.dev2.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.6.12.dev2.dist-info/RECORD,,
+geoseeq-0.6.13.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.6.13.dist-info/METADATA,sha256=yt0Gn0_0cxRUm4UuiWaDm_uF2epCCktxslPiD3S6Bd4,4932
+geoseeq-0.6.13.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+geoseeq-0.6.13.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.6.13.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.6.13.dist-info/RECORD,,