geoseeq 0.6.12.dev2__tar.gz → 0.6.13.dev1__tar.gz

{geoseeq-0.6.12.dev2 → geoseeq-0.6.13.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.12.dev2
+Version: 0.6.13.dev1
 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 → geoseeq-0.6.13.dev1}/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('0.6.13dev1')  # remember to update pyproject.toml
 
 
 @main.group('advanced')

{geoseeq-0.6.12.dev2 → geoseeq-0.6.13.dev1}/geoseeq/id_constructors/from_ids.py

@@ -27,6 +27,7 @@ from geoseeq.knex import with_knex
 
 def _generic_from_id(knex, id, from_uuid_func, from_name_func):
     """Return the object which the id points to."""
+    logger.info(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-0.6.12.dev2 → geoseeq-0.6.13.dev1}/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.info(f"Checking for knex in args: {args}, kwargs: {kwargs}")
         any_knex = any([isinstance(arg, Knex) for arg in args])
         if any_knex:
+            logger.info("knex found in args")
             return func(*args, **kwargs)
         else:
+            logger.info("knex not found in args")
             varnames = [
                 varname for varname in func.__code__.co_varnames
                 if varname != "knex"
             ]
             kwargs.update(zip(varnames, args))
             if "knex" not in kwargs:
+                logger.info("knex not found in kwargs")
                 profile = kwargs.pop("profile", "")
                 kwargs['knex'] = Knex.load_profile(profile=profile)
             # reorder kwargs to match the function signature

{geoseeq-0.6.12.dev2 → geoseeq-0.6.13.dev1}/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 → geoseeq-0.6.13.dev1}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: geoseeq
-Version: 0.6.12.dev2
+Version: 0.6.13.dev1
 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 → geoseeq-0.6.13.dev1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "geoseeq"
-version = "0.6.12dev2"
+version = "0.6.13dev1"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]