geoseeq 0.5.6a15__tar.gz → 0.5.6a16__tar.gz

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a15
+Version: 0.5.6a16
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/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('0.5.6a15')  # remember to update setup
+    click.echo('0.5.6a16')  # remember to update setup
 
 
 @main.group('advanced')
@@ -101,4 +101,20 @@ def cli_config(yes, api_token, endpoint, profile, overwrite):
             click.echo('You must accept the EULA to use the GeoSeeq API.')
             return
     set_profile(api_token, endpoint=endpoint, profile=profile, overwrite=overwrite)
-    click.echo(f'Profile configured.')
+    click.echo(f'Profile configured.')
+
+
+@main.command('clear-cache')
+@yes_option
+def cli_clear_cache(yes):
+    """Clear the local cache.
+
+    ---
+    
+    Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
+    Run `geoseeq eula show` to view the EULA.
+    """
+    from geoseeq.file_system_cache import GEOSEEQ_CACHE_DIR
+    import shutil
+    if yes or click.confirm('Are you sure you want to clear the cache?'):
+        shutil.rmtree(GEOSEEQ_CACHE_DIR, ignore_errors=True)

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/geoseeq/cli/upload/upload.py

@@ -40,7 +40,7 @@ hidden_option = click.option('--hidden/--no-hidden', default=False, help='Upload
 @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)
-@click.option('--chunk-size-mb', default=5, help='Size of chunks to upload in MB', show_default=True)
+@click.option('--chunk-size-mb', default=-1, help='Size of chunks to upload in MB', show_default=True)
 @ignore_errors_option
 @yes_option
 @private_option
@@ -122,8 +122,8 @@ def cli_upload_file(state, cores, threads_per_upload, num_retries, chunk_size_mb
         use_cache=state.use_cache,
         num_retries=num_retries,
         ignore_errors=ignore_errors,
-        session=knex.new_session(),
-        chunk_size_mb=chunk_size_mb,
+        session=None, #knex.new_session(),
+        chunk_size_mb=chunk_size_mb if chunk_size_mb > 0 else None,
     )
     for geoseeq_file_name, file_path in name_pairs:
         if isfile(file_path):

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/geoseeq/result/file_upload.py

@@ -175,6 +175,7 @@ class ResultFileUpload:
         attempts = 0
         while attempts < max_retries:
             try:
+                # url = url.replace("s3.wasabisys.com", "s3.us-east-1.wasabisys.com")
                 logger.debug(f"Uploading part {num + 1} to {url}. Size: {len(file_chunk)} bytes.")
                 if session:
                     http_response = session.put(url, data=file_chunk)
@@ -192,7 +193,7 @@ class ResultFileUpload:
                     raise e
 
                 retry_time = min(8 ** attempts, 120)  # exponential backoff, max 120s
-                retry_time *= 0.8 + (random() * 0.4)  # randomize to avoid thundering herd
+                retry_time *= 0.6 + (random() * 0.8)  # randomize to avoid thundering herd
                 logger.debug(f"Retrying upload for part {num + 1} in {retry_time} seconds.")
                 time.sleep(retry_time)
             
@@ -250,7 +251,7 @@ class ResultFileUpload:
         filepath,
         file_size,
         optional_fields=None,
-        chunk_size=FIVE_MB,
+        chunk_size=None,
         max_retries=3,
         session=None,
         progress_tracker=None,
@@ -259,6 +260,11 @@ class ResultFileUpload:
     ):
         """Upload a file to S3 using the multipart upload process."""
         logger.info(f"Uploading {filepath} to S3 using multipart upload.")
+        if not chunk_size:
+            chunk_size = FIVE_MB
+            if file_size >= 10 * FIVE_MB:
+                chunk_size = 5 * FIVE_MB
+        logger.debug(f"Using chunk size of {chunk_size} bytes.")
         resumable_upload_tracker = None
         if use_cache and file_size > 10 * FIVE_MB:  # only use resumable upload tracker for larger files
             resumable_upload_tracker = ResumableUploadTracker(filepath, chunk_size)

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/geoseeq/upload_download_manager.py

@@ -23,7 +23,7 @@ def _upload_one_file(args):
      link_type, overwrite, log_level, parallel_uploads,
      use_cache, no_new_versions, threads_per_upload,
      num_retries, ignore_errors, chunk_size_mb) = args
-    chunk_size = chunk_size_mb * 1024 * 1024
+    chunk_size = chunk_size_mb * 1024 * 1024 if chunk_size_mb else None
     if parallel_uploads:
         _make_in_process_logger(log_level)
     try:

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a15
+Version: 0.5.6a16
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a15 → geoseeq-0.5.6a16}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "geoseeq"
-version = "0.5.6a15"
+version = "0.5.6a16"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]