geoseeq 0.6.12.dev1__tar.gz → 0.6.12.dev2__tar.gz
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- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/PKG-INFO +1 -1
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/main.py +1 -1
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/upload_download_manager.py +12 -11
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq.egg-info/PKG-INFO +1 -1
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/pyproject.toml +1 -1
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/LICENSE +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/README.md +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/app.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/blob_constructors.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/bulk_creators.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/constants.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/copy.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/detail.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/download.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/fastq_utils.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/get_eula.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/manage.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/progress_bar.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/project.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/raw.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/run.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/search.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/shared_params/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/shared_params/common_state.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/shared_params/config.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/shared_params/id_handlers.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/shared_params/obj_getters.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/shared_params/opts_and_args.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/upload/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/upload/upload.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/upload/upload_advanced.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/upload/upload_reads.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/user.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/utils.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/cli/view.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/constants.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/contrib/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/contrib/ncbi/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/contrib/ncbi/api.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/contrib/ncbi/bioproject.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/contrib/ncbi/cli.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/contrib/ncbi/setup_logging.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/file_system_cache.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/from_blobs.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/from_ids.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/from_names.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/from_uuids.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/resolvers.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/id_constructors/utils.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/knex.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/organization.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/pipeline.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/constants.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/highcharts.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/map/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/map/base_layer.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/map/map.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/map/overlay.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/plotting/selectable.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/project.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/remote_object.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/bioinfo.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/file_chunker.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/file_download.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/file_upload.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/result_file.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/result_folder.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/resumable_download_tracker.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/resumable_upload_tracker.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/result/utils.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/sample.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/search.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/user.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/utils.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/checksum.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/cli.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/clone.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/constants.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/vc_cache.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/vc_dir.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/vc_sample.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/vc/vc_stub.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq/work_orders.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq.egg-info/SOURCES.txt +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq.egg-info/dependency_links.txt +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq.egg-info/entry_points.txt +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq.egg-info/requires.txt +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/geoseeq.egg-info/top_level.txt +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/setup.cfg +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/setup.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/tests/__init__.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/tests/test_api_client.py +0 -0
- {geoseeq-0.6.12.dev1 → geoseeq-0.6.12.dev2}/tests/test_plotting.py +0 -0
@@ -54,7 +54,7 @@ def version():
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Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
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Run `geoseeq eula show` to view the EULA.
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"""
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click.echo('0.6.
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click.echo('0.6.12dev2') # remember to update pyproject.toml
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@main.group('advanced')
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@@ -127,7 +127,7 @@ class GeoSeeqUploadManager:
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def _download_one_file(args):
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original_url,
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+
original_url, file_path, key, callback, pbar, ignore_errors, head, log_level, parallel_downloads = args
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if parallel_downloads:
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_make_in_process_logger(log_level)
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if isinstance(original_url, ResultFile):
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@@ -142,7 +142,7 @@ def _download_one_file(args):
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callback_result = callback(local_path)
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else:
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callback_result = None
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return local_path,
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+
return local_path, key, callback_result
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except Exception as e:
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if ignore_errors:
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logger.error(f"Error downloading {url}: {e}")
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@@ -161,13 +161,13 @@ class GeoSeeqDownloadManager:
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self._result_files = []
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def add_download(self, url, file_path=None, progress_tracker=None, callback=None):
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def add_download(self, url, file_path=None, progress_tracker=None, callback=None, key=None):
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if not file_path:
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if isinstance(url, ResultFile):
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file_path = url.get_local_filename()
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else:
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raise ValueError("file_path must be provided if url is not a ResultFile object.")
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self._result_files.append((url, file_path, callback))
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self._result_files.append((url, file_path, key, callback))
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def add_result_folder_download(self, result_folder, local_folder_path, hidden_files=True):
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@@ -178,14 +178,14 @@ class GeoSeeqDownloadManager:
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def get_preview_string(self):
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out = ["Download Preview:"]
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for url, file_path, _ in self._result_files:
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for url, file_path, _, _ in self._result_files:
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out.append(f"{url} -> {file_path}")
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return "\n".join(out)
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def get_url_string(self):
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self._convert_result_files_to_urls()
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out = []
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for url, _, _ in self._result_files:
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for url, _, _, _ in self._result_files:
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out.append(url)
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return "\n".join(out)
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@@ -195,23 +195,24 @@ class GeoSeeqDownloadManager:
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def _convert_result_files_to_urls(self):
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self._result_files = [(
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url.get_download_url() if isinstance(url, ResultFile) else url,
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url, # original url
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file_path,
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key,
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callback
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) for url, file_path, callback in self._result_files]
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) for url, file_path, key, callback in self._result_files]
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def download_files(self):
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"""Return a list of 3-ples (local_path,
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"""Return a list of 3-ples (local_path, key, callback_result).
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If no key was provided the key is None
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If no callback was provided with the file callback result is None
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"""
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self._convert_result_files_to_urls()
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download_args = [(
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url,
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url, file_path, key, callback,
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self.progress_tracker_factory(file_path),
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self.ignore_errors, self.head, self.log_level,
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self.n_parallel_downloads > 1
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) for url,
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) for url, file_path, key, callback in self._result_files]
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out = []
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if self.n_parallel_downloads == 1:
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logger.info(f"Downloading files in series.")
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