implement metadata search functions (#8)

Refactor, renaming, tests, documentation.

src/gypsum_client/__init__.py

@@ -15,29 +15,29 @@
 finally:
     del version, PackageNotFoundError
 
-from .abort_upload import abort_upload
+
 from .auth import access_token, set_access_token
-from .clone_version import clone_version
-from .complete_upload import complete_upload
-from .create_assets import create_project
-from .fetch_assets import (
+from .clone_operations import clone_version
+from .create_operations import create_project
+from .fetch_metadata_database import fetch_metadata_database
+from .fetch_metadata_schema import fetch_metadata_schema
+from .fetch_operations import (
     fetch_latest,
     fetch_manifest,
     fetch_permissions,
     fetch_quota,
     fetch_summary,
     fetch_usage,
 )
-from .fetch_metadata_database import fetch_metadata_database
-from .fetch_metadata_schema import fetch_metadata_schema
-from .list_assets import list_assets, list_files, list_projects, list_versions
+from .list_operations import list_assets, list_files, list_projects, list_versions
 from .prepare_directory_for_upload import prepare_directory_upload
-from .probation import approve_probation, reject_probation
-from .refresh_ops import refresh_latest, refresh_usage
-from .remove_assets import remove_asset, remove_project, remove_version
+from .probation_operations import approve_probation, reject_probation
+from .refresh_operations import refresh_latest, refresh_usage
+from .remove_operations import remove_asset, remove_project, remove_version
 from .resolve_links import resolve_links
 from .s3_config import public_s3_config
-from .save_assets import save_version
-from .save_file import save_file
-from .set_ops import set_permissions, set_quota
-from .upload_assets import upload_directory, upload_files
+from .save_operations import save_file, save_version
+from .search_metadata import define_text_query, search_metadata_text
+from .set_operations import set_permissions, set_quota
+from .upload_api_operations import abort_upload, complete_upload, start_upload
+from .upload_file_actions import upload_directory, upload_files

src/gypsum_client/_utils.py

@@ -145,7 +145,7 @@ def _save_file(
     if overwrite is True or not os.path.exists(destination):
         os.makedirs(os.path.dirname(destination), exist_ok=True)
 
-        _lock = FileLock(destination + ".lock")
+        _lock = FileLock(destination + ".LOCK")
         with _lock:
             with tempfile.NamedTemporaryFile(
                 dir=os.path.dirname(destination), delete=False
@@ -224,7 +224,7 @@ def _acquire_lock(cache: str, project: str, asset: str, version: str):
         _path = os.path.join(cache, "status", project, asset, version)
         os.makedirs(os.path.dirname(_path), exist_ok=True)
 
-        _lock = FileLock(_path + ".lock")
+        _lock = FileLock(_path + ".LOCK")
         _lock.acquire()
         IS_LOCKED["locks"][_key] = _lock
 

src/gypsum_client/auth.py

@@ -64,7 +64,7 @@ def _token_func(x):
         cache_path = _token_cache_path(cache_dir)
 
         if os.path.exists(cache_path):
-            _lock = FileLock(cache_path + ".lock")
+            _lock = FileLock(cache_path + ".LOCK")
             with _lock:
                 with open(cache_path, "r") as file:
                     dump = file.read().splitlines()
@@ -204,7 +204,7 @@ def set_access_token(
         cache_path = _token_cache_path(cache_dir)
         os.makedirs(os.path.dirname(cache_path), exist_ok=True)
 
-        _lock = FileLock(cache_path + ".lock")
+        _lock = FileLock(cache_path + ".LOCK")
         with _lock:
             with open(cache_path, "w") as file:
                 file.write("\n".join([token, name, str(expiry)]))

src/gypsum_client/clone_version.py → src/gypsum_client/clone_operations.py

@@ -3,8 +3,8 @@
 import shutil
 
 from ._utils import BUCKET_CACHE_NAME, _cache_directory, _rest_url
-from .fetch_assets import fetch_manifest
-from .save_assets import save_version
+from .fetch_operations import fetch_manifest
+from .save_operations import save_version
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"

src/gypsum_client/config.py

@@ -2,5 +2,7 @@
 __copyright__ = "Jayaram Kancherla"
 __license__ = "MIT"
 
+## Set this to False if SSL certificates are not properly setup on your machine.
+## essentially sets verify=False on all requests going out.
 
 REQUESTS_MOD = {"verify": True}

src/gypsum_client/fetch_metadata_database.py

@@ -61,7 +61,7 @@ def fetch_metadata_database(
         if os.path.exists(cache_path) and not overwrite:
             old_lastmod_raw = None
 
-            _lock = FileLock(cache_path + ".lock")
+            _lock = FileLock(cache_path + ".LOCK")
             if not _lock.is_locked:
                 old_lastmod_raw = open(cache_path + ".modified").readlines()
 
@@ -71,7 +71,7 @@ def fetch_metadata_database(
             if new_lastmod is not None and old_lastmod == new_lastmod:
                 return cache_path
 
-    _lock = FileLock(cache_path + ".lock")
+    _lock = FileLock(cache_path + ".LOCK")
     with _lock:
         mod_path = cache_path + ".modified"
         _download_and_rename_file(base_url + "modified", mod_path)

src/gypsum_client/fetch_metadata_schema.py

@@ -44,11 +44,11 @@ def fetch_metadata_schema(
             os.makedirs(os.path.dirname(cache_path), exist_ok=True)
 
         if os.path.exists(cache_path) and not overwrite:
-            _lock = FileLock(cache_path + ".lock")
+            _lock = FileLock(cache_path + ".LOCK")
             if not _lock.is_locked:
                 return cache_path
 
-    _lock = FileLock(cache_path + ".lock")
+    _lock = FileLock(cache_path + ".LOCK")
     with _lock:
         url = "https://artifactdb.github.io/bioconductor-metadata-index/" + name
         response = requests.get(url, verify=REQUESTS_MOD["verify"])

src/gypsum_client/resolve_links.py

@@ -10,8 +10,7 @@
     _release_lock,
     _rest_url,
 )
-from .fetch_assets import fetch_manifest
-from .save_file import save_file
+from .fetch_operations import fetch_manifest
 
 __author__ = "Jayaram Kancherla"
 __copyright__ = "Jayaram Kancherla"
@@ -54,6 +53,8 @@ def resolve_links(
     Returns:
         True if all links are resolved.
     """
+    from .save_operations import save_file
+
     cache_dir = _cache_directory(cache_dir)
     _acquire_lock(cache_dir, project, asset, version)
 

src/gypsum_client/s3_config.py

@@ -58,7 +58,7 @@ def public_s3_config(
 
             cache_path = _config_cache_path(cache_dir)
             if os.path.exists(cache_path):
-                _lock = FileLock(cache_path + ".lock")
+                _lock = FileLock(cache_path + ".LOCK")
                 with _lock:
                     with open(cache_dir, "r") as f:
                         creds = json.load(f)
@@ -79,7 +79,7 @@ def public_s3_config(
         config_path = _config_cache_path(cache_dir)
         os.makedirs(os.path.dirname(config_path), exist_ok=True)
 
-        with FileLock(config_path + ".lock"):
+        with FileLock(config_path + ".LOCK"):
             with open(config_path, "w") as f:
                 json.dump(creds, f)