geoseeq 0.5.6a2__tar.gz → 0.5.6a4__tar.gz

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a2
+Version: 0.5.6a4
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/geoseeq/cli/main.py

@@ -14,7 +14,7 @@ from .search import cli_search
 from geoseeq.vc.cli import cli_vc
 from geoseeq.knex import DEFAULT_ENDPOINT
 from geoseeq.utils import set_profile
-from .shared_params.opts_and_args import overwrite_option
+from .shared_params.opts_and_args import overwrite_option, yes_option
 from .detail import cli_detail
 from .run import cli_app
 from .get_eula import cli_eula
@@ -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('0.5.6a2')  # remember to update setup
+    click.echo('0.5.6a4')  # remember to update setup
 
 
 @main.group('advanced')
@@ -74,9 +74,12 @@ def cli_experimental():
 cli_experimental.add_command(cli_vc)
 
 @main.command('config')
+@yes_option
+@click.option('--api-token', default=None, help='The API token to use.')
+@click.option('--endpoint', default=None, help='The endpoint to use.')
 @click.option('-p', '--profile', default=None, help='The profile name to use.')
 @overwrite_option
-def cli_config(profile, overwrite):
+def cli_config(yes, api_token, endpoint, profile, overwrite):
     """Configure the GeoSeeq API.
 
     ---
@@ -84,13 +87,16 @@ def cli_config(profile, overwrite):
     Use of this tool implies acceptance of the GeoSeeq End User License Agreement.
     Run `geoseeq eula show` to view the EULA.
     """
-    if not profile:
+    if not profile and not yes:
         profile = click.prompt(f'Set custom profile name? (Leave blank for default)', default="").strip(' \"\'')
-    endpoint = click.prompt(f'Enter the URL to use for GeoSeeq (Most users can use the default)', default=DEFAULT_ENDPOINT).strip(' \"\'')
-    api_token = click.prompt(f'Enter your GeoSeeq API token', hide_input=True).strip(' \"\'')
-    eula_accepted = click.confirm(f'Have you read and accepted the GeoSeeq End User License Agreement? Use `geoseeq eula show` to view the EULA.')
-    if not eula_accepted:
-        click.echo('You must accept the EULA to use the GeoSeeq API.')
-        return
+    if not endpoint and not yes:
+        endpoint = click.prompt(f'Enter the URL to use for GeoSeeq (Most users can use the default)', default=DEFAULT_ENDPOINT).strip(' \"\'')
+    if not api_token:
+        api_token = click.prompt(f'Enter your GeoSeeq API token', hide_input=True).strip(' \"\'')
+    if not yes:
+        eula_accepted = click.confirm(f'Have you read and accepted the GeoSeeq End User License Agreement? Use `geoseeq eula show` to view the EULA.')
+        if not eula_accepted:
+            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.')

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/geoseeq/cli/shared_params/common_state.py

@@ -2,7 +2,7 @@ import logging
 
 import click
 from geoseeq.knex import DEFAULT_ENDPOINT
-
+import geoseeq.file_system_cache
 from geoseeq import Knex
 from geoseeq.utils import load_auth_profile
 
@@ -17,6 +17,7 @@ class State(object):
         self.outfile = None
         self.log_level = 20
         self._knex = None
+        self.use_cache = True
 
     def get_knex(self):
         logger.setLevel(self.log_level)
@@ -37,8 +38,8 @@ def log_level_option(f):
         state.log_level = value
         return value
     return click.option('-l', '--log-level',
-                        type=click.Choice(['CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG']),
-                        default='WARNING',
+                        type=click.Choice(['CRITICAL', 'ERROR', 'WARN', 'INFO', 'DEBUG']),
+                        default='WARN',
                         envvar='GEOSEEQ_CLI_LOG_LEVEL',
                         expose_value=False,
                         callback=callback)(f)
@@ -103,11 +104,25 @@ def outfile_option(f):
                         callback=callback)(f)
 
 
+def cache_option(f):
+    def callback(ctx, param, value):
+        state = ctx.ensure_object(State)
+        state.use_cache = value
+        geoseeq.file_system_cache.USE_GEOSEEQ_CACHE = value
+        return value
+    return click.option('--use-cache/--no-cache',
+                        default=True,
+                        expose_value=False,
+                        help='Cache data from the geoseeq server.',
+                        callback=callback)(f)
+
+
 def common_options(f):
     f = outfile_option(f)
     f = log_level_option(f)
     f = endpoint_option(f)
     f = profile_option(f)
+    f = cache_option(f)
     return f
 
 

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/geoseeq/file_system_cache.py

@@ -1,15 +1,20 @@
 import json
 import logging
 import os
+from os.path import join, abspath
 from glob import glob
 from hashlib import sha256
 from random import randint
 from time import time
 
-logger = logging.getLogger(__name__)  # Same name as calling module
+logger = logging.getLogger("geoseeq_api")  # Same name as calling module
 logger.addHandler(logging.NullHandler())  # No output unless configured by calling program
-CACHED_BLOB_TIME = 3 * 60 * 60  # 3 hours in seconds
-CACHE_DIR = os.environ.get('GEOSEEQ_API_CACHE_DIR', '.')
+CACHED_BLOB_TIME = 5 * 60 # 5 minutes in seconds
+CACHE_DIR = join(
+    os.environ.get('XDG_CACHE_HOME', join(os.environ["HOME"], ".cache")),
+    "geoseeq"
+)
+USE_GEOSEEQ_CACHE = None
 
 
 def hash_obj(obj):
@@ -30,8 +35,31 @@ def time_since_file_cached(blob_filepath):
 class FileSystemCache:
 
     def __init__(self, timeout=CACHED_BLOB_TIME):
-        self.no_cache = 'false' in os.environ.get('USE_GEOSEEQ_CACHE', 'TRUE').lower()
         self.timeout = timeout
+        self._no_cache = False
+        self.setup()
+
+    @property
+    def cache_dir_path(self):
+        return abspath(f'{CACHE_DIR}/geoseeq_api_cache/v1/')
+
+    def setup(self):
+        if self.no_cache:
+            return
+        try:
+            os.makedirs(self.cache_dir_path, exist_ok=True)
+            open(join(self.cache_dir_path, 'flag'), 'w').close()
+        except Exception as e:
+            logger.warning(f'Could not create cache directory. {e}')
+            self._no_cache = True
+    
+    @property
+    def no_cache(self):
+        if self._no_cache or not USE_GEOSEEQ_CACHE:
+            logger.debug('Cache is disabled.')
+            return True
+        logger.debug('Cache is enabled.')
+        return not USE_GEOSEEQ_CACHE
 
     def clear_blob(self, obj):
         if self.no_cache:
@@ -46,8 +74,7 @@ class FileSystemCache:
                 pass
 
     def get_cached_blob_filepath(self, obj):
-        path_base = f'{CACHE_DIR}/.geoseeq_api_cache/v1/geoseeq_api_cache__{hash_obj(obj)}'
-        os.makedirs(os.path.dirname(path_base), exist_ok=True)
+        path_base = join(self.cache_dir_path, f'geoseeq_api_cache__{hash_obj(obj)}')
         paths = sorted(glob(f'{path_base}__*.json'))
         if paths:
             return paths[-1], True

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/geoseeq/id_constructors/from_blobs.py

@@ -93,6 +93,7 @@ def sample_result_file_from_blob(knex, blob, already_fetched=True, modified=Fals
     arf.load_blob(blob)
     ar._already_fetched = already_fetched
     ar._modified = modified
+    arf.cache_blob(blob)
     return arf
 
 
@@ -110,6 +111,7 @@ def project_result_file_from_blob(knex, blob, already_fetched=True, modified=Fal
     arf.load_blob(blob)
     ar._already_fetched = already_fetched
     ar._modified = modified
+    arf.cache_blob(blob)
     return arf
 
 

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/geoseeq/id_constructors/from_ids.py

@@ -28,6 +28,7 @@ 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."""
     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)
     if is_name(id):
         return from_name_func(knex, id)

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a2
+Version: 0.5.6a4
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "geoseeq"
-version = "0.5.6a2"
+version = "0.5.6a4"
 authors = [
   { name="David C. Danko", email="dcdanko@biotia.io" },
 ]

{geoseeq-0.5.6a2 → geoseeq-0.5.6a4}/setup.py

@@ -5,7 +5,7 @@ import setuptools
 
 setuptools.setup(
     name='geoseeq',
-    version='0.5.6a1',  # remember to update version string in CLI as well
+    version='0.5.6a3',  # remember to update version string in CLI as well
     author="David C. Danko",
     author_email='dcdanko@biotia.io',
     description=open('README.md').read(),