geoseeq 0.5.6a1__py3-none-any.whl → 0.5.6a3__py3-none-any.whl

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('0.5.6a1')  # remember to update setup
+    click.echo('0.5.6a3')  # 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:
+        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/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/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/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/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-0.5.6a1.dist-info → geoseeq-0.5.6a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.5.6a1
+Version: 0.5.6a3
 Summary: GeoSeeq command line tools and python API
 Author: David C. Danko
 Author-email: "David C. Danko" <dcdanko@biotia.io>

{geoseeq-0.5.6a1.dist-info → geoseeq-0.5.6a3.dist-info}/RECORD

@@ -3,7 +3,7 @@ geoseeq/app.py,sha256=Y6d1UzxFLfE3RNccATbFCVi6kH3eFmzwoUbeR2Ry09A,2387
 geoseeq/blob_constructors.py,sha256=AkWpDQY0EdGMxF1p6eRspyHKubcUdiW4it-_Q7S2QWk,188
 geoseeq/bulk_creators.py,sha256=pdn-Dv7yv5SFv-PfDuQbuOnw2W4-BfIfRJVRAhM8U6s,2115
 geoseeq/constants.py,sha256=h9RURz4xs2bZyDrSGocej7ANJvRLr_H1H7JRxpNUXJM,431
-geoseeq/file_system_cache.py,sha256=7pdM-1VncOvjkYv2pOocPHOXnEWz0jKhH6sm1LaXtoU,3405
+geoseeq/file_system_cache.py,sha256=fZrvqWmUtTLFOpm_qG0fz1Q0GWnw_yVOAcFVPloc75c,4101
 geoseeq/knex.py,sha256=6fPO8F8yxgBgBXZiliMJvYYjgf_16chfJPyWLe-kpPk,7898
 geoseeq/organization.py,sha256=a9xmGDE0tQsjPJfyFkYnWagxZ8xpdeckkwvkhH6LNIk,2462
 geoseeq/pipeline.py,sha256=89mhWaecsKnm6tyRkdkaVp4dmZh62_v42Ze0oXf8OTY,9873
@@ -22,7 +22,7 @@ geoseeq/cli/detail.py,sha256=q8Suu-j2k18knfSVFG-SWWGNsKM-n8y9RMA3LcIIi9Y,4132
 geoseeq/cli/download.py,sha256=ldpqpnRe00utb1EL1T_5CyPbFrZbtauIvOSOHtxz9qc,17656
 geoseeq/cli/fastq_utils.py,sha256=-bmeQLaiMBm57zWOF0R5OlWTU0_3sh1JBC1RYw2BOFM,3083
 geoseeq/cli/get_eula.py,sha256=79mbUwyiF7O1r0g6UTxG9kJGQEqKuH805E6eLkPC6Y4,997
-geoseeq/cli/main.py,sha256=RVAeSDuObgZpdMOh6R3yW7PWEBbZxCUQZ_WroI68Urk,2910
+geoseeq/cli/main.py,sha256=EaKUewWBNapS9s71DPK-a1SX1POzvsGY5A3CB6ZDNFk,3199
 geoseeq/cli/manage.py,sha256=wGXAcVaXqE5JQEU8Jh6OlHr02nB396bpS_SFcOZdrEo,5929
 geoseeq/cli/progress_bar.py,sha256=p1Xl01nkYxSBZCB30ue2verIIi22W93m3ZAMAxipD0g,738
 geoseeq/cli/run.py,sha256=bx2AV6VIqOSTlxUda78xl0XxcZ8TXlQx02-e7iLQPwI,3838
@@ -31,7 +31,7 @@ geoseeq/cli/user.py,sha256=fARv_5vx-QYT765Hsjgwr6J5ddA_viCPQdv9iUoVX6w,925
 geoseeq/cli/utils.py,sha256=f0wX5-19uDrYZ8d-aBLplqfbGOkr5BH8x3AMSAyPCes,2873
 geoseeq/cli/view.py,sha256=P-o2YKBkTrPzSI-JOv7xROc63HLSUygZNZsjp9TGvSw,6783
 geoseeq/cli/shared_params/__init__.py,sha256=ckNHGCBJUpJbQmcYi7lW-lsC0xKud6CCMznwcG5Vte4,325
-geoseeq/cli/shared_params/common_state.py,sha256=XhyVPr7lw56GIyCrmlaFzZVyCeYfNMtakP8XARF3OKE,3555
+geoseeq/cli/shared_params/common_state.py,sha256=jiHZtL3TATMjEoqhbO7HT8KkLJr1QPsy7ZHT4qcoQ1E,4095
 geoseeq/cli/shared_params/config.py,sha256=HQ0xQh_jdt3EKI5VXYqQXzo-s8Rm6YlziMyVX-kg598,1072
 geoseeq/cli/shared_params/id_handlers.py,sha256=501K9sCVkI0YGDQ62vXk_DM5lMMDrdB5spIS3cw9x9U,9299
 geoseeq/cli/shared_params/obj_getters.py,sha256=ZSkt6LnDkVFlNVYKgLrjzg60-6BthZMr3eeD3HNqzac,2741
@@ -47,8 +47,8 @@ geoseeq/contrib/ncbi/bioproject.py,sha256=_oThTd_iLDOC8cLOlJKAatSr362OBYZCEV3Yrq
 geoseeq/contrib/ncbi/cli.py,sha256=j9zEcaZPTryK3a4xluRxigcJKDhRpRxbp3KZSx-Bfhk,2400
 geoseeq/contrib/ncbi/setup_logging.py,sha256=Tp1bY1U0f-o739aHpvVYriG2qdd1lFvCYBXZeXQgt-w,175
 geoseeq/id_constructors/__init__.py,sha256=w5E0PNQ9UuAxBeZbDI7KBnUoERd85gGz3nScz45bd2o,126
-geoseeq/id_constructors/from_blobs.py,sha256=3JVmVf1hZI4B9Nwk9Ht_KLjM94hzFHqD_IgY29BdRcM,5652
-geoseeq/id_constructors/from_ids.py,sha256=zBAKTzv1ZY9kCKl1QBTWsKg610nCVQgJ0IA9c1umd40,3050
+geoseeq/id_constructors/from_blobs.py,sha256=aj7M7NRpKGs3u3xUvuFJwmJdFeIcJPmaI2_bhwbFfEs,5702
+geoseeq/id_constructors/from_ids.py,sha256=bbAJX4LnuN70v9bny6N-jAwOudb2-ztHvlMBgRuSDz0,3151
 geoseeq/id_constructors/from_names.py,sha256=RqgFjDsAwQcidMkZwX7oB00OvBAKTiilHYetTPogJ40,4174
 geoseeq/id_constructors/from_uuids.py,sha256=5NrQoRBNBfiB48SIB6QFZvO0lxNrxAHbu1MDkNRSu_4,3305
 geoseeq/id_constructors/resolvers.py,sha256=8hp5xJSCoZrAXtMT54Hp4okt63l909XqJU3IQx-VCgc,2676
@@ -80,8 +80,9 @@ geoseeq/vc/vc_stub.py,sha256=IQr8dI0zsWKVAeY_5ybDD6n49_3othcgfHS3P0O9tuY,3110
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_api_client.py,sha256=TS5njc5pcPP_Ycy-ljcfPVT1hQRBsFVdQ0lCqBmoesU,12810
 tests/test_plotting.py,sha256=TcTu-2ARr8sxZJ7wPQxmbs3-gHw7uRvsgrhhhg0qKik,784
-geoseeq-0.5.6a1.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
-geoseeq-0.5.6a1.dist-info/METADATA,sha256=H66w27KgQL6Bq5pzO38uOv-hJpVBdbHYZyyYtik2EP4,4805
-geoseeq-0.5.6a1.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-geoseeq-0.5.6a1.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
-geoseeq-0.5.6a1.dist-info/RECORD,,
+geoseeq-0.5.6a3.dist-info/LICENSE,sha256=IuhIl1XCxXLPLJT_coN1CNqQU4Khlq7x4IdW7ioOJD8,1067
+geoseeq-0.5.6a3.dist-info/METADATA,sha256=NbqTL5rlxCyYeDboJ6cmx6Ee8hvCrXkzHQei-xgCUEk,4805
+geoseeq-0.5.6a3.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+geoseeq-0.5.6a3.dist-info/entry_points.txt,sha256=yF-6KDM8zXib4Al0qn49TX-qM7PUkWUIcYtsgt36rjM,45
+geoseeq-0.5.6a3.dist-info/top_level.txt,sha256=zZk7mmeaqAYqFJG8nq2DTgSQPbflRjJwkDIhNURPDEU,14
+geoseeq-0.5.6a3.dist-info/RECORD,,

geoseeq-0.5.6a3.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+geoseeq = geoseeq.cli:main