geoseeq 0.4.1__tar.gz → 0.5.1__tar.gz

{geoseeq-0.4.1 → geoseeq-0.5.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.4.1
+Version: 0.5.1
 Summary: # Geoseeq API Client
 Author: David C. Danko
 Author-email: dcdanko@biotia.io

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/cli/main.py

@@ -13,7 +13,7 @@ from .view import cli_view
 from .search import cli_search
 from geoseeq.vc.cli import cli_vc
 from geoseeq.knex import DEFAULT_ENDPOINT
-from .shared_params.config import set_profile
+from geoseeq.utils import set_profile
 from .shared_params.opts_and_args import overwrite_option
 from .detail import cli_detail
 from .run import cli_app
@@ -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('0.4.1')  # remember to update setup
+    click.echo('0.5.1')  # remember to update setup
 
 
 @main.group('advanced')

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/cli/shared_params/common_state.py

@@ -4,7 +4,7 @@ import click
 from geoseeq.knex import DEFAULT_ENDPOINT
 
 from geoseeq import Knex
-from .config import load_profile
+from geoseeq.utils import load_auth_profile
 
 logger = logging.getLogger('geoseeq_api')
 

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/cli/shared_params/opts_and_args.py

@@ -24,4 +24,4 @@ org_id_arg = click.argument('org_id', nargs=1)
 project_id_arg = click.argument('project_id', nargs=1)
 pipeline_id_arg = click.argument('pipeline_id', nargs=1)
 sample_ids_arg = click.argument('sample_ids', nargs=-1)
-folder_id_arg = click.argument('folder_id', nargs=1)
+folder_id_arg = click.argument('folder_id', nargs=1)

geoseeq-0.5.1/geoseeq/constants.py

@@ -0,0 +1,10 @@
+from os import environ
+from os.path import join
+
+FIVE_MB = 5 * (1024 ** 2)
+FASTQ_MODULE_NAMES = ['short_read::paired_end', 'short_read::single_end', 'long_read::nanopore']
+DEFAULT_ENDPOINT = "https://backend.geoseeq.com"
+
+CONFIG_FOLDER = environ.get("XDG_CONFIG_HOME", join(environ["HOME"], ".config"))
+CONFIG_DIR = environ.get("GEOSEEQ_CONFIG_DIR", join(CONFIG_FOLDER, "geoseeq"))
+PROFILES_PATH = join(CONFIG_DIR, "profiles.json")

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/id_constructors/from_blobs.py

@@ -1,6 +1,8 @@
 from geoseeq import GeoseeqNotFoundError
+from geoseeq.knex import with_knex
 
 
+@with_knex
 def org_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return an Organization object from a blob."""
     from geoseeq.organization import Organization  # import here to avoid circular import
@@ -11,6 +13,7 @@ def org_from_blob(knex, blob, already_fetched=True, modified=False):
     return org
 
 
+@with_knex
 def project_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a Project object from a blob."""
     org = org_from_blob(
@@ -27,6 +30,7 @@ def project_from_blob(knex, blob, already_fetched=True, modified=False):
 sample_group_from_blob = project_from_blob  # Alias
 
 
+@with_knex
 def sample_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a Sample object from a blob."""
     lib = sample_group_from_blob(
@@ -40,6 +44,7 @@ def sample_from_blob(knex, blob, already_fetched=True, modified=False):
     return sample
 
 
+@with_knex
 def project_result_folder_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a ProjectResultFolder object from a blob."""
     group = project_from_blob(
@@ -58,6 +63,7 @@ def project_result_folder_from_blob(knex, blob, already_fetched=True, modified=F
 sample_group_ar_from_blob = project_result_folder_from_blob  # Alias
 
 
+@with_knex
 def sample_result_folder_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a SampleResultFolder object from a blob."""
     sample = sample_from_blob(
@@ -76,6 +82,7 @@ def sample_result_folder_from_blob(knex, blob, already_fetched=True, modified=Fa
 sample_ar_from_blob = sample_result_folder_from_blob  # Alias
 
 
+@with_knex
 def sample_result_file_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a SampleResultFile object from a blob."""
     ar = sample_result_folder_from_blob(
@@ -92,6 +99,7 @@ def sample_result_file_from_blob(knex, blob, already_fetched=True, modified=Fals
 sample_ar_field_from_blob = sample_result_file_from_blob  # Alias
 
 
+@with_knex
 def project_result_file_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a ProjectResultFile object from a blob."""
     ar = project_result_folder_from_blob(
@@ -108,6 +116,7 @@ def project_result_file_from_blob(knex, blob, already_fetched=True, modified=Fal
 sample_group_ar_field_from_blob = project_result_file_from_blob  # Alias
 
 
+@with_knex
 def pipeline_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a Pipeline object from a blob."""
     from geoseeq.pipeline import Pipeline  # import here to avoid circular import
@@ -120,6 +129,7 @@ def pipeline_from_blob(knex, blob, already_fetched=True, modified=False):
 app_from_blob = pipeline_from_blob  # Alias
 
 
+@with_knex
 def pipeline_run_from_blob(knex, blob, already_fetched=True, modified=False):
     """Return a Pipeline run object from a blob."""
     from geoseeq.pipeline import PipelineRun  # import here to avoid circular import

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/id_constructors/from_ids.py

@@ -22,6 +22,7 @@ from .from_names import (
     result_file_from_name,
 )
 from .utils import is_grn_or_uuid, is_name
+from geoseeq.knex import with_knex
 
 
 def _generic_from_id(knex, id, from_uuid_func, from_name_func):
@@ -33,31 +34,37 @@ def _generic_from_id(knex, id, from_uuid_func, from_name_func):
     raise ValueError(f'"{id}" is not a GRN, UUID, or name')
 
 
+@with_knex
 def org_from_id(knex, id):
     """Return the organization object which the id points to."""
     return _generic_from_id(knex, id, org_from_uuid, org_from_name)
 
 
+@with_knex
 def project_from_id(knex, id):
     """Return the project object which the id points to."""
     return _generic_from_id(knex, id, project_from_uuid, project_from_name)
 
 
+@with_knex
 def sample_from_id(knex, id):
     """Return the sample object which the id points to."""
     return _generic_from_id(knex, id, sample_from_uuid, sample_from_name)
 
 
+@with_knex
 def sample_result_folder_from_id(knex, id):
     """Return the sample result folder object which the id points to."""
     return _generic_from_id(knex, id, sample_result_folder_from_uuid, sample_result_folder_from_name)
 
 
+@with_knex
 def project_result_folder_from_id(knex, id):
     """Return the project result folder object which the id points to."""
     return _generic_from_id(knex, id, project_result_folder_from_uuid, project_result_folder_from_name)
 
 
+@with_knex
 def result_folder_from_id(knex, id):
     """Return a result folder object which the id points to.
     
@@ -66,16 +73,19 @@ def result_folder_from_id(knex, id):
     return _generic_from_id(knex, id, result_folder_from_uuid, result_folder_from_name)
 
 
+@with_knex
 def sample_result_file_from_id(knex, id):
     """Return the sample result file object which the id points to."""
     return _generic_from_id(knex, id, sample_result_file_from_uuid, sample_result_file_from_name)
 
 
+@with_knex
 def project_result_file_from_id(knex, id):
     """Return the project result file object which the id points to."""
     return _generic_from_id(knex, id, project_result_file_from_uuid, project_result_file_from_name)
 
 
+@with_knex
 def result_file_from_id(knex, id):
     """Return a result file object which the id points to.
     

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/id_constructors/from_names.py

@@ -14,8 +14,10 @@ This makes them more human-readable, but not reliable for permanent references.
 """
 from geoseeq.organization import Organization
 from geoseeq import GeoseeqNotFoundError
+from geoseeq.knex import with_knex
 
 
+@with_knex
 def org_from_name(knex, name):
     """Return the organization object which the name points to.
     
@@ -28,6 +30,7 @@ def org_from_name(knex, name):
     return org
 
 
+@with_knex
 def project_from_name(knex, name):
     """Return the project object which the name points to.
     
@@ -41,6 +44,7 @@ def project_from_name(knex, name):
     return proj
 
 
+@with_knex
 def sample_from_name(knex, name):
     """Return the sample object which the name points to.
     
@@ -54,6 +58,7 @@ def sample_from_name(knex, name):
     return sample
 
 
+@with_knex
 def sample_result_folder_from_name(knex, name):
     """Return the sample result folder object which the name points to.
     
@@ -67,6 +72,7 @@ def sample_result_folder_from_name(knex, name):
     return ar
 
 
+@with_knex
 def project_result_folder_from_name(knex, name):
     """Return the project result folder object which the name points to.
     
@@ -80,6 +86,7 @@ def project_result_folder_from_name(knex, name):
     return rf
 
 
+@with_knex
 def result_folder_from_name(knex, name):
     """Return a result folder object which the name points to.
     
@@ -95,6 +102,7 @@ def result_folder_from_name(knex, name):
         return project_result_folder_from_name(knex, name)
 
 
+@with_knex
 def sample_result_file_from_name(knex, name):
     """Return the sample result file object which the name points to.
     
@@ -108,6 +116,7 @@ def sample_result_file_from_name(knex, name):
     return r_file
 
 
+@with_knex
 def project_result_file_from_name(knex, name):
     """Return the project result file object which the name points to.
     
@@ -121,6 +130,7 @@ def project_result_file_from_name(knex, name):
     return r_file
 
 
+@with_knex
 def result_file_from_name(knex, name):
     """Return a result file object which the name points to.
     

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/id_constructors/from_uuids.py

@@ -1,8 +1,9 @@
 from geoseeq import GeoseeqNotFoundError
-
+from geoseeq.knex import with_knex
 from .from_blobs import *
 
 
+@with_knex
 def org_from_uuid(knex, uuid):
     """Return the organization object which the uuid points to."""
     blob = knex.get(f"organizations/{uuid}")
@@ -10,6 +11,7 @@ def org_from_uuid(knex, uuid):
     return org
 
 
+@with_knex
 def project_from_uuid(knex, uuid):
     """Return the project object which the uuid points to."""
     blob = knex.get(f"sample_groups/{uuid}")
@@ -20,6 +22,7 @@ def project_from_uuid(knex, uuid):
 sample_group_from_uuid = project_from_uuid  # Alias
 
 
+@with_knex
 def sample_from_uuid(knex, uuid):
     """Return the sample object which the uuid points to."""
     blob = knex.get(f"samples/{uuid}")
@@ -27,6 +30,7 @@ def sample_from_uuid(knex, uuid):
     return sample
 
 
+@with_knex
 def sample_result_folder_from_uuid(knex, uuid):
     """Return the sample result folder object which the uuid points to."""
     blob = knex.get(f"sample_ars/{uuid}")
@@ -37,6 +41,7 @@ def sample_result_folder_from_uuid(knex, uuid):
 sample_ar_from_uuid = sample_result_folder_from_uuid  # Alias
 
 
+@with_knex
 def project_result_folder_from_uuid(knex, uuid):
     """Return the project result folder object which the uuid points to."""
     blob = knex.get(f"sample_group_ars/{uuid}")
@@ -47,6 +52,7 @@ def project_result_folder_from_uuid(knex, uuid):
 sample_group_ar_from_uuid = project_result_folder_from_uuid  # Alias
 
 
+@with_knex
 def result_folder_from_uuid(knex, uuid):
     """Return a result folder object which the uuid points to.
 
@@ -58,6 +64,7 @@ def result_folder_from_uuid(knex, uuid):
         return project_result_folder_from_uuid(knex, uuid)
 
 
+@with_knex
 def sample_result_file_from_uuid(knex, uuid):
     """Return the sample result file object which the uuid points to."""
     blob = knex.get(f"sample_ar_fields/{uuid}")
@@ -68,6 +75,7 @@ def sample_result_file_from_uuid(knex, uuid):
 sample_ar_field_from_uuid = sample_result_file_from_uuid  # Alias
 
 
+@with_knex
 def project_result_file_from_uuid(knex, uuid):
     """Return the project result file object which the uuid points to."""
     blob = knex.get(f"sample_group_ar_fields/{uuid}")
@@ -78,6 +86,7 @@ def project_result_file_from_uuid(knex, uuid):
 sample_group_ar_field_from_uuid = project_result_file_from_uuid  # Alias
 
 
+@with_knex
 def result_file_from_uuid(knex, uuid):
     """Return a result file object which the uuid points to.
 
@@ -89,6 +98,7 @@ def result_file_from_uuid(knex, uuid):
         return project_result_file_from_uuid(knex, uuid)
     
 
+@with_knex
 def pipeline_from_uuid(knex, uuid):
     """Return the pipeline object which the uuid points to."""
     blob = knex.get(f"pipelines/{uuid}")
@@ -99,6 +109,7 @@ def pipeline_from_uuid(knex, uuid):
 app_from_uuid = pipeline_from_uuid  # Alias
 
 
+@with_knex
 def pipeline_run_from_uuid(knex, uuid):
     """Return a pipeline run object which the uuid points to."""
     blob = knex.get(f"app_runs/{uuid}")

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/id_constructors/resolvers.py

@@ -22,8 +22,10 @@ from .from_names import (
     result_file_from_name,
 )
 from .utils import is_name, is_grn
+from geoseeq.knex import with_knex
 
 
+@with_knex
 def resolve_id(knex, id):
     """Return the object which the id points to."""
     if is_grn(id):
@@ -33,6 +35,7 @@ def resolve_id(knex, id):
     raise ValueError(f'"{id}" is not a GRN, or name. UUIDs cannot be resolved without a type')
 
 
+@with_knex
 def resolve_name(knex, name):
     """Return the object which the name points to."""
     assert is_name(name), f'"{name}" is not a name'
@@ -56,6 +59,7 @@ def resolve_name(knex, name):
     raise GeoseeqNotFoundError(f'Name "{name}" not found')
 
 
+@with_knex
 def resolve_grn(knex, grn):
     """Return the object which the grn points to."""
     assert is_grn(grn), f'"{grn}" is not a GRN'

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/knex.py

@@ -2,8 +2,8 @@ import logging
 import requests
 from os import environ
 from .file_system_cache import FileSystemCache
-
-DEFAULT_ENDPOINT = "https://backend.geoseeq.com"
+from geoseeq.utils import load_auth_profile
+from geoseeq.constants import DEFAULT_ENDPOINT
 
 
 logger = logging.getLogger("geoseeq_api")  # Same name as calling module
@@ -205,3 +205,36 @@ class Knex:
         response = self.sess.delete(f"{self.endpoint_url}/{url}", json=json)
         logger.debug(f"DELETE request response:\n{response}")
         return self._handle_response(response, json_response=False, **kwargs)
+
+    @classmethod
+    def load_profile(cls, profile=""):
+        """Return a knex authenticated with a profile."""
+        endpoint, token = load_auth_profile(profile)
+        knex = cls(endpoint)
+        knex.add_api_token(token)
+        return knex
+    
+
+def with_knex(func):
+    def wrapper(*args, **kwargs):
+        # check if any of the arguments are a knex instance
+        any_knex = any([isinstance(arg, Knex) for arg in args])
+        if any_knex:
+            return func(*args, **kwargs)
+        else:
+            varnames = [
+                varname for varname in func.__code__.co_varnames
+                if varname != "knex"
+            ]
+            kwargs.update(zip(varnames, args))
+            if "knex" not in kwargs:
+                profile = kwargs.pop("profile", "")
+                kwargs['knex'] = Knex.load_profile(profile=profile)
+            # reorder kwargs to match the function signature
+            reordered = {
+                key: kwargs[key] for key in func.__code__.co_varnames
+                if key in kwargs
+            }
+            return func(**reordered)
+    return wrapper
+        

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq/utils.py

@@ -4,11 +4,47 @@ import logging
 from ftplib import FTP
 from threading import Timer
 from .file_system_cache import FileSystemCache
+from os.path import join, exists
+import json
+from os import environ, makedirs
+from .constants import CONFIG_DIR, PROFILES_PATH, DEFAULT_ENDPOINT
 
 logger = logging.getLogger('geoseeq_api')  # Same name as calling module
 logger.addHandler(logging.NullHandler())  # No output unless configured by calling program
 
 
+def load_auth_profile(profile=""):
+    """Return an endpoit and a token"""
+    profile = profile or "__default__"
+    with open(PROFILES_PATH, "r") as f:
+        profiles = json.load(f)
+    if profile in profiles:
+        return profiles[profile]["endpoint"], profiles[profile]["token"]
+    raise KeyError(f"Profile {profile} not found.")
+
+
+def set_profile(token, endpoint=DEFAULT_ENDPOINT, profile="", overwrite=False):
+    """Write a profile to a config file.
+    
+    Raises KeyError if profile already exists.
+    """
+    if not exists(PROFILES_PATH):
+        makedirs(CONFIG_DIR)
+        with open(PROFILES_PATH, "w") as f:
+            json.dump({}, f)
+    with open(PROFILES_PATH, "r") as f:
+        profiles = json.load(f)
+    profile = profile or "__default__"
+    if profile in profiles and not overwrite:
+        raise KeyError(f"Profile {profile} already exists.")
+    profiles[profile] = {
+        "token": token,
+        "endpoint": endpoint,
+    }
+    with open(PROFILES_PATH, "w") as f:
+        json.dump(profiles, f, indent=4)
+
+
 def paginated_iterator(knex, initial_url, error_handler=None):
     cache = FileSystemCache()
     result = cache.get_cached_blob(initial_url)

{geoseeq-0.4.1 → geoseeq-0.5.1}/geoseeq.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: geoseeq
-Version: 0.4.1
+Version: 0.5.1
 Summary: # Geoseeq API Client
 Author: David C. Danko
 Author-email: dcdanko@biotia.io

{geoseeq-0.4.1 → geoseeq-0.5.1}/setup.py

@@ -5,7 +5,7 @@ import setuptools
 
 setuptools.setup(
     name='geoseeq',
-    version='0.4.1',  # remember to update version string in CLI as well
+    version='0.5.1',  # remember to update version string in CLI as well
     author="David C. Danko",
     author_email='dcdanko@biotia.io',
     description=open('README.md').read(),

geoseeq-0.4.1/geoseeq/constants.py

@@ -1,2 +0,0 @@
-FIVE_MB = 5 * (1024 ** 2)
-FASTQ_MODULE_NAMES = ['short_read::paired_end', 'short_read::single_end', 'long_read::nanopore']