Merge pull request #28 from databio/drs

work toward implementing drs

bbconf/__init__.py

@@ -1,9 +1,6 @@
-import logmuse
-
 from bbconf._version import __version__
 from bbconf.bbconf import *
 from bbconf.const import *
 
 __all__ = ["BedBaseConf", "get_bedbase_cfg"]
 
-logmuse.init_logger("bbconf")

bbconf/bbconf.py

@@ -43,14 +43,16 @@
 from bbconf.exceptions import MissingConfigDataError, BedBaseConfError
 from bbconf.helpers import raise_missing_key, get_bedbase_cfg
 
-os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"  # to suppress verbose warnings tensorflow
+# os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"  # to suppress verbose warnings tensorflow
 from geniml.text2bednn import text2bednn
 from geniml.search import QdrantBackend
 from sentence_transformers import SentenceTransformer
 from geniml.region2vec import Region2VecExModel
 from geniml.io import RegionSet
 
-_LOGGER = getLogger(PKG_NAME)
+_LOGGER = getLogger(__name__)
+
+DRS_ACCESS_URL = "{server_url}/objects/{object_id}/access/{access_id}"
 
 
 class BedBaseConf:
@@ -593,3 +595,37 @@ def get_prefixed_uri(self, postfix: str, remote_class: str = "http") -> str:
         :return: full uri path
         """
         return os.path.join(self.prefix(remote_class), postfix)
+
+    def get_bed_drs_metadata(object_id: str) -> dict:
+        bed_metadata = self.bed.retrieve(object_id)
+        drs_dict = {
+            "id": object_id,
+            "size": bed_metadata["file_size"],
+            "created_time": bed_metadata["created_time"],
+            "checksums": object_id,
+            "access_methods": [],
+        }
+        # add access method for each remote class
+        for access_id in keys(self.config[CFG_REMOTE_KEY]):
+            access_dict = {
+                "type": "https",
+                "access_id": access_id,
+                "access_url": DRS_ACCESS_URL.format(
+                    server_url=self.config["access_methods"][access_id]["server_url"],
+                    object_id=object_id,
+                    access_id=access_id,
+                ),
+            }
+            access_dict["region"] = (
+                self.config["access_methods"][access_id]["region"] or None
+            )
+            drs_dict["access_methods"].append(access_dict)
+        return drs_dict
+
+    def get_bed_url(object_id: str, access_id: str) -> str:
+        access_url = DRS_ACCESS_URL.format(
+            server_url=self.config["access_methods"][access_id]["server_url"],
+            object_id=object_id,
+            access_id=access_id,
+        )
+        return access_url

interactive_testing.py

@@ -0,0 +1,31 @@
+# This provides a short script to explore bbconf interactively
+# First you have to set the env vars with something like:
+# source ../bedbase.org/environment/production.env
+
+from bbconf import BedBaseConf
+
+import logging
+import sys
+
+def set_up_interactive_logger(package=None) -> logging.Logger:
+    """Set up a logger for interactive testing"""
+    _LOGGER = logging.getLogger(package)
+    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+    stream = logging.StreamHandler(sys.stdout)
+    stream.setFormatter(formatter)
+    stream.setLevel(logging.DEBUG)
+    _LOGGER.addHandler(stream)
+    _LOGGER.setLevel(logging.DEBUG)
+    return _LOGGER
+
+_LOGGER = set_up_interactive_logger()
+_LOGGER.debug("Test log message")
+
+
+bbc = BedBaseConf("../bedbase.org/config/bedbase.yaml")
+
+bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984")
+
+bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984", "bedfile")
+
+bbc.bed.retrieve("78c0e4753d04b238fc07e4ebe5a02984", result_identifier="bedfile")

requirements/requirements-all.txt

@@ -1,4 +1,3 @@
-logmuse
 yacman>=0.9.1
 pipestat>=0.6.0a2
 #pipestat @ git+https://github.com/pepkit/pipestat@dev#egg=pipestat