nmdc-runtime 1.0.12__py3-none-any.whl → 1.0.14__py3-none-any.whl

nmdc_runtime/site/translation/gold_translator.py

@@ -1,6 +1,6 @@
 import collections
 import re
-from typing import List, Union
+from typing import List, Tuple, Union
 from nmdc_schema import nmdc
 
 from nmdc_runtime.site.translation.translator import JSON_OBJECT, Translator
@@ -188,37 +188,48 @@ class GoldStudyTranslator(Translator):
     def _get_quantity_value(
         self,
         gold_entity: JSON_OBJECT,
-        gold_field: str,
+        gold_field: Union[str, Tuple[str, str]],
         unit: Union[str, None] = None,
     ) -> Union[nmdc.QuantityValue, None]:
         """Get any field of a GOLD entity object as a QuantityValue
 
         This method extracts any single field of a GOLD entity object (study, biosample, etc)
         and if it is not `None` returns it as an `nmdc:QuantityValue`. A has_numeric_value will
-        be inferred from the gold_field value in gold_entity. The inference is done only if the
-        unit is meters. Support for other units will be added incrementally. A unit can optionally
-        be provided, otherwise the unit will be `None`. If the value of the field is `None`,
-        `None` will be returned.
+        be inferred from the gold_field value in gold_entity if it is a simple string value. If
+        it is a tuple of two fields, a has_minimum_numeric_value and has_maximum_numeric_value
+        will be inferred from the gold_field values in gold_entity.
 
         :param gold_entity: GOLD entity object
-        :param gold_field: Name of the field to extract
+        :param gold_field: Name of the field to extract, or a tuple of two fields to extract a range
         :param unit: An optional unit as a string, defaults to None
         :return: QuantityValue object
         """
+        if isinstance(gold_field, tuple):
+            minimum_numeric_value = gold_entity.get(gold_field[0])
+            maximum_numeric_value = gold_entity.get(gold_field[1])
+
+            if minimum_numeric_value is None and maximum_numeric_value is None:
+                return None
+            elif minimum_numeric_value is not None and maximum_numeric_value is None:
+                return nmdc.QuantityValue(
+                    has_raw_value=field_value,
+                    has_numeric_value=nmdc.Double(minimum_numeric_value),
+                    has_unit=unit,
+                )
+            else:
+                return nmdc.QuantityValue(
+                    has_minimum_numeric_value=nmdc.Double(minimum_numeric_value),
+                    has_maximum_numeric_value=nmdc.Double(maximum_numeric_value),
+                    has_unit=unit,
+                )
+
         field_value = gold_entity.get(gold_field)
         if field_value is None:
             return None
 
-        numeric_value = None
-        # TODO: in the future we will need better handling
-        # to parse out the numerical portion of the quantity value
-        # ex. temp might be 3 C, and we will need to parse out 3.0 from it
-        if unit == "meters":
-            numeric_value = nmdc.Double(field_value)
-
         return nmdc.QuantityValue(
             has_raw_value=field_value,
-            has_numeric_value=numeric_value,
+            has_numeric_value=nmdc.Double(field_value),
             has_unit=unit,
         )
 
@@ -390,7 +401,7 @@ class GoldStudyTranslator(Translator):
         """
         return nmdc.Study(
             description=gold_study.get("description"),
-            gold_study_identifiers=self._get_curie("GOLD", gold_study["studyGoldId"]),
+            gold_study_identifiers=self._get_curie("gold", gold_study["studyGoldId"]),
             id=nmdc_study_id,
             name=gold_study.get("studyName"),
             principal_investigator=self._get_pi(gold_study),
@@ -427,7 +438,7 @@ class GoldStudyTranslator(Translator):
             collected_from=nmdc_field_site_id,
             collection_date=self._get_collection_date(gold_biosample),
             depth=self._get_quantity_value(
-                gold_biosample, "depthInMeters", unit="meters"
+                gold_biosample, ("depthInMeters", "depthInMeters2"), unit="meters"
             ),
             description=gold_biosample.get("description"),
             diss_oxygen=self._get_quantity_value(gold_biosample, "oxygenConcentration"),
@@ -440,7 +451,7 @@ class GoldStudyTranslator(Translator):
             env_local_scale=self._get_env_term_value(gold_biosample, "envoLocalScale"),
             env_medium=self._get_env_term_value(gold_biosample, "envoMedium"),
             geo_loc_name=self._get_text_value(gold_biosample, "geoLocation"),
-            gold_biosample_identifiers=self._get_curie("GOLD", gold_biosample_id),
+            gold_biosample_identifiers=self._get_curie("gold", gold_biosample_id),
             habitat=gold_biosample.get("habitat"),
             host_name=gold_biosample.get("hostName"),
             host_taxid=self._get_text_value(gold_biosample, "hostNcbiTaxid"),
@@ -498,7 +509,7 @@ class GoldStudyTranslator(Translator):
             id=nmdc_omics_processing_id,
             name=gold_project.get("projectName"),
             gold_sequencing_project_identifiers=self._get_curie(
-                "GOLD", gold_project_id
+                "gold", gold_project_id
             ),
             ncbi_project_name=gold_project.get("projectName"),
             type="nmdc:OmicsProcessing",

{nmdc_runtime-1.0.12.dist-info → nmdc_runtime-1.0.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nmdc-runtime
-Version: 1.0.12
+Version: 1.0.14
 Summary: A runtime system for NMDC data management and orchestration
 Home-page: https://github.com/microbiomedata/nmdc-runtime
 Author: Donny Winston
@@ -137,10 +137,10 @@ make up-dev
 Docker Compose is used to start local MongoDB and PostgresSQL (used by Dagster) instances, as well
 as a Dagster web server (dagit) and daemon (dagster-daemon).
 
-The Dagit web server is viewable at http://localhost:3000/.
+The Dagit web server is viewable at http://127.0.0.1:3000/. 
 
-The FastAPI service is viewable at http://localhost:8000/ -- e.g., rendered documentation at
-http://localhost:8000/redoc/.
+The FastAPI service is viewable at http://127.0.0.1:8000/ -- e.g., rendered documentation at
+http://127.0.0.1:8000/redoc/.
 
 ## Local Testing
 

{nmdc_runtime-1.0.12.dist-info → nmdc_runtime-1.0.14.dist-info}/RECORD

@@ -60,7 +60,7 @@ nmdc_runtime/site/terminusdb/schema.py,sha256=3e39rHUSZsNbN_F0SHHNsvcEGRWtYa6O9K
 nmdc_runtime/site/translation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 nmdc_runtime/site/translation/emsl.py,sha256=l6Q9Jj3RNJFQNYAU_TtKTJ7cyFcR93xBRs_lLdX0bMQ,1244
 nmdc_runtime/site/translation/gold.py,sha256=R3W99sdQb7Pgu_esN7ruIC-tyREQD_idJ4xCzkqWuGw,1622
-nmdc_runtime/site/translation/gold_translator.py,sha256=NypSTCiTFMWEWiUyUJ8oRFbIZ_O60FhHDRgJ1miL4QQ,25842
+nmdc_runtime/site/translation/gold_translator.py,sha256=vqTmZ5dqmaExIgA8nXpBYCs0d2OedNZgwbWJrt5Tm_M,26441
 nmdc_runtime/site/translation/jgi.py,sha256=bh73r0uq5BT3ywXwIa1OEKKtz9LbFsSng472tdr-xtg,875
 nmdc_runtime/site/translation/neon_translator.py,sha256=RjLMm2VHm1ASFr8J7p-EEWqPiE4KpUWtQdbTLsKha58,43440
 nmdc_runtime/site/translation/submission_portal_translator.py,sha256=qHMWqe3IwqhTYuwMYLmHHkewkWvJHC5nmsuwO3CFBP4,27608
@@ -71,9 +71,9 @@ nmdc_runtime/site/validation/emsl.py,sha256=TgckqKkFquHDLso77sn-jZRu5ZaBevGCt5p8
 nmdc_runtime/site/validation/gold.py,sha256=kJ1L081SZb-8qKpF731r5aQOueM206SUfUYMTTNTFMc,802
 nmdc_runtime/site/validation/jgi.py,sha256=lBo-FCtEYedT74CpW-Kdj512Ib963ik-4YIYmY5puDo,1298
 nmdc_runtime/site/validation/util.py,sha256=GGbMDSwR090sr_E_fHffCN418gpYESaiot6XghS7OYk,3349
-nmdc_runtime-1.0.12.dist-info/LICENSE,sha256=VWiv65r7gHGjgtr3jMJYVmQny5GRpQ6H-W9sScb1x70,2408
-nmdc_runtime-1.0.12.dist-info/METADATA,sha256=V8f9F5Kgrcjij1mpf2ri8SGcoaB84fFk6u8rx5S-lE8,7424
-nmdc_runtime-1.0.12.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-nmdc_runtime-1.0.12.dist-info/entry_points.txt,sha256=nfH6-K9tDKv7va8ENfShsBnxVQoYJdEe7HHdwtkbh1Y,289
-nmdc_runtime-1.0.12.dist-info/top_level.txt,sha256=b0K1s09L_iHH49ueBKaLrB5-lh6cyrSv9vL6x4Qvyz8,13
-nmdc_runtime-1.0.12.dist-info/RECORD,,
+nmdc_runtime-1.0.14.dist-info/LICENSE,sha256=VWiv65r7gHGjgtr3jMJYVmQny5GRpQ6H-W9sScb1x70,2408
+nmdc_runtime-1.0.14.dist-info/METADATA,sha256=O9nKIzZVMbCcPZUVDRUkky4UmdWlxTbePQnierx4mrY,7425
+nmdc_runtime-1.0.14.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+nmdc_runtime-1.0.14.dist-info/entry_points.txt,sha256=nfH6-K9tDKv7va8ENfShsBnxVQoYJdEe7HHdwtkbh1Y,289
+nmdc_runtime-1.0.14.dist-info/top_level.txt,sha256=b0K1s09L_iHH49ueBKaLrB5-lh6cyrSv9vL6x4Qvyz8,13
+nmdc_runtime-1.0.14.dist-info/RECORD,,