From 3591df9f5ec65100453fb0e512224623b919d1ce Mon Sep 17 00:00:00 2001 From: Danny Mandel Date: Tue, 17 Sep 2024 15:47:27 -0700 Subject: [PATCH 1/4] Move the SESARTransformer to the latest version of the iSamples Core JSON constants --- isamples_sesar/metadata_constants.py | 46 ++++++++++++++++ isamples_sesar/sesar_transformer.py | 82 +++++++++++++++------------- 2 files changed, 89 insertions(+), 39 deletions(-) create mode 100644 isamples_sesar/metadata_constants.py diff --git a/isamples_sesar/metadata_constants.py b/isamples_sesar/metadata_constants.py new file mode 100644 index 0000000..5a358c4 --- /dev/null +++ b/isamples_sesar/metadata_constants.py @@ -0,0 +1,46 @@ +""" +String constants used in metadata transformation +""" + +METADATA_SCHEMA = "$schema" +METADATA_AT_ID = "@id" +METADATA_LABEL = "label" +METADATA_IDENTIFIER = "identifier" +METADATA_SAMPLE_IDENTIFIER = "sample_identifier" +METADATA_DESCRIPTION = "description" +METADATA_HAS_CONTEXT_CATEGORY = "has_context_category" +METADATA_HAS_CONTEXT_CATEGORY_CONFIDENCE = "has_context_category_confidence" +METADATA_HAS_MATERIAL_CATEGORY = "has_material_category" +METADATA_HAS_MATERIAL_CATEGORY_CONFIDENCE = "has_material_category_confidence" +METADATA_HAS_SAMPLE_OBJECT_TYPE = "has_sample_object_type" +METADATA_HAS_SAMPLE_OBJECT_TYPE_CONFIDENCE = "has_sample_object_type_confidence" +METADATA_INFORMAL_CLASSIFICATION = "informal_classification" +METADATA_KEYWORDS = "keywords" +METADATA_KEYWORD = "keyword" +METADATA_SCHEME_NAME = "scheme_name" +METADATA_KEYWORD_URI = "keyword_uri" +METADATA_PRODUCED_BY = "produced_by" +METADATA_RESPONSIBILITY = "responsibility" +METADATA_HAS_FEATURE_OF_INTEREST = "has_feature_of_interest" +METADATA_RESULT_TIME = "result_time" +METADATA_SAMPLING_SITE = "sampling_site" +METADATA_SAMPLE_LOCATION = "sample_location" +METADATA_LOCATION = "location" +METADATA_ELEVATION = "elevation" +METADATA_LATITUDE = "latitude" +METADATA_LONGITUDE = "longitude" +METADATA_PLACE_NAME = "place_name" +METADATA_SUBSAMPLE = "subsample" +METADATA_REGISTRANT = "registrant" +METADATA_SAMPLING_PURPOSE = "sampling_purpose" +METADATA_CURATION = "curation" +METADATA_ACCESS_CONSTRAINTS = "access_constraints" +METADATA_CURATION_LOCATION = "curation_location" +METADATA_RELATED_RESOURCE = "related_resource" +METADATA_RELATIONSHIP = "relationship" +METADATA_TARGET = "target" +METADATA_AUTHORIZED_BY = "authorized_by" +METADATA_COMPLIES_WITH = "complies_with" +METADATA_ROLE = "role" +METADATA_NAME = "name" +METADATA_LAST_MODIFIED_TIME = "last_modified_time" \ No newline at end of file diff --git a/isamples_sesar/sesar_transformer.py b/isamples_sesar/sesar_transformer.py index cf83d77..6626a92 100644 --- a/isamples_sesar/sesar_transformer.py +++ b/isamples_sesar/sesar_transformer.py @@ -2,6 +2,14 @@ from typing import Optional import logging import h3 + +from .metadata_constants import METADATA_LABEL, METADATA_SAMPLE_IDENTIFIER, METADATA_DESCRIPTION, \ + METADATA_HAS_CONTEXT_CATEGORY, METADATA_HAS_MATERIAL_CATEGORY, METADATA_HAS_SAMPLE_OBJECT_TYPE, \ + METADATA_INFORMAL_CLASSIFICATION, METADATA_KEYWORDS, METADATA_AT_ID, METADATA_PRODUCED_BY, \ + METADATA_HAS_FEATURE_OF_INTEREST, METADATA_RESPONSIBILITY, METADATA_RESULT_TIME, METADATA_SAMPLING_SITE, \ + METADATA_SAMPLE_LOCATION, METADATA_ELEVATION, METADATA_LATITUDE, METADATA_LONGITUDE, METADATA_PLACE_NAME, \ + METADATA_REGISTRANT, METADATA_SAMPLING_PURPOSE, METADATA_CURATION, METADATA_ACCESS_CONSTRAINTS, \ + METADATA_CURATION_LOCATION, METADATA_RELATED_RESOURCE, METADATA_AUTHORIZED_BY, METADATA_COMPLIES_WITH from .sample import Sample from .mapper import ( @@ -39,53 +47,49 @@ def transform(self) -> typing.Dict: specimen_categories = self.has_specimen_categories() transformed_record = { "$schema": "iSamplesSchemaCore1.0.json", - "@id": self.id_string(), - "label": self.sample_label(), - "sampleidentifier": self.sample_identifier_string(), - "description": self.sample_description(), - "hasContextCategory": context_categories, + METADATA_AT_ID: self.id_string(), + METADATA_LABEL: self.sample_label(), + METADATA_SAMPLE_IDENTIFIER: self.sample_identifier_string(), + METADATA_DESCRIPTION: self.sample_description(), + METADATA_HAS_CONTEXT_CATEGORY: context_categories, # "hasContextCategoryConfidence": self.has_context_category_confidences(context_categories), - "hasMaterialCategory": material_categories, + METADATA_HAS_MATERIAL_CATEGORY: material_categories, # "hasMaterialCategoryConfidence": self.has_material_category_confidences(material_categories), - "hasSpecimenCategory": specimen_categories, + METADATA_HAS_SAMPLE_OBJECT_TYPE: specimen_categories, # "hasSpecimenCategoryConfidence": self.has_specimen_category_confidences(specimen_categories), - "informalClassification": self.informal_classification(), - "keywords": self.keywords(), - "producedBy": { - "@id": self.produced_by_id_string(), - "label": self.produced_by_label(), - "description": self.produced_by_description(), - "hasFeatureOfInterest": self.produced_by_feature_of_interest(), - "responsibility": self.produced_by_responsibilities(), - "resultTime": self.produced_by_result_time(), - "samplingSite": { - "description": self.sampling_site_description(), - "label": self.sampling_site_label(), - "location": { - "elevation": self.sampling_site_elevation(), - "latitude": self.sampling_site_latitude(), - "longitude": self.sampling_site_longitude(), + METADATA_INFORMAL_CLASSIFICATION: self.informal_classification(), + METADATA_KEYWORDS: self.keywords(), + METADATA_PRODUCED_BY: { + METADATA_AT_ID: self.produced_by_id_string(), + METADATA_LABEL: self.produced_by_label(), + METADATA_DESCRIPTION: self.produced_by_description(), + METADATA_HAS_FEATURE_OF_INTEREST: self.produced_by_feature_of_interest(), + METADATA_RESPONSIBILITY: self.produced_by_responsibilities(), + METADATA_RESULT_TIME: self.produced_by_result_time(), + METADATA_SAMPLING_SITE: { + METADATA_DESCRIPTION: self.sampling_site_description(), + METADATA_LABEL: self.sampling_site_label(), + METADATA_SAMPLE_LOCATION: { + METADATA_ELEVATION: self.sampling_site_elevation(), + METADATA_LATITUDE: self.sampling_site_latitude(), + METADATA_LONGITUDE: self.sampling_site_longitude(), }, - "placeName": self.sampling_site_place_names(), + METADATA_PLACE_NAME: self.sampling_site_place_names(), }, }, - "registrant": self.sample_registrant(), - "samplingPurpose": self.sample_sampling_purpose(), - "curation": { - "label": self.curation_label(), - "description": self.curation_description(), - "accessConstraints": self.curation_access_constraints(), - "curationLocation": self.curation_location(), - "responsibility": self.curation_responsibility(), + METADATA_REGISTRANT: self.sample_registrant(), + METADATA_SAMPLING_PURPOSE: self.sample_sampling_purpose(), + METADATA_CURATION: { + METADATA_LABEL: self.curation_label(), + METADATA_DESCRIPTION: self.curation_description(), + METADATA_ACCESS_CONSTRAINTS: self.curation_access_constraints(), + METADATA_CURATION_LOCATION: self.curation_location(), + METADATA_RESPONSIBILITY: self.curation_responsibility(), }, - "relatedResource": self.related_resources(), - "authorizedBy": self.authorized_by(), - "compliesWith": self.complies_with(), + METADATA_RELATED_RESOURCE: self.related_resources(), + METADATA_AUTHORIZED_BY: self.authorized_by(), + METADATA_COMPLIES_WITH: self.complies_with(), } - for index in range(0, 15): - h3_at_resolution = self.h3_function()(self.sample.latitude, self.sample.longitude, index) - field_name = f"producedBy_samplingSite_location_h3_{index}" - transformed_record[field_name] = h3_at_resolution return transformed_record def has_context_categories(self) -> typing.List[str]: From 9d00343ff13a54eb8155437882d247237a90f5e8 Mon Sep 17 00:00:00 2001 From: Danny Mandel Date: Fri, 20 Sep 2024 10:31:48 -0700 Subject: [PATCH 2/4] Update the code to use the iSamples API package --- examples/EOI00002H.json | 91 +- examples/IEDUT103B.json | 91 +- examples/IEEJR000M.json | 87 +- examples/IEJEN0040.json | 87 +- examples/IERVTL1I7.json | 91 +- examples/ODP02Q1IZ.json | 95 +- isamples_sesar/metadata_constants.py | 46 - isamples_sesar/sesar_transformer.py | 71 +- poetry.lock | 3978 +++++++++++++++----------- pyproject.toml | 1 + tests/test_isamples_metadata.py | 76 +- 11 files changed, 2637 insertions(+), 2077 deletions(-) delete mode 100644 isamples_sesar/metadata_constants.py diff --git a/examples/EOI00002H.json b/examples/EOI00002H.json index c5f25cf..f1d1134 100644 --- a/examples/EOI00002H.json +++ b/examples/EOI00002H.json @@ -1,36 +1,19 @@ { "$schema": "iSamplesSchemaCore1.0.json", "@id": "https://data.isamples.org/digitalsample/igsn/10.58052/EOI00002H", - "authorizedBy": [], - "compliesWith": [], - "curation": { - "accessConstraints": "Not Provided", - "curationLocation": "Not Provided", - "description": "Not Provided", - "label": "Not Provided", - "responsibility": [ - { - "contact_information": "andra.bobbitt@noaa.gov", - "name": "Andra Bobbitt", - "role": "sample owner" - }, - { - "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/", - "role": "metadata publisher" - } - ] - }, + "label": "J730-GTHFS-16", + "sample_identifier": "igsn:10.58052/EOI00002H", "description": "Gas. Sampler:Fluid:GTHFS. HFS gastight. Red-center-9. T=250C", - "hasContextCategory": [ + "has_context_category": [ "Subsurface fluid reservoir" ], - "hasMaterialCategory": [ + "has_material_category": [ "Gaseous material" ], - "hasSpecimenCategory": [ + "has_sample_object_type": [ "Other solid object" ], - "informalClassification": [ + "informal_classification": [ "Not Provided" ], "keywords": [ @@ -39,53 +22,55 @@ "scheme_name": "SESAR: Sample Type" } ], - "label": "J730-GTHFS-16", - "producedBy": { + "produced_by": { "@id": "", - "description": "cruiseFieldPrgrm:TN300. launchPlatformName:Jason II. Collection method:Sampler:Fluid:GTHFS. HFS gastight. Red-center-9. T=250C. launch type:ROV, navigation type:USBL", - "hasFeatureOfInterest": "volcano", "label": "Sampler:Fluid:GTHFS, TN300", + "description": "cruiseFieldPrgrm:TN300. launchPlatformName:Jason II. Collection method:Sampler:Fluid:GTHFS. HFS gastight. Red-center-9. T=250C. launch type:ROV, navigation type:USBL", + "has_feature_of_interest": "volcano", "responsibility": [ { - "name": "Evans_Leigh", - "role": "collector" + "role": "collector", + "name": "Evans_Leigh" }, { - "name": "TN300", - "role": "sponsor" + "role": "sponsor", + "name": "TN300" } ], - "resultTime": "2013-09-14", - "samplingSite": { + "result_time": "2013-09-14", + "sampling_site": { "description": "Trevi:Jason Tmax=257.9 C. In the direct flow at this small anhydrite mound (anhydrite knocked over).", "label": "Not Provided", - "location": { + "sample_location": { "elevation": "-1520.0 m", "latitude": 45.946265, "longitude": -129.983725 }, - "placeName": [ + "place_name": [ "Axial Seamount" ] } }, - "producedBy_samplingSite_location_h3_0": "8029fffffffffff", - "producedBy_samplingSite_location_h3_1": "8128fffffffffff", - "producedBy_samplingSite_location_h3_10": "8a28ed791baffff", - "producedBy_samplingSite_location_h3_11": "8b28ed791ba9fff", - "producedBy_samplingSite_location_h3_12": "8c28ed791ba97ff", - "producedBy_samplingSite_location_h3_13": "8d28ed791ba967f", - "producedBy_samplingSite_location_h3_14": "8e28ed791ba9647", - "producedBy_samplingSite_location_h3_2": "8228effffffffff", - "producedBy_samplingSite_location_h3_3": "8328edfffffffff", - "producedBy_samplingSite_location_h3_4": "8428ed7ffffffff", - "producedBy_samplingSite_location_h3_5": "8528ed7bfffffff", - "producedBy_samplingSite_location_h3_6": "8628ed797ffffff", - "producedBy_samplingSite_location_h3_7": "8728ed791ffffff", - "producedBy_samplingSite_location_h3_8": "8828ed791bfffff", - "producedBy_samplingSite_location_h3_9": "8928ed791bbffff", "registrant": "Andra Bobbitt", - "relatedResource": [], - "sampleidentifier": "igsn:10.58052/EOI00002H", - "samplingPurpose": "Not Provided" + "sampling_purpose": "Not Provided", + "curation": { + "label": "Not Provided", + "description": "Not Provided", + "access_constraints": "Not Provided", + "curation_location": "Not Provided", + "responsibility": [ + { + "role": "sample owner", + "name": "Andra Bobbitt", + "contact_information": "andra.bobbitt@noaa.gov" + }, + { + "role": "metadata publisher", + "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/" + } + ] + }, + "related_resource": [], + "authorized_by": [], + "complies_with": [] } \ No newline at end of file diff --git a/examples/IEDUT103B.json b/examples/IEDUT103B.json index 4b48931..dc715e8 100644 --- a/examples/IEDUT103B.json +++ b/examples/IEDUT103B.json @@ -1,37 +1,20 @@ { "$schema": "iSamplesSchemaCore1.0.json", "@id": "https://data.isamples.org/digitalsample/igsn/10.58052/IEDUT103B", - "authorizedBy": [], - "compliesWith": [], - "curation": { - "accessConstraints": "Not Provided", - "curationLocation": "University of Florida Department of Geological Sciences", - "description": "Not Provided", - "label": "Not Provided", - "responsibility": [ - { - "contact_information": "dutton3@wisc.edu", - "name": "Andrea Dutton", - "role": "sample owner" - }, - { - "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/", - "role": "metadata publisher" - } - ] - }, + "label": "JAM42", + "sample_identifier": "igsn:10.58052/IEDUT103B", "description": "Macrobiology>Coral>Biology. Coring>HandHeldCorer. piece of short core", - "hasContextCategory": [ + "has_context_category": [ "Not Provided" ], - "hasMaterialCategory": [ + "has_material_category": [ "Organic material", "Biogenic non-organic material" ], - "hasSpecimenCategory": [ + "has_sample_object_type": [ "Not Provided" ], - "informalClassification": [ + "informal_classification": [ "Not Provided" ], "keywords": [ @@ -44,32 +27,31 @@ "scheme_name": "taxon: species" } ], - "label": "JAM42", - "producedBy": { + "produced_by": { "@id": "", - "description": "cruiseFieldPrgrm:UF Jamaica 2015 Fieldwork. Collection method:Coring>HandHeldCorer. piece of short core", - "hasFeatureOfInterest": "Reef", "label": "Coring>HandHeldCorer, UF Jamaica 2015 Fieldwork", + "description": "cruiseFieldPrgrm:UF Jamaica 2015 Fieldwork. Collection method:Coring>HandHeldCorer. piece of short core", + "has_feature_of_interest": "Reef", "responsibility": [ { - "name": "Andrea Dutton", - "role": "collector" + "role": "collector", + "name": "Andrea Dutton" }, { - "name": "UF Jamaica 2015 Fieldwork", - "role": "sponsor" + "role": "sponsor", + "name": "UF Jamaica 2015 Fieldwork" } ], - "resultTime": "2015-06-19", - "samplingSite": { + "result_time": "2015-06-19", + "sampling_site": { "description": "Between Buccaneer Villa, Treasure Beach, and Great Bay", "label": "Treasure Beach", - "location": { + "sample_location": { "elevation": "1.626 m", "latitude": 17.88451, "longitude": -77.77107 }, - "placeName": [ + "place_name": [ "Limestone Falmouth Formation ", "Saint Elizabeth", "Cornwall", @@ -77,23 +59,26 @@ ] } }, - "producedBy_samplingSite_location_h3_0": "8067fffffffffff", - "producedBy_samplingSite_location_h3_1": "8145bffffffffff", - "producedBy_samplingSite_location_h3_10": "8a45b29884e7fff", - "producedBy_samplingSite_location_h3_11": "8b45b29884e1fff", - "producedBy_samplingSite_location_h3_12": "8c45b29884e15ff", - "producedBy_samplingSite_location_h3_13": "8d45b29884e147f", - "producedBy_samplingSite_location_h3_14": "8e45b29884e1457", - "producedBy_samplingSite_location_h3_2": "8245b7fffffffff", - "producedBy_samplingSite_location_h3_3": "8345b2fffffffff", - "producedBy_samplingSite_location_h3_4": "8445b29ffffffff", - "producedBy_samplingSite_location_h3_5": "8545b29bfffffff", - "producedBy_samplingSite_location_h3_6": "8645b298fffffff", - "producedBy_samplingSite_location_h3_7": "8745b2988ffffff", - "producedBy_samplingSite_location_h3_8": "8845b29885fffff", - "producedBy_samplingSite_location_h3_9": "8945b29884fffff", "registrant": "Andrea Dutton", - "relatedResource": [], - "sampleidentifier": "igsn:10.58052/IEDUT103B", - "samplingPurpose": "Paleosea-level" + "sampling_purpose": "Paleosea-level", + "curation": { + "label": "Not Provided", + "description": "Not Provided", + "access_constraints": "Not Provided", + "curation_location": "University of Florida Department of Geological Sciences", + "responsibility": [ + { + "role": "sample owner", + "name": "Andrea Dutton", + "contact_information": "dutton3@wisc.edu" + }, + { + "role": "metadata publisher", + "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/" + } + ] + }, + "related_resource": [], + "authorized_by": [], + "complies_with": [] } \ No newline at end of file diff --git a/examples/IEEJR000M.json b/examples/IEEJR000M.json index b3813a7..f0d4884 100644 --- a/examples/IEEJR000M.json +++ b/examples/IEEJR000M.json @@ -1,36 +1,19 @@ { "$schema": "iSamplesSchemaCore1.0.json", "@id": "https://data.isamples.org/digitalsample/igsn/10.58052/IEEJR000M", - "authorizedBy": [], - "compliesWith": [], - "curation": { - "accessConstraints": "Not Provided", - "curationLocation": "The University of Texas at Austin", - "description": "Not Provided", - "label": "Not Provided", - "responsibility": [ - { - "contact_information": "ejramos@utexas.edu", - "name": "Evan Ramos", - "role": "sample owner" - }, - { - "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/", - "role": "metadata publisher" - } - ] - }, + "label": "16ER6F3", + "sample_identifier": "igsn:10.58052/IEEJR000M", "description": "Metamorphic>Meta-Carbonate>Rock. Manual>Hammer", - "hasContextCategory": [ + "has_context_category": [ "Earth interior" ], - "hasMaterialCategory": [ + "has_material_category": [ "Rock" ], - "hasSpecimenCategory": [ + "has_sample_object_type": [ "Other solid object" ], - "informalClassification": [ + "informal_classification": [ "Not Provided" ], "keywords": [ @@ -43,28 +26,27 @@ "scheme_name": "taxon: species" } ], - "label": "16ER6F3", - "producedBy": { + "produced_by": { "@id": "", - "description": "Collection method:Manual>Hammer", - "hasFeatureOfInterest": "Metamorphic aureole", "label": "Manual>Hammer", + "description": "Collection method:Manual>Hammer", + "has_feature_of_interest": "Metamorphic aureole", "responsibility": [ { - "name": "Jade Star Lackey", - "role": "collector" + "role": "collector", + "name": "Jade Star Lackey" } ], - "resultTime": "2021-01-19", - "samplingSite": { + "result_time": "2021-01-19", + "sampling_site": { "description": "Not Provided", "label": "Not Provided", - "location": { + "sample_location": { "elevation": "Not Provided", "latitude": 36.461666, "longitude": -118.583888 }, - "placeName": [ + "place_name": [ "Mineral King", "Sequoia National Forest", "California", @@ -73,23 +55,26 @@ ] } }, - "producedBy_samplingSite_location_h3_0": "8029fffffffffff", - "producedBy_samplingSite_location_h3_1": "8129bffffffffff", - "producedBy_samplingSite_location_h3_10": "8a29aa8f66dffff", - "producedBy_samplingSite_location_h3_11": "8b29aa8f66dbfff", - "producedBy_samplingSite_location_h3_12": "8c29aa8f66dbbff", - "producedBy_samplingSite_location_h3_13": "8d29aa8f66dbaff", - "producedBy_samplingSite_location_h3_14": "8e29aa8f66dbaef", - "producedBy_samplingSite_location_h3_2": "8229affffffffff", - "producedBy_samplingSite_location_h3_3": "8329aafffffffff", - "producedBy_samplingSite_location_h3_4": "8429aa9ffffffff", - "producedBy_samplingSite_location_h3_5": "8529aa8ffffffff", - "producedBy_samplingSite_location_h3_6": "8629aa8f7ffffff", - "producedBy_samplingSite_location_h3_7": "8729aa8f2ffffff", - "producedBy_samplingSite_location_h3_8": "8829aa8f2dfffff", - "producedBy_samplingSite_location_h3_9": "8929aa8f2d7ffff", "registrant": "Evan Ramos", - "relatedResource": [], - "sampleidentifier": "igsn:10.58052/IEEJR000M", - "samplingPurpose": "Not Provided" + "sampling_purpose": "Not Provided", + "curation": { + "label": "Not Provided", + "description": "Not Provided", + "access_constraints": "Not Provided", + "curation_location": "The University of Texas at Austin", + "responsibility": [ + { + "role": "sample owner", + "name": "Evan Ramos", + "contact_information": "ejramos@utexas.edu" + }, + { + "role": "metadata publisher", + "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/" + } + ] + }, + "related_resource": [], + "authorized_by": [], + "complies_with": [] } \ No newline at end of file diff --git a/examples/IEJEN0040.json b/examples/IEJEN0040.json index 97247dc..e12fd90 100644 --- a/examples/IEJEN0040.json +++ b/examples/IEJEN0040.json @@ -1,36 +1,19 @@ { "$schema": "iSamplesSchemaCore1.0.json", "@id": "https://data.isamples.org/digitalsample/igsn/10.58052/IEJEN0040", - "authorizedBy": [], - "compliesWith": [], - "curation": { - "accessConstraints": "Not Provided", - "curationLocation": "Lamont-Doherty Earth Observatory", - "description": "Not Provided", - "label": "Not Provided", - "responsibility": [ - { - "contact_information": "jnichols@ldeo.columbia.edu", - "name": "Jonathan Nichols", - "role": "sample owner" - }, - { - "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/", - "role": "metadata publisher" - } - ] - }, + "label": "Goldfin ~20 m moss from 30 cm hummock", + "sample_identifier": "igsn:10.58052/IEJEN0040", "description": "Biology", - "hasContextCategory": [ + "has_context_category": [ "Not Provided" ], - "hasMaterialCategory": [ + "has_material_category": [ "Organic material" ], - "hasSpecimenCategory": [ + "has_sample_object_type": [ "Other solid object" ], - "informalClassification": [ + "informal_classification": [ "Not Provided" ], "keywords": [ @@ -39,49 +22,51 @@ "scheme_name": "SESAR: Sample Type" } ], - "label": "Goldfin ~20 m moss from 30 cm hummock", - "producedBy": { + "produced_by": { "@id": "", - "description": "Not Provided", - "hasFeatureOfInterest": "peatland", "label": "Not Provided", + "description": "Not Provided", + "has_feature_of_interest": "peatland", "responsibility": [ { - "name": "Miriam Jones", - "role": "collector" + "role": "collector", + "name": "Miriam Jones" } ], - "resultTime": "2017-09-01", - "samplingSite": { + "result_time": "2017-09-01", + "sampling_site": { "description": "Not Provided", "label": "Not Provided", - "location": { + "sample_location": { "elevation": "Not Provided", "latitude": 60.25455, "longitude": -149.35756666667 }, - "placeName": [ + "place_name": [ "Gold Fin" ] } }, - "producedBy_samplingSite_location_h3_0": "800dfffffffffff", - "producedBy_samplingSite_location_h3_1": "810c7ffffffffff", - "producedBy_samplingSite_location_h3_10": "8a0c42d0e837fff", - "producedBy_samplingSite_location_h3_11": "8b0c42d0e832fff", - "producedBy_samplingSite_location_h3_12": "8c0c42d0e8327ff", - "producedBy_samplingSite_location_h3_13": "8d0c42d0e8326ff", - "producedBy_samplingSite_location_h3_14": "8e0c42d0e8326e7", - "producedBy_samplingSite_location_h3_2": "820c47fffffffff", - "producedBy_samplingSite_location_h3_3": "830c42fffffffff", - "producedBy_samplingSite_location_h3_4": "840c42dffffffff", - "producedBy_samplingSite_location_h3_5": "850c42d3fffffff", - "producedBy_samplingSite_location_h3_6": "860c42d0fffffff", - "producedBy_samplingSite_location_h3_7": "870c42d0effffff", - "producedBy_samplingSite_location_h3_8": "880c42d0e9fffff", - "producedBy_samplingSite_location_h3_9": "890c42d0e83ffff", "registrant": "Jonathan Nichols", - "relatedResource": [], - "sampleidentifier": "igsn:10.58052/IEJEN0040", - "samplingPurpose": "Not Provided" + "sampling_purpose": "Not Provided", + "curation": { + "label": "Not Provided", + "description": "Not Provided", + "access_constraints": "Not Provided", + "curation_location": "Lamont-Doherty Earth Observatory", + "responsibility": [ + { + "role": "sample owner", + "name": "Jonathan Nichols", + "contact_information": "jnichols@ldeo.columbia.edu" + }, + { + "role": "metadata publisher", + "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/" + } + ] + }, + "related_resource": [], + "authorized_by": [], + "complies_with": [] } \ No newline at end of file diff --git a/examples/IERVTL1I7.json b/examples/IERVTL1I7.json index d1b4fee..a619a0b 100644 --- a/examples/IERVTL1I7.json +++ b/examples/IERVTL1I7.json @@ -1,36 +1,19 @@ { "$schema": "iSamplesSchemaCore1.0.json", "@id": "https://data.isamples.org/digitalsample/igsn/10.58052/IERVTL1I7", - "authorizedBy": [], - "compliesWith": [], - "curation": { - "accessConstraints": "Not Provided", - "curationLocation": "Not Provided", - "description": "Not Provided", - "label": "Not Provided", - "responsibility": [ - { - "contact_information": "wfsfa-data@lbl.gov", - "name": "Watershed Function SFA Data Team", - "role": "sample owner" - }, - { - "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/", - "role": "metadata publisher" - } - ] - }, + "label": "0744", + "sample_identifier": "igsn:10.58052/IERVTL1I7", "description": "Gas. Headspace equilibration method", - "hasContextCategory": [ + "has_context_category": [ "Subsurface fluid reservoir" ], - "hasMaterialCategory": [ + "has_material_category": [ "Gaseous material" ], - "hasSpecimenCategory": [ + "has_sample_object_type": [ "Other solid object" ], - "informalClassification": [ + "informal_classification": [ "Not Provided" ], "keywords": [ @@ -39,51 +22,53 @@ "scheme_name": "SESAR: Sample Type" } ], - "label": "0744", - "producedBy": { + "produced_by": { "@id": "igsn:10.58052/IERVTNTEZ", - "description": "cruiseFieldPrgrm:SLAC-SFA. Collection method:Headspace equilibration method", - "hasFeatureOfInterest": "floodplain, aquifer", "label": "Headspace equilibration method, SLAC-SFA", + "description": "cruiseFieldPrgrm:SLAC-SFA. Collection method:Headspace equilibration method", + "has_feature_of_interest": "floodplain, aquifer", "responsibility": [ { - "name": "Zach Perzan", - "role": "collector" + "role": "collector", + "name": "Zach Perzan" }, { - "name": "SLAC-SFA", - "role": "sponsor" + "role": "sponsor", + "name": "SLAC-SFA" } ], - "resultTime": "2019-05-24", - "samplingSite": { + "result_time": "2019-05-24", + "sampling_site": { "description": "Not Provided", "label": "Not Provided", - "location": { + "sample_location": { "elevation": "Not Provided", "latitude": 42.988396, "longitude": -108.400284 }, - "placeName": [] + "place_name": [] } }, - "producedBy_samplingSite_location_h3_0": "8027fffffffffff", - "producedBy_samplingSite_location_h3_1": "8126bffffffffff", - "producedBy_samplingSite_location_h3_10": "8a26b56364a7fff", - "producedBy_samplingSite_location_h3_11": "8b26b56364a3fff", - "producedBy_samplingSite_location_h3_12": "8c26b56364a31ff", - "producedBy_samplingSite_location_h3_13": "8d26b56364a30ff", - "producedBy_samplingSite_location_h3_14": "8e26b56364a30c7", - "producedBy_samplingSite_location_h3_2": "8226b7fffffffff", - "producedBy_samplingSite_location_h3_3": "8326b5fffffffff", - "producedBy_samplingSite_location_h3_4": "8426b57ffffffff", - "producedBy_samplingSite_location_h3_5": "8526b57bfffffff", - "producedBy_samplingSite_location_h3_6": "8626b5637ffffff", - "producedBy_samplingSite_location_h3_7": "8726b5636ffffff", - "producedBy_samplingSite_location_h3_8": "8826b56365fffff", - "producedBy_samplingSite_location_h3_9": "8926b56364bffff", "registrant": "SLAC SFA", - "relatedResource": [], - "sampleidentifier": "igsn:10.58052/IERVTL1I7", - "samplingPurpose": "2018 inundation tracer tests" + "sampling_purpose": "2018 inundation tracer tests", + "curation": { + "label": "Not Provided", + "description": "Not Provided", + "access_constraints": "Not Provided", + "curation_location": "Not Provided", + "responsibility": [ + { + "role": "sample owner", + "name": "Watershed Function SFA Data Team", + "contact_information": "wfsfa-data@lbl.gov" + }, + { + "role": "metadata publisher", + "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/" + } + ] + }, + "related_resource": [], + "authorized_by": [], + "complies_with": [] } \ No newline at end of file diff --git a/examples/ODP02Q1IZ.json b/examples/ODP02Q1IZ.json index 110c9d0..ad0206a 100644 --- a/examples/ODP02Q1IZ.json +++ b/examples/ODP02Q1IZ.json @@ -1,40 +1,19 @@ { "$schema": "iSamplesSchemaCore1.0.json", "@id": "https://data.isamples.org/digitalsample/igsn/10.60471/ODP02Q1IZ", - "authorizedBy": [], - "compliesWith": [], - "curation": { - "accessConstraints": "Not Provided", - "curationLocation": "Integrated Ocean Drilling Program (IODP)", - "description": "Not Provided", - "label": "Not Provided", - "responsibility": [ - { - "name": "Integrated Ocean Drilling Program (TAMU)", - "role": "curator" - }, - { - "contact_information": "information@iodp.tamu.edu", - "name": "Integrated Ocean Drilling Program (TAMU)", - "role": "sample owner" - }, - { - "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/", - "role": "metadata publisher" - } - ] - }, + "label": "Sample 178-1098B-1H-3 (26-27 cm.)", + "sample_identifier": "igsn:10.60471/ODP02Q1IZ", "description": "Janus sample_id: 63151", - "hasContextCategory": [ + "has_context_category": [ "Not Provided" ], - "hasMaterialCategory": [ + "has_material_category": [ "Not Provided" ], - "hasSpecimenCategory": [ + "has_sample_object_type": [ "Other solid object" ], - "informalClassification": [ + "informal_classification": [ "Not Provided" ], "keywords": [ @@ -43,47 +22,53 @@ "scheme_name": "SESAR: Sample Type" } ], - "label": "Sample 178-1098B-1H-3 (26-27 cm.)", - "producedBy": { + "produced_by": { "@id": "igsn:10.60471/ODP01LAMY", - "description": "cruiseFieldPrgrm:ODP Leg 178. Janus sample_id: 63151", - "hasFeatureOfInterest": "Not Provided", "label": "ODP Leg 178", + "description": "cruiseFieldPrgrm:ODP Leg 178. Janus sample_id: 63151", + "has_feature_of_interest": "Not Provided", "responsibility": [ { - "name": "ODP Leg 178", - "role": "sponsor" + "role": "sponsor", + "name": "ODP Leg 178" } ], - "resultTime": "2006-08-11", - "samplingSite": { + "result_time": "2006-08-11", + "sampling_site": { "description": "Not Provided", "label": "Not Provided", - "location": { + "sample_location": { "elevation": "-1010.6 m", "latitude": -64.86194, "longitude": -64.20799 }, - "placeName": [] + "place_name": [] } }, - "producedBy_samplingSite_location_h3_0": "80dffffffffffff", - "producedBy_samplingSite_location_h3_1": "81df3ffffffffff", - "producedBy_samplingSite_location_h3_10": "8adf35928cf7fff", - "producedBy_samplingSite_location_h3_11": "8bdf35928cf0fff", - "producedBy_samplingSite_location_h3_12": "8cdf35928cf05ff", - "producedBy_samplingSite_location_h3_13": "8ddf35928cf0cff", - "producedBy_samplingSite_location_h3_14": "8edf35928cf0cdf", - "producedBy_samplingSite_location_h3_2": "82df37fffffffff", - "producedBy_samplingSite_location_h3_3": "83e89bfffffffff", - "producedBy_samplingSite_location_h3_4": "84df359ffffffff", - "producedBy_samplingSite_location_h3_5": "85df3593fffffff", - "producedBy_samplingSite_location_h3_6": "86df3592fffffff", - "producedBy_samplingSite_location_h3_7": "87df35928ffffff", - "producedBy_samplingSite_location_h3_8": "88df35928dfffff", - "producedBy_samplingSite_location_h3_9": "89df35928cfffff", "registrant": "Integrated Ocean Drilling Program (TAMU)", - "relatedResource": [], - "sampleidentifier": "igsn:10.60471/ODP02Q1IZ", - "samplingPurpose": "Not Provided" + "sampling_purpose": "Not Provided", + "curation": { + "label": "Not Provided", + "description": "Not Provided", + "access_constraints": "Not Provided", + "curation_location": "Integrated Ocean Drilling Program (IODP)", + "responsibility": [ + { + "role": "curator", + "name": "Integrated Ocean Drilling Program (TAMU)" + }, + { + "role": "sample owner", + "name": "Integrated Ocean Drilling Program (TAMU)", + "contact_information": "information@iodp.tamu.edu" + }, + { + "role": "metadata publisher", + "contact_information": "info@geosamples.org; url: https://www.geosamples.org/contact/" + } + ] + }, + "related_resource": [], + "authorized_by": [], + "complies_with": [] } \ No newline at end of file diff --git a/isamples_sesar/metadata_constants.py b/isamples_sesar/metadata_constants.py deleted file mode 100644 index 5a358c4..0000000 --- a/isamples_sesar/metadata_constants.py +++ /dev/null @@ -1,46 +0,0 @@ -""" -String constants used in metadata transformation -""" - -METADATA_SCHEMA = "$schema" -METADATA_AT_ID = "@id" -METADATA_LABEL = "label" -METADATA_IDENTIFIER = "identifier" -METADATA_SAMPLE_IDENTIFIER = "sample_identifier" -METADATA_DESCRIPTION = "description" -METADATA_HAS_CONTEXT_CATEGORY = "has_context_category" -METADATA_HAS_CONTEXT_CATEGORY_CONFIDENCE = "has_context_category_confidence" -METADATA_HAS_MATERIAL_CATEGORY = "has_material_category" -METADATA_HAS_MATERIAL_CATEGORY_CONFIDENCE = "has_material_category_confidence" -METADATA_HAS_SAMPLE_OBJECT_TYPE = "has_sample_object_type" -METADATA_HAS_SAMPLE_OBJECT_TYPE_CONFIDENCE = "has_sample_object_type_confidence" -METADATA_INFORMAL_CLASSIFICATION = "informal_classification" -METADATA_KEYWORDS = "keywords" -METADATA_KEYWORD = "keyword" -METADATA_SCHEME_NAME = "scheme_name" -METADATA_KEYWORD_URI = "keyword_uri" -METADATA_PRODUCED_BY = "produced_by" -METADATA_RESPONSIBILITY = "responsibility" -METADATA_HAS_FEATURE_OF_INTEREST = "has_feature_of_interest" -METADATA_RESULT_TIME = "result_time" -METADATA_SAMPLING_SITE = "sampling_site" -METADATA_SAMPLE_LOCATION = "sample_location" -METADATA_LOCATION = "location" -METADATA_ELEVATION = "elevation" -METADATA_LATITUDE = "latitude" -METADATA_LONGITUDE = "longitude" -METADATA_PLACE_NAME = "place_name" -METADATA_SUBSAMPLE = "subsample" -METADATA_REGISTRANT = "registrant" -METADATA_SAMPLING_PURPOSE = "sampling_purpose" -METADATA_CURATION = "curation" -METADATA_ACCESS_CONSTRAINTS = "access_constraints" -METADATA_CURATION_LOCATION = "curation_location" -METADATA_RELATED_RESOURCE = "related_resource" -METADATA_RELATIONSHIP = "relationship" -METADATA_TARGET = "target" -METADATA_AUTHORIZED_BY = "authorized_by" -METADATA_COMPLIES_WITH = "complies_with" -METADATA_ROLE = "role" -METADATA_NAME = "name" -METADATA_LAST_MODIFIED_TIME = "last_modified_time" \ No newline at end of file diff --git a/isamples_sesar/sesar_transformer.py b/isamples_sesar/sesar_transformer.py index 6626a92..3753b39 100644 --- a/isamples_sesar/sesar_transformer.py +++ b/isamples_sesar/sesar_transformer.py @@ -2,14 +2,9 @@ from typing import Optional import logging import h3 +from isamples_api.controlled_vocabulary import VocabularyTerm +from isamples_api.transformer import AbstractTransformer -from .metadata_constants import METADATA_LABEL, METADATA_SAMPLE_IDENTIFIER, METADATA_DESCRIPTION, \ - METADATA_HAS_CONTEXT_CATEGORY, METADATA_HAS_MATERIAL_CATEGORY, METADATA_HAS_SAMPLE_OBJECT_TYPE, \ - METADATA_INFORMAL_CLASSIFICATION, METADATA_KEYWORDS, METADATA_AT_ID, METADATA_PRODUCED_BY, \ - METADATA_HAS_FEATURE_OF_INTEREST, METADATA_RESPONSIBILITY, METADATA_RESULT_TIME, METADATA_SAMPLING_SITE, \ - METADATA_SAMPLE_LOCATION, METADATA_ELEVATION, METADATA_LATITUDE, METADATA_LONGITUDE, METADATA_PLACE_NAME, \ - METADATA_REGISTRANT, METADATA_SAMPLING_PURPOSE, METADATA_CURATION, METADATA_ACCESS_CONSTRAINTS, \ - METADATA_CURATION_LOCATION, METADATA_RELATED_RESOURCE, METADATA_AUTHORIZED_BY, METADATA_COMPLIES_WITH from .sample import Sample from .mapper import ( @@ -22,7 +17,7 @@ ) -class Transformer(): +class Transformer(AbstractTransformer): NOT_PROVIDED = "Not Provided" @@ -34,64 +29,6 @@ def __init__(self, sample: Sample): self.sample = sample self._material_prediction_results: Optional[list] = None - def transform(self) -> typing.Dict: - """Do the actual work of transforming a Sesar record into an iSamples record. - - Arguments: - sample -- The Sesar record to be transformed - Return value: - The Sesar record transformed into an iSamples record - """ - context_categories = self.has_context_categories() - material_categories = self.has_material_categories() - specimen_categories = self.has_specimen_categories() - transformed_record = { - "$schema": "iSamplesSchemaCore1.0.json", - METADATA_AT_ID: self.id_string(), - METADATA_LABEL: self.sample_label(), - METADATA_SAMPLE_IDENTIFIER: self.sample_identifier_string(), - METADATA_DESCRIPTION: self.sample_description(), - METADATA_HAS_CONTEXT_CATEGORY: context_categories, - # "hasContextCategoryConfidence": self.has_context_category_confidences(context_categories), - METADATA_HAS_MATERIAL_CATEGORY: material_categories, - # "hasMaterialCategoryConfidence": self.has_material_category_confidences(material_categories), - METADATA_HAS_SAMPLE_OBJECT_TYPE: specimen_categories, - # "hasSpecimenCategoryConfidence": self.has_specimen_category_confidences(specimen_categories), - METADATA_INFORMAL_CLASSIFICATION: self.informal_classification(), - METADATA_KEYWORDS: self.keywords(), - METADATA_PRODUCED_BY: { - METADATA_AT_ID: self.produced_by_id_string(), - METADATA_LABEL: self.produced_by_label(), - METADATA_DESCRIPTION: self.produced_by_description(), - METADATA_HAS_FEATURE_OF_INTEREST: self.produced_by_feature_of_interest(), - METADATA_RESPONSIBILITY: self.produced_by_responsibilities(), - METADATA_RESULT_TIME: self.produced_by_result_time(), - METADATA_SAMPLING_SITE: { - METADATA_DESCRIPTION: self.sampling_site_description(), - METADATA_LABEL: self.sampling_site_label(), - METADATA_SAMPLE_LOCATION: { - METADATA_ELEVATION: self.sampling_site_elevation(), - METADATA_LATITUDE: self.sampling_site_latitude(), - METADATA_LONGITUDE: self.sampling_site_longitude(), - }, - METADATA_PLACE_NAME: self.sampling_site_place_names(), - }, - }, - METADATA_REGISTRANT: self.sample_registrant(), - METADATA_SAMPLING_PURPOSE: self.sample_sampling_purpose(), - METADATA_CURATION: { - METADATA_LABEL: self.curation_label(), - METADATA_DESCRIPTION: self.curation_description(), - METADATA_ACCESS_CONSTRAINTS: self.curation_access_constraints(), - METADATA_CURATION_LOCATION: self.curation_location(), - METADATA_RESPONSIBILITY: self.curation_responsibility(), - }, - METADATA_RELATED_RESOURCE: self.related_resources(), - METADATA_AUTHORIZED_BY: self.authorized_by(), - METADATA_COMPLIES_WITH: self.complies_with(), - } - return transformed_record - def has_context_categories(self) -> typing.List[str]: material_type = self._material_type() primary_location_type = self.sample.primary_location_type @@ -118,7 +55,7 @@ def has_material_categories(self) -> typing.List[str]: # return [] return MaterialCategoryMetaMapper.categories(material) - def has_specimen_categories(self) -> typing.List[str]: + def has_material_sample_object_type_categories(self) -> typing.List[str]: sample_type = self.sample.sample_type.name return SpecimenCategoryMetaMapper.categories(sample_type) diff --git a/poetry.lock b/poetry.lock index d370156..8cce342 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.0 and should not be changed by hand. 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"https://github.com/isamplesorg/isamples_inabox.git", rev = "develop"} +isamples-export-client = {git = "https://github.com/isamplesorg/export_client.git", rev="partner_api_support"} [tool.poetry.group.dev.dependencies] flake8 = "^6.1.0" diff --git a/tests/test_isamples_metadata.py b/tests/test_isamples_metadata.py index 98bda0e..0754dc0 100644 --- a/tests/test_isamples_metadata.py +++ b/tests/test_isamples_metadata.py @@ -20,42 +20,46 @@ def test_example(sesar_session: Session, igsn): transformed_test_data = Transformer(sample).transform() igsn_suffix = igsn.split("/")[1] - json_file = open("examples/" + igsn_suffix + ".json") - expected_data = json.load(json_file) - json_file.close() - - check_id(transformed_test_data, expected_data) - check_label(transformed_test_data, expected_data) - check_sample_identifier(transformed_test_data, expected_data) - check_description(transformed_test_data, expected_data) - check_context_category(transformed_test_data, expected_data) - check_material_category(transformed_test_data, expected_data) - check_specimen_category(transformed_test_data, expected_data) - check_informal_classification(transformed_test_data, expected_data) - check_keywords(transformed_test_data, expected_data) - check_produced_by_id(transformed_test_data, expected_data) - check_produced_by_label(transformed_test_data, expected_data) - check_produced_by_description(transformed_test_data, expected_data) - check_produced_by_feature(transformed_test_data, expected_data) - check_produced_by_responsibility(transformed_test_data, expected_data) - check_produced_by_time(transformed_test_data, expected_data) - check_sampling_site_description(transformed_test_data, expected_data) - check_sampling_site_label(transformed_test_data, expected_data) - check_sampling_site_place_name(transformed_test_data, expected_data) - check_sampling_site_elevation(transformed_test_data, expected_data) - check_sampling_site_latitude(transformed_test_data, expected_data) - check_sampling_site_longitude(transformed_test_data, expected_data) - check_registrant(transformed_test_data, expected_data) - check_sampling_purpose(transformed_test_data, expected_data) - check_curation_label(transformed_test_data, expected_data) - check_curation_description(transformed_test_data, expected_data) - check_curation_access_constraints(transformed_test_data, expected_data) - check_curation_location(transformed_test_data, expected_data) - check_curation_responsibility(transformed_test_data, expected_data) - check_related_resource(transformed_test_data, expected_data) - check_authorized_by(transformed_test_data, expected_data) - check_complies_with(transformed_test_data, expected_data) - check_geo_to_h3(transformed_test_data, expected_data) + file_path = "examples/" + igsn_suffix + ".json" + with open(file_path, "w", encoding="UTF-8") as f: + json.dump(transformed_test_data, f, indent=4) + # json.dump(transformed_test_data) + # json_file = open() + # expected_data = json.load(json_file) + # json_file.close() + + # check_id(transformed_test_data, expected_data) + # check_label(transformed_test_data, expected_data) + # check_sample_identifier(transformed_test_data, expected_data) + # check_description(transformed_test_data, expected_data) + # check_context_category(transformed_test_data, expected_data) + # check_material_category(transformed_test_data, expected_data) + # check_specimen_category(transformed_test_data, expected_data) + # check_informal_classification(transformed_test_data, expected_data) + # check_keywords(transformed_test_data, expected_data) + # check_produced_by_id(transformed_test_data, expected_data) + # check_produced_by_label(transformed_test_data, expected_data) + # check_produced_by_description(transformed_test_data, expected_data) + # check_produced_by_feature(transformed_test_data, expected_data) + # check_produced_by_responsibility(transformed_test_data, expected_data) + # check_produced_by_time(transformed_test_data, expected_data) + # check_sampling_site_description(transformed_test_data, expected_data) + # check_sampling_site_label(transformed_test_data, expected_data) + # check_sampling_site_place_name(transformed_test_data, expected_data) + # check_sampling_site_elevation(transformed_test_data, expected_data) + # check_sampling_site_latitude(transformed_test_data, expected_data) + # check_sampling_site_longitude(transformed_test_data, expected_data) + # check_registrant(transformed_test_data, expected_data) + # check_sampling_purpose(transformed_test_data, expected_data) + # check_curation_label(transformed_test_data, expected_data) + # check_curation_description(transformed_test_data, expected_data) + # check_curation_access_constraints(transformed_test_data, expected_data) + # check_curation_location(transformed_test_data, expected_data) + # check_curation_responsibility(transformed_test_data, expected_data) + # check_related_resource(transformed_test_data, expected_data) + # check_authorized_by(transformed_test_data, expected_data) + # check_complies_with(transformed_test_data, expected_data) + # check_geo_to_h3(transformed_test_data, expected_data) def check_id(test_data, expected_data): From 876b099fe0d9a6df15bdd29c75bfee69e1fa2e2f Mon Sep 17 00:00:00 2001 From: Danny Mandel Date: Fri, 20 Sep 2024 13:13:52 -0700 Subject: [PATCH 3/4] flake8 --- isamples_sesar/sesar_transformer.py | 6 ++-- scripts/sesar_things.py | 51 +++++++++++++++++------------ 2 files changed, 33 insertions(+), 24 deletions(-) diff --git a/isamples_sesar/sesar_transformer.py b/isamples_sesar/sesar_transformer.py index 3753b39..6fbf7da 100644 --- a/isamples_sesar/sesar_transformer.py +++ b/isamples_sesar/sesar_transformer.py @@ -29,7 +29,7 @@ def __init__(self, sample: Sample): self.sample = sample self._material_prediction_results: Optional[list] = None - def has_context_categories(self) -> typing.List[str]: + def has_context_categories(self) -> list[VocabularyTerm]: material_type = self._material_type() primary_location_type = self.sample.primary_location_type return ContextCategoryMetaMapper.categories( @@ -44,7 +44,7 @@ def has_context_categories(self) -> typing.List[str]: # return None # Disabled pending resolution of https://github.com/isamplesorg/isamples_inabox/issues/255 - def has_material_categories(self) -> typing.List[str]: + def has_material_categories(self) -> list[VocabularyTerm]: material = self._material_type() # TODO: implement predictions # if not material: @@ -55,7 +55,7 @@ def has_material_categories(self) -> typing.List[str]: # return [] return MaterialCategoryMetaMapper.categories(material) - def has_material_sample_object_type_categories(self) -> typing.List[str]: + def has_material_sample_object_type_categories(self) -> list[VocabularyTerm]: sample_type = self.sample.sample_type.name return SpecimenCategoryMetaMapper.categories(sample_type) diff --git a/scripts/sesar_things.py b/scripts/sesar_things.py index f288e9b..05fb44b 100644 --- a/scripts/sesar_things.py +++ b/scripts/sesar_things.py @@ -44,47 +44,54 @@ def load_sesar_entries(sesar_db_session, isb_db_session, start_from=None): bulk_updater.finish() print(f"Num newer={num_newer}\n\n") + def ingest_precalculated_vocab(isb_db_session, json_file): count = 0 - with fileinput.FileInput(json_file, inplace = True, backup ='.bak') as file: + with fileinput.FileInput(json_file, inplace=True, backup='.bak') as file: for line in file: if line[:4] == 'done': print(line, end='') continue precalculated_data = json.loads(line) - if precalculated_data == None: + if precalculated_data is None: continue specimen_category = precalculated_data["has_specimen_category"] material_category = precalculated_data["has_material_category"] context_category = precalculated_data["has_context_category"] igsn_suffix = precalculated_data["sample_identifier"][5:] - if (igsn_suffix[:3] == 'UKB'): - doi_prefix = '10.60665/' - elif (igsn_suffix[:3] == 'ODP'): - doi_prefix = '10.60471/' - elif (igsn_suffix[:5] == 'IEJAA'): - doi_prefix = '10.60471/' - elif (igsn_suffix[:3] == 'NHB'): - doi_prefix = '10.58151/' - elif (igsn_suffix[:3] == 'UGS'): - doi_prefix = '10.58136/' - elif (igsn_suffix[:3] == 'CNR'): - doi_prefix = '' - else: - doi_prefix = '10.58052/' + doi_prefix = _calculate_doi_prefix(igsn_suffix) igsn = 'igsn:' + doi_prefix + igsn_suffix current_record = get_thing_with_id(isb_db_session, igsn) - if current_record != None: + if current_record is not None: resolved_content_copy = current_record.resolved_content.copy() resolved_content_copy["hasSpecimenCategory"] = specimen_category resolved_content_copy["hasMaterialCategory"] = material_category resolved_content_copy["hasContextCategory"] = context_category current_record.resolved_content = resolved_content_copy - save_or_update_thing(isb_db_session,current_record) - print('done'+line, end='') - count+=1 + save_or_update_thing(isb_db_session, current_record) + print('done' + line, end='') + count += 1 print('samples updated: ' + str(count)) + +def _calculate_doi_prefix(igsn_suffix): + if (igsn_suffix[:3] == 'UKB'): + doi_prefix = '10.60665/' + elif (igsn_suffix[:3] == 'ODP'): + doi_prefix = '10.60471/' + elif (igsn_suffix[:5] == 'IEJAA'): + doi_prefix = '10.60471/' + elif (igsn_suffix[:3] == 'NHB'): + doi_prefix = '10.58151/' + elif (igsn_suffix[:3] == 'UGS'): + doi_prefix = '10.58136/' + elif (igsn_suffix[:3] == 'CNR'): + doi_prefix = '' + else: + doi_prefix = '10.58052/' + return doi_prefix + + @click.group() @click.option( "-d", "--sesar_db_url", default=None, help="SQLAlchemy SESAR database URL for retrieving data" @@ -120,7 +127,7 @@ def main(ctx, sesar_db_url, isb_db_url, solr_url, verbosity): "-d", "--modification_date", type=click.DateTime(formats=["%Y-%m-%d"]), - default=(datetime.datetime.now()-datetime.timedelta(days=1)).date().strftime("%Y-%m-%d"), # default to last day for daily script + default=(datetime.datetime.now() - datetime.timedelta(days=1)).date().strftime("%Y-%m-%d"), # default to last day for daily script help="""The modified date to use when considering delta updates. Records with a last modified before this date will be ignored""" ) @@ -154,6 +161,7 @@ def populate_isb_core_solr(ctx): ) logger.info(f"Total keys= {len(allkeys)}") + @main.command("ingest_json") @click.option( "-d", @@ -170,5 +178,6 @@ def ingest_json(ctx, json_file): ingest_precalculated_vocab(isb_session, json_file) isb_session.close() + if __name__ == "__main__": main() From 5ef7c2536dc3155956c5bac781b14a0152b1f815 Mon Sep 17 00:00:00 2001 From: Danny Mandel Date: Fri, 20 Sep 2024 13:38:30 -0700 Subject: [PATCH 4/4] Reinstantiate checks --- tests/test_isamples_metadata.py | 169 +++++++++++++++----------------- 1 file changed, 77 insertions(+), 92 deletions(-) diff --git a/tests/test_isamples_metadata.py b/tests/test_isamples_metadata.py index 0754dc0..982d20f 100644 --- a/tests/test_isamples_metadata.py +++ b/tests/test_isamples_metadata.py @@ -1,5 +1,13 @@ import pytest import json + +from isamples_api.metadata_constants import METADATA_SAMPLE_IDENTIFIER, METADATA_DESCRIPTION, \ + METADATA_HAS_CONTEXT_CATEGORY, METADATA_HAS_SAMPLE_OBJECT_TYPE, METADATA_INFORMAL_CLASSIFICATION, METADATA_KEYWORDS, \ + METADATA_PRODUCED_BY, METADATA_AT_ID, METADATA_LABEL, METADATA_HAS_FEATURE_OF_INTEREST, METADATA_RESPONSIBILITY, \ + METADATA_HAS_MATERIAL_CATEGORY, METADATA_RESULT_TIME, METADATA_SAMPLING_SITE, METADATA_PLACE_NAME, \ + METADATA_LOCATION, METADATA_ELEVATION, METADATA_LATITUDE, METADATA_LONGITUDE, METADATA_REGISTRANT, \ + METADATA_SAMPLING_PURPOSE, METADATA_CURATION, METADATA_ACCESS_CONSTRAINTS, METADATA_CURATION_LOCATION, \ + METADATA_RELATED_RESOURCE, METADATA_AUTHORIZED_BY, METADATA_COMPLIES_WITH, METADATA_SAMPLE_LOCATION from sqlmodel import Session from isamples_sesar.sesar_transformer import Transformer from isamples_sesar.sqlmodel_database import ( @@ -21,45 +29,40 @@ def test_example(sesar_session: Session, igsn): igsn_suffix = igsn.split("/")[1] file_path = "examples/" + igsn_suffix + ".json" - with open(file_path, "w", encoding="UTF-8") as f: - json.dump(transformed_test_data, f, indent=4) - # json.dump(transformed_test_data) - # json_file = open() - # expected_data = json.load(json_file) - # json_file.close() - - # check_id(transformed_test_data, expected_data) - # check_label(transformed_test_data, expected_data) - # check_sample_identifier(transformed_test_data, expected_data) - # check_description(transformed_test_data, expected_data) - # check_context_category(transformed_test_data, expected_data) - # check_material_category(transformed_test_data, expected_data) - # check_specimen_category(transformed_test_data, expected_data) - # check_informal_classification(transformed_test_data, expected_data) - # check_keywords(transformed_test_data, expected_data) - # check_produced_by_id(transformed_test_data, expected_data) - # check_produced_by_label(transformed_test_data, expected_data) - # check_produced_by_description(transformed_test_data, expected_data) - # check_produced_by_feature(transformed_test_data, expected_data) - # check_produced_by_responsibility(transformed_test_data, expected_data) - # check_produced_by_time(transformed_test_data, expected_data) - # check_sampling_site_description(transformed_test_data, expected_data) - # check_sampling_site_label(transformed_test_data, expected_data) - # check_sampling_site_place_name(transformed_test_data, expected_data) - # check_sampling_site_elevation(transformed_test_data, expected_data) - # check_sampling_site_latitude(transformed_test_data, expected_data) - # check_sampling_site_longitude(transformed_test_data, expected_data) - # check_registrant(transformed_test_data, expected_data) - # check_sampling_purpose(transformed_test_data, expected_data) - # check_curation_label(transformed_test_data, expected_data) - # check_curation_description(transformed_test_data, expected_data) - # check_curation_access_constraints(transformed_test_data, expected_data) - # check_curation_location(transformed_test_data, expected_data) - # check_curation_responsibility(transformed_test_data, expected_data) - # check_related_resource(transformed_test_data, expected_data) - # check_authorized_by(transformed_test_data, expected_data) - # check_complies_with(transformed_test_data, expected_data) - # check_geo_to_h3(transformed_test_data, expected_data) + with open(file_path, "r", encoding="UTF-8") as f: + expected_data = json.load(f) + + check_id(transformed_test_data, expected_data) + check_label(transformed_test_data, expected_data) + check_sample_identifier(transformed_test_data, expected_data) + check_description(transformed_test_data, expected_data) + check_context_category(transformed_test_data, expected_data) + check_material_category(transformed_test_data, expected_data) + check_specimen_category(transformed_test_data, expected_data) + check_informal_classification(transformed_test_data, expected_data) + check_keywords(transformed_test_data, expected_data) + check_produced_by_id(transformed_test_data, expected_data) + check_produced_by_label(transformed_test_data, expected_data) + check_produced_by_description(transformed_test_data, expected_data) + check_produced_by_feature(transformed_test_data, expected_data) + check_produced_by_responsibility(transformed_test_data, expected_data) + check_produced_by_time(transformed_test_data, expected_data) + check_sampling_site_description(transformed_test_data, expected_data) + check_sampling_site_label(transformed_test_data, expected_data) + check_sampling_site_place_name(transformed_test_data, expected_data) + check_sampling_site_elevation(transformed_test_data, expected_data) + check_sampling_site_latitude(transformed_test_data, expected_data) + check_sampling_site_longitude(transformed_test_data, expected_data) + check_registrant(transformed_test_data, expected_data) + check_sampling_purpose(transformed_test_data, expected_data) + check_curation_label(transformed_test_data, expected_data) + check_curation_description(transformed_test_data, expected_data) + check_curation_access_constraints(transformed_test_data, expected_data) + check_curation_location(transformed_test_data, expected_data) + check_curation_responsibility(transformed_test_data, expected_data) + check_related_resource(transformed_test_data, expected_data) + check_authorized_by(transformed_test_data, expected_data) + check_complies_with(transformed_test_data, expected_data) def check_id(test_data, expected_data): @@ -71,143 +74,125 @@ def check_label(test_data, expected_data): def check_sample_identifier(test_data, expected_data): - assert test_data["sampleidentifier"] == expected_data["sampleidentifier"] + assert test_data[METADATA_SAMPLE_IDENTIFIER] == expected_data[METADATA_SAMPLE_IDENTIFIER] def check_description(test_data, expected_data): - assert test_data["description"] == expected_data["description"] + assert test_data[METADATA_DESCRIPTION] == expected_data[METADATA_DESCRIPTION] def check_context_category(test_data, expected_data): - assert test_data["hasContextCategory"] == expected_data["hasContextCategory"] + assert test_data[METADATA_HAS_CONTEXT_CATEGORY] == expected_data[METADATA_HAS_CONTEXT_CATEGORY] # assert test_data["hasContextCategoryConfidence"] == expected_data["hasContextCategoryConfidence"] def check_material_category(test_data, expected_data): - assert test_data["hasMaterialCategory"] == expected_data["hasMaterialCategory"] + assert test_data[METADATA_HAS_MATERIAL_CATEGORY] == expected_data[METADATA_HAS_MATERIAL_CATEGORY] # assert test_data["hasMaterialCategoryConfidence"] == expected_data["hasMaterialCategoryConfidence"] def check_specimen_category(test_data, expected_data): - assert test_data["hasSpecimenCategory"] == expected_data["hasSpecimenCategory"] + assert test_data[METADATA_HAS_SAMPLE_OBJECT_TYPE] == expected_data[METADATA_HAS_SAMPLE_OBJECT_TYPE] # assert test_data["hasSpecimenCategoryConfidence"] == expected_data["hasSpecimenCategoryConfidence"] def check_informal_classification(test_data, expected_data): - assert test_data["informalClassification"] == expected_data["informalClassification"] + assert test_data[METADATA_INFORMAL_CLASSIFICATION] == expected_data[METADATA_INFORMAL_CLASSIFICATION] def check_keywords(test_data, expected_data): - assert test_data["keywords"] == expected_data["keywords"] + assert test_data[METADATA_KEYWORDS] == expected_data[METADATA_KEYWORDS] def check_produced_by_id(test_data, expected_data): - assert test_data["producedBy"]["@id"] == expected_data["producedBy"]["@id"] + assert test_data[METADATA_PRODUCED_BY][METADATA_AT_ID] == expected_data[METADATA_PRODUCED_BY][METADATA_AT_ID] def check_produced_by_label(test_data, expected_data): - assert test_data["producedBy"]["label"] == expected_data["producedBy"]["label"] + assert test_data[METADATA_PRODUCED_BY][METADATA_LABEL] == expected_data[METADATA_PRODUCED_BY][METADATA_LABEL] def check_produced_by_description(test_data, expected_data): - assert test_data["producedBy"]["description"] == expected_data["producedBy"]["description"] + assert test_data[METADATA_PRODUCED_BY][METADATA_DESCRIPTION] == expected_data[METADATA_PRODUCED_BY][METADATA_DESCRIPTION] def check_produced_by_feature(test_data, expected_data): - assert test_data["producedBy"]["hasFeatureOfInterest"] == expected_data["producedBy"]["hasFeatureOfInterest"] + assert test_data[METADATA_PRODUCED_BY][METADATA_HAS_FEATURE_OF_INTEREST] == expected_data[METADATA_PRODUCED_BY][METADATA_HAS_FEATURE_OF_INTEREST] def check_produced_by_responsibility(test_data, expected_data): - assert test_data["producedBy"]["responsibility"] == expected_data["producedBy"]["responsibility"] + assert test_data[METADATA_PRODUCED_BY][METADATA_RESPONSIBILITY] == expected_data[METADATA_PRODUCED_BY][METADATA_RESPONSIBILITY] def check_produced_by_time(test_data, expected_data): - assert test_data["producedBy"]["resultTime"] == expected_data["producedBy"]["resultTime"] + assert test_data[METADATA_PRODUCED_BY][METADATA_RESULT_TIME] == expected_data[METADATA_PRODUCED_BY][METADATA_RESULT_TIME] def check_sampling_site_description(test_data, expected_data): - assert test_data["producedBy"]["samplingSite"]["description"] == \ - expected_data["producedBy"]["samplingSite"]["description"] + assert test_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_DESCRIPTION] == \ + expected_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_DESCRIPTION] def check_sampling_site_label(test_data, expected_data): - assert test_data["producedBy"]["samplingSite"]["label"] == \ - expected_data["producedBy"]["samplingSite"]["label"] + assert test_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_LABEL] == \ + expected_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_LABEL] def check_sampling_site_place_name(test_data, expected_data): - assert test_data["producedBy"]["samplingSite"]["placeName"] == \ - expected_data["producedBy"]["samplingSite"]["placeName"] + assert test_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_PLACE_NAME] == \ + expected_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_PLACE_NAME] def check_sampling_site_elevation(test_data, expected_data): - assert test_data["producedBy"]["samplingSite"]["location"]["elevation"] == \ - expected_data["producedBy"]["samplingSite"]["location"]["elevation"] + assert test_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_SAMPLE_LOCATION][METADATA_ELEVATION] == \ + expected_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_SAMPLE_LOCATION][METADATA_ELEVATION] def check_sampling_site_latitude(test_data, expected_data): - assert test_data["producedBy"]["samplingSite"]["location"]["latitude"] == \ - expected_data["producedBy"]["samplingSite"]["location"]["latitude"] + assert test_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_SAMPLE_LOCATION][METADATA_LATITUDE] == \ + expected_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_SAMPLE_LOCATION][METADATA_LATITUDE] def check_sampling_site_longitude(test_data, expected_data): - assert test_data["producedBy"]["samplingSite"]["location"]["longitude"] == \ - expected_data["producedBy"]["samplingSite"]["location"]["longitude"] + assert test_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_SAMPLE_LOCATION][METADATA_LONGITUDE] == \ + expected_data[METADATA_PRODUCED_BY][METADATA_SAMPLING_SITE][METADATA_SAMPLE_LOCATION][METADATA_LONGITUDE] def check_registrant(test_data, expected_data): - assert test_data["registrant"] == expected_data["registrant"] + assert test_data[METADATA_REGISTRANT] == expected_data[METADATA_REGISTRANT] def check_sampling_purpose(test_data, expected_data): - assert test_data["samplingPurpose"] == expected_data["samplingPurpose"] + assert test_data[METADATA_SAMPLING_PURPOSE] == expected_data[METADATA_SAMPLING_PURPOSE] def check_curation_label(test_data, expected_data): - assert test_data["curation"]["label"] == expected_data["curation"]["label"] + assert test_data[METADATA_CURATION][METADATA_LABEL] == expected_data[METADATA_CURATION][METADATA_LABEL] def check_curation_description(test_data, expected_data): - assert test_data["curation"]["description"] == expected_data["curation"]["description"] + assert test_data[METADATA_CURATION][METADATA_DESCRIPTION] == expected_data[METADATA_CURATION][METADATA_DESCRIPTION] def check_curation_access_constraints(test_data, expected_data): - assert test_data["curation"]["accessConstraints"] == expected_data["curation"]["accessConstraints"] + assert test_data[METADATA_CURATION][METADATA_ACCESS_CONSTRAINTS] == expected_data[METADATA_CURATION][METADATA_ACCESS_CONSTRAINTS] def check_curation_location(test_data, expected_data): - assert test_data["curation"]["curationLocation"] == expected_data["curation"]["curationLocation"] + assert test_data[METADATA_CURATION][METADATA_CURATION_LOCATION] == expected_data[METADATA_CURATION][METADATA_CURATION_LOCATION] def check_curation_responsibility(test_data, expected_data): - assert test_data["curation"]["responsibility"] == expected_data["curation"]["responsibility"] + assert test_data[METADATA_CURATION][METADATA_RESPONSIBILITY] == expected_data[METADATA_CURATION][METADATA_RESPONSIBILITY] def check_related_resource(test_data, expected_data): - assert test_data["relatedResource"] == expected_data["relatedResource"] + assert test_data[METADATA_RELATED_RESOURCE] == expected_data[METADATA_RELATED_RESOURCE] def check_authorized_by(test_data, expected_data): - assert test_data["authorizedBy"] == expected_data["authorizedBy"] + assert test_data[METADATA_AUTHORIZED_BY] == expected_data[METADATA_AUTHORIZED_BY] def check_complies_with(test_data, expected_data): - assert test_data["compliesWith"] == expected_data["compliesWith"] - - -def check_geo_to_h3(test_data, expected_data): - assert test_data["producedBy_samplingSite_location_h3_0"] == expected_data["producedBy_samplingSite_location_h3_0"] - assert test_data["producedBy_samplingSite_location_h3_1"] == expected_data["producedBy_samplingSite_location_h3_1"] - assert test_data["producedBy_samplingSite_location_h3_2"] == expected_data["producedBy_samplingSite_location_h3_2"] - assert test_data["producedBy_samplingSite_location_h3_3"] == expected_data["producedBy_samplingSite_location_h3_3"] - assert test_data["producedBy_samplingSite_location_h3_4"] == expected_data["producedBy_samplingSite_location_h3_4"] - assert test_data["producedBy_samplingSite_location_h3_5"] == expected_data["producedBy_samplingSite_location_h3_5"] - assert test_data["producedBy_samplingSite_location_h3_6"] == expected_data["producedBy_samplingSite_location_h3_6"] - assert test_data["producedBy_samplingSite_location_h3_7"] == expected_data["producedBy_samplingSite_location_h3_7"] - assert test_data["producedBy_samplingSite_location_h3_8"] == expected_data["producedBy_samplingSite_location_h3_8"] - assert test_data["producedBy_samplingSite_location_h3_9"] == expected_data["producedBy_samplingSite_location_h3_9"] - assert test_data["producedBy_samplingSite_location_h3_10"] == expected_data["producedBy_samplingSite_location_h3_10"] - assert test_data["producedBy_samplingSite_location_h3_11"] == expected_data["producedBy_samplingSite_location_h3_11"] - assert test_data["producedBy_samplingSite_location_h3_12"] == expected_data["producedBy_samplingSite_location_h3_12"] - assert test_data["producedBy_samplingSite_location_h3_13"] == expected_data["producedBy_samplingSite_location_h3_13"] - assert test_data["producedBy_samplingSite_location_h3_14"] == expected_data["producedBy_samplingSite_location_h3_14"] + assert test_data[METADATA_COMPLIES_WITH] == expected_data[METADATA_COMPLIES_WITH]