From 965d83b0525c724c96739bc526e6969895ea0883 Mon Sep 17 00:00:00 2001 From: "makena.dettmann@pnnl.gov" Date: Mon, 15 Sep 2025 11:12:16 -0700 Subject: [PATCH 1/3] updating valid emsl data --- src/sample_data/valid/emsl-example.json | 19 +++++++ src/sample_data/valid/monet-example.json | 64 ++++++++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 src/sample_data/valid/emsl-example.json create mode 100644 src/sample_data/valid/monet-example.json diff --git a/src/sample_data/valid/emsl-example.json b/src/sample_data/valid/emsl-example.json new file mode 100644 index 0000000..7de78f2 --- /dev/null +++ b/src/sample_data/valid/emsl-example.json @@ -0,0 +1,19 @@ +{ + "ber_data_source": "EMSL", + "coordinates": { + "depth": null, + "altitude": null, + "latitude": 40.0867, + "elevation": null, + "longitude": -83.2392 + }, + "entity_type": [ + "sample" + ], + "description": "BH_Madison", + "id": "EMSL:fcbde351-29e1-40eb-b0c9-ea4e36ac4dc0", + "name": null, + "alt_ids": null, + "part_of_collection": null, + "uri": "https://sc-data.emsl.pnnl.gov/emsl?projectId=61875" +} \ No newline at end of file diff --git a/src/sample_data/valid/monet-example.json b/src/sample_data/valid/monet-example.json new file mode 100644 index 0000000..0c099f7 --- /dev/null +++ b/src/sample_data/valid/monet-example.json @@ -0,0 +1,64 @@ +{ + "ber_data_source": "MONET", + "coordinates": { + "latitude": 39.0855, + "longitude": -96.5845 + }, + "entity_type": [ + "sample" + ], + "description": null, + "id": "fca44f53-14cb-42cf-bc9a-73af11a80c8b", + "name": "MONet Core 60933_19_BOTTOM", + "alt_ids": null, + "alt_names": null, + "part_of_collection": null, + "uri": "https://sc-data.emsl.pnnl.gov/monet", + "properties": [ + { + "attribute": { + "id": "MIXS:0000332", + "label": "soil_type" + }, + "raw_value": "Mollisol" + }, + { + "attribute": { + "id": "MIXS:0000011", + "label": "collection_date" + }, + "raw_value": "2023-10-23 15:23:00" + }, + { + "attribute": { + "label": "ecoregion" + }, + "raw_value": "prairie_peninsula" + }, + { + "attribute": { + "label": "elevation", + "id": "PATO:0001687" + }, + "numeric_value": 387.08, + "unit": "m", + "raw_value": "387.08 m" + }, + { + "attribute": { + "label": "toc_avg" + }, + "raw_value": "1324.18 mg per kg", + "unit": "mg per kg", + "numeric_value": 1324.18 + }, + { + "attribute": { + "label": "tn_avg" + }, + "raw_value": "39.34 mg per kg", + "unit": "mg per kg", + "numeric_value": 39.34 + } + ] +} \ No newline at end of file From 9773d136b42b5177c5467f9b350d33580fe761b3 Mon Sep 17 00:00:00 2001 From: "makena.dettmann@pnnl.gov" Date: Mon, 15 Sep 2025 12:00:31 -0700 Subject: [PATCH 2/3] Fix example names --- .../valid/Entity-emsl-example-00001.yaml | 32 ++++------ .../valid/Entity-monet-example-00001.yaml | 46 +++++++++++-- src/sample_data/valid/emsl-example.json | 19 ------ src/sample_data/valid/monet-example.json | 64 ------------------- 4 files changed, 51 insertions(+), 110 deletions(-) delete mode 100644 src/sample_data/valid/emsl-example.json delete mode 100644 src/sample_data/valid/monet-example.json diff --git a/src/sample_data/valid/Entity-emsl-example-00001.yaml b/src/sample_data/valid/Entity-emsl-example-00001.yaml index 87e369e..103bd68 100644 --- a/src/sample_data/valid/Entity-emsl-example-00001.yaml +++ b/src/sample_data/valid/Entity-emsl-example-00001.yaml @@ -1,23 +1,15 @@ +alt_ids: .nan ber_data_source: EMSL coordinates: - latitude: 34 - longitude: 118 + altitude: null + depth: null + elevation: null + latitude: 40.0867 + longitude: -83.2392 +description: BH_Madison entity_type: - - sample -properties: - - attribute: - label: altitude - id: MIXS:0000094 - numeric_value: 2947.3 - unit: UO:0000008 - raw_value: 2974.3m - - attribute: - label: elevation - id: MIXS:0000093 - raw_value: 2.2 cm - numeric_value: 2.2 - unit: UO:0000009 -description: Clostridium thermocellum protein extracts -id: EMSL:c9405190-e962-4ba5-93f0-e3ff499f4488 -name: EMSL Sample c9405190-e962-4ba5-93f0-e3ff499f4488 -uri: https://sc-data.emsl.pnnl.gov/?projectId=61815 +- sample +id: EMSL:fcbde351-29e1-40eb-b0c9-ea4e36ac4dc0 +name: .nan +part_of_collection: .nan +uri: https://sc-data.emsl.pnnl.gov/emsl?projectId=61875 diff --git a/src/sample_data/valid/Entity-monet-example-00001.yaml b/src/sample_data/valid/Entity-monet-example-00001.yaml index 5aaa532..beb42a7 100644 --- a/src/sample_data/valid/Entity-monet-example-00001.yaml +++ b/src/sample_data/valid/Entity-monet-example-00001.yaml @@ -1,9 +1,41 @@ -ber_data_source: EMSL +alt_ids: null +alt_names: null +ber_data_source: MONET coordinates: - latitude: 40.0867 - longitude: -83.2392 + latitude: 39.0855 + longitude: -96.5845 +description: null entity_type: - - sample -description: BH_Madison -id: EMSL:fcbde351-29e1-40eb-b0c9-ea4e36ac4dc0 -uri: https://sc-data.emsl.pnnl.gov/emsl?projectId=61875 +- sample +id: fca44f53-14cb-42cf-bc9a-73af11a80c8b +name: MONet Core 60933_19_BOTTOM +part_of_collection: null +properties: +- attribute: + id: MIXS:0000332 + label: soil_type + raw_value: Mollisol +- attribute: + id: MIXS:0000011 + label: collection_date + raw_value: '2023-10-23 15:23:00' +- attribute: + label: ecoregion + raw_value: prairie_peninsula +- attribute: + id: PATO:0001687 + label: elevation + numeric_value: 387.08 + raw_value: 387.08 m + unit: m +- attribute: + label: toc_avg + numeric_value: 1324.18 + raw_value: 1324.18 mg per kg + unit: mg per kg +- attribute: + label: tn_avg + numeric_value: 39.34 + raw_value: 39.34 mg per kg + unit: mg per kg +uri: https://sc-data.emsl.pnnl.gov/monet diff --git a/src/sample_data/valid/emsl-example.json b/src/sample_data/valid/emsl-example.json deleted file mode 100644 index 7de78f2..0000000 --- a/src/sample_data/valid/emsl-example.json +++ /dev/null @@ -1,19 +0,0 @@ -{ - "ber_data_source": "EMSL", - "coordinates": { - "depth": null, - "altitude": null, - "latitude": 40.0867, - "elevation": null, - "longitude": -83.2392 - }, - "entity_type": [ - "sample" - ], - "description": "BH_Madison", - "id": "EMSL:fcbde351-29e1-40eb-b0c9-ea4e36ac4dc0", - "name": null, - "alt_ids": null, - "part_of_collection": null, - "uri": "https://sc-data.emsl.pnnl.gov/emsl?projectId=61875" -} \ No newline at end of file diff --git a/src/sample_data/valid/monet-example.json b/src/sample_data/valid/monet-example.json deleted file mode 100644 index 0c099f7..0000000 --- a/src/sample_data/valid/monet-example.json +++ /dev/null @@ -1,64 +0,0 @@ -{ - "ber_data_source": "MONET", - "coordinates": { - "latitude": 39.0855, - "longitude": -96.5845 - }, - "entity_type": [ - "sample" - ], - "description": null, - "id": "fca44f53-14cb-42cf-bc9a-73af11a80c8b", - "name": "MONet Core 60933_19_BOTTOM", - "alt_ids": null, - "alt_names": null, - "part_of_collection": null, - "uri": "https://sc-data.emsl.pnnl.gov/monet", - "properties": [ - { - "attribute": { - "id": "MIXS:0000332", - "label": "soil_type" - }, - "raw_value": "Mollisol" - }, - { - "attribute": { - "id": "MIXS:0000011", - "label": "collection_date" - }, - "raw_value": "2023-10-23 15:23:00" - }, - { - "attribute": { - "label": "ecoregion" - }, - "raw_value": "prairie_peninsula" - }, - { - "attribute": { - "label": "elevation", - "id": "PATO:0001687" - }, - "numeric_value": 387.08, - "unit": "m", - "raw_value": "387.08 m" - }, - { - "attribute": { - "label": "toc_avg" - }, - "raw_value": "1324.18 mg per kg", - "unit": "mg per kg", - "numeric_value": 1324.18 - }, - { - "attribute": { - "label": "tn_avg" - }, - "raw_value": "39.34 mg per kg", - "unit": "mg per kg", - "numeric_value": 39.34 - } - ] -} \ No newline at end of file From ba543b8dcd3774bc704e9f13cba4fe2c36dd4d36 Mon Sep 17 00:00:00 2001 From: "makena.dettmann@pnnl.gov" Date: Mon, 15 Sep 2025 12:07:22 -0700 Subject: [PATCH 3/3] fix nan issues --- src/sample_data/valid/Entity-emsl-example-00001.yaml | 6 ------ src/sample_data/valid/Entity-monet-example-00001.yaml | 4 ---- 2 files changed, 10 deletions(-) diff --git a/src/sample_data/valid/Entity-emsl-example-00001.yaml b/src/sample_data/valid/Entity-emsl-example-00001.yaml index 103bd68..7290acc 100644 --- a/src/sample_data/valid/Entity-emsl-example-00001.yaml +++ b/src/sample_data/valid/Entity-emsl-example-00001.yaml @@ -1,15 +1,9 @@ -alt_ids: .nan ber_data_source: EMSL coordinates: - altitude: null - depth: null - elevation: null latitude: 40.0867 longitude: -83.2392 description: BH_Madison entity_type: - sample id: EMSL:fcbde351-29e1-40eb-b0c9-ea4e36ac4dc0 -name: .nan -part_of_collection: .nan uri: https://sc-data.emsl.pnnl.gov/emsl?projectId=61875 diff --git a/src/sample_data/valid/Entity-monet-example-00001.yaml b/src/sample_data/valid/Entity-monet-example-00001.yaml index beb42a7..5ab2232 100644 --- a/src/sample_data/valid/Entity-monet-example-00001.yaml +++ b/src/sample_data/valid/Entity-monet-example-00001.yaml @@ -1,15 +1,11 @@ -alt_ids: null -alt_names: null ber_data_source: MONET coordinates: latitude: 39.0855 longitude: -96.5845 -description: null entity_type: - sample id: fca44f53-14cb-42cf-bc9a-73af11a80c8b name: MONet Core 60933_19_BOTTOM -part_of_collection: null properties: - attribute: id: MIXS:0000332