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add transformer functions and mappers #2

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Oct 11, 2023
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2 changes: 1 addition & 1 deletion .flake8
Original file line number Diff line number Diff line change
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[flake8]
max-line-length = 110
max-line-length = 120
80 changes: 80 additions & 0 deletions examples/EOI00002H.json
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It would be good to formalize these as tests. Will post a link to how we do this in iSamples…

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Let me know if you have any questions on these.

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You would need to make some test files with the raw SESAR source records as well.

Original file line number Diff line number Diff line change
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{
"$schema": "iSamplesSchemaCore1.0.json",
"@id": "https://data.isamples.org/digitalsample/igsn/10.58052/EOI00002H",
"authorizedBy": [],
"compliesWith": [],
"curation": {
"accessConstraints": "Not Provided",
"curationLocation": "Not Provided",
"description": "Not Provided",
"label": "Not Provided",
"responsibility": [
{
"contact_information": "[email protected]",
"name": "Andra Bobbitt",
"role": "sample owner"
},
{
"contact_information": "[email protected]; url: https://www.geosamples.org/contact/",
"role": "metadata publisher"
}
]
},
"description": "Gas. Sampler:Fluid:GTHFS. HFS gastight. Red-center-9. T=250C",
"hasContextCategory": [
"Subsurface fluid reservoir"
],
"hasMaterialCategory": [
"Gaseous material"
],
"hasSpecimenCategory": [
"Other solid object"
],
"informalClassification": [
"Not Provided"
],
"keywords": [
{
"keyword": "Individual Sample",
"scheme_name": "SESAR: Sample Type"
}
],
"label": "J730-GTHFS-16",
"producedBy": {
"@id": "",
"description": "cruiseFieldPrgrm:TN300. launchPlatformName:Jason II. Collection method:Sampler:Fluid:GTHFS. HFS gastight. Red-center-9. T=250C. launch type:ROV, navigation type:USBL",
"hasFeatureOfInterest": "volcano",
"label": "Sampler:Fluid:GTHFS, TN300",
"responsibility": [
{
"name": "Evans_Leigh",
"role": "collector"
},
{
"name": "Andra Bobbitt",
"role": "sample owner"
},
{
"name": "TN300",
"role": "sponsor"
}
],
"resultTime": "2013-09-14",
"samplingSite": {
"description": "Trevi:Jason Tmax=257.9 C. In the direct flow at this small anhydrite mound (anhydrite knocked over).",
"label": "Not Provided",
"location": {
"elevation": "-1520.0 m",
"latitude": 45.946265,
"longitude": -129.983725
},
"placeName": [
"Axial Seamount"
]
}
},
"registrant": "Andra Bobbitt",
"relatedResource": [],
"sampleidentifier": "IGSN:10.58052/EOI00002H",
"samplingPurpose": "Not Provided"
}
88 changes: 88 additions & 0 deletions examples/IEDUT103B.json
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{
"$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": "[email protected]",
"name": "Andrea Dutton",
"role": "sample owner"
},
{
"contact_information": "[email protected]; url: https://www.geosamples.org/contact/",
"role": "metadata publisher"
}
]
},
"description": "Macrobiology>Coral>Biology. Coring>HandHeldCorer. piece of short core",
"hasContextCategory": [
"Not Provided"
],
"hasMaterialCategory": [
"Organic material",
"Biogenic non-organic material"
],
"hasSpecimenCategory": [
"Not Provided"
],
"informalClassification": [
"Not Provided"
],
"keywords": [
{
"keyword": "Individual Sample>Cylinder",
"scheme_name": "SESAR: Sample Type"
},
{
"keyword": "Pseudodiploria strigosa",
"scheme_name": "taxon: species"
}
],
"label": "JAM42",
"producedBy": {
"@id": "",
"description": "cruiseFieldPrgrm:UF Jamaica 2015 Fieldwork. Collection method:Coring>HandHeldCorer. piece of short core",
"hasFeatureOfInterest": "Reef",
"label": "Coring>HandHeldCorer, UF Jamaica 2015 Fieldwork",
"responsibility": [
{
"name": "Andrea Dutton",
"role": "collector"
},
{
"name": "Andrea Dutton",
"role": "sample owner"
},
{
"name": "UF Jamaica 2015 Fieldwork",
"role": "sponsor"
}
],
"resultTime": "2015-06-19",
"samplingSite": {
"description": "Between Buccaneer Villa, Treasure Beach, and Great Bay",
"label": "Treasure Beach",
"location": {
"elevation": "1.626 m",
"latitude": 17.88451,
"longitude": -77.77107
},
"placeName": [
"Limestone Falmouth Formation ",
"Saint Elizabeth",
"Cornwall",
"Treasure Beach"
]
}
},
"registrant": "Andrea Dutton",
"relatedResource": [],
"sampleidentifier": "IGSN:10.58052/IEDUT103B",
"samplingPurpose": "Paleosea-level"
}
84 changes: 84 additions & 0 deletions examples/IEEJR000M.json
Original file line number Diff line number Diff line change
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{
"$schema": "iSamplesSchemaCore1.0.json",
"@id": "https://data.isamples.org/digitalsample/igsn/10.58052/IEEJR000M",
"authorizedBy": [],
"compliesWith": [],
"curation": {
"accessConstraints": "Not Provided",
"curationLocation": "The University of Texas at Austin",
"description": "Not Provided",
"label": "Not Provided",
"responsibility": [
{
"contact_information": "[email protected]",
"name": "Evan Ramos",
"role": "sample owner"
},
{
"contact_information": "[email protected]; url: https://www.geosamples.org/contact/",
"role": "metadata publisher"
}
]
},
"description": "Metamorphic>Meta-Carbonate>Rock. Manual>Hammer",
"hasContextCategory": [
"Earth interior"
],
"hasMaterialCategory": [
"Rock"
],
"hasSpecimenCategory": [
"Other solid object"
],
"informalClassification": [
"Not Provided"
],
"keywords": [
{
"keyword": "Individual Sample",
"scheme_name": "SESAR: Sample Type"
},
{
"keyword": "Marble",
"scheme_name": "taxon: species"
}
],
"label": "16ER6F3",
"producedBy": {
"@id": "",
"description": "Collection method:Manual>Hammer",
"hasFeatureOfInterest": "Metamorphic aureole",
"label": "Manual>Hammer",
"responsibility": [
{
"name": "Jade Star Lackey",
"role": "collector"
},
{
"name": "Evan Ramos",
"role": "sample owner"
}
],
"resultTime": "2021-01-19",
"samplingSite": {
"description": "Not Provided",
"label": "Not Provided",
"location": {
"elevation": "Not Provided",
"latitude": 36.461666,
"longitude": -118.583888
},
"placeName": [
"Mineral King",
"Sequoia National Forest",
"California",
"Tulare",
"Silver City"
]
}
},
"registrant": "Evan Ramos",
"relatedResource": [],
"sampleidentifier": "IGSN:10.58052/IEEJR000M",
"samplingPurpose": "Not Provided"
}
76 changes: 76 additions & 0 deletions examples/IEJEN0040.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,76 @@
{
"$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": "[email protected]",
"name": "Jonathan Nichols",
"role": "sample owner"
},
{
"contact_information": "[email protected]; url: https://www.geosamples.org/contact/",
"role": "metadata publisher"
}
]
},
"description": "Biology",
"hasContextCategory": [
"Not Provided"
],
"hasMaterialCategory": [
"Organic material"
],
"hasSpecimenCategory": [
"Other solid object"
],
"informalClassification": [
"Not Provided"
],
"keywords": [
{
"keyword": "Grab",
"scheme_name": "SESAR: Sample Type"
}
],
"label": "Goldfin ~20 m moss from 30 cm hummock",
"producedBy": {
"@id": "",
"description": "Not Provided",
"hasFeatureOfInterest": "peatland",
"label": "Not Provided",
"responsibility": [
{
"name": "Miriam Jones",
"role": "collector"
},
{
"name": "Jonathan Nichols",
"role": "sample owner"
}
],
"resultTime": "2017-09-01",
"samplingSite": {
"description": "Not Provided",
"label": "Not Provided",
"location": {
"elevation": "Not Provided",
"latitude": 60.25455,
"longitude": -149.35756666667
},
"placeName": [
"Gold Fin"
]
}
},
"registrant": "Jonathan Nichols",
"relatedResource": [],
"sampleidentifier": "IGSN:10.58052/IEJEN0040",
"samplingPurpose": "Not Provided"
}
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