Merge pull request #9 from GenomicsStandardsConsortium/initial-assets

initial assets

assets/compare_mims_and_soil_slots.txt

@@ -0,0 +1,155 @@
+conflicting slot's usage in Mims:
+name: conflicting
+pattern: ^[a-zA-Z]+$
+
+conflicting slot's usage in Soil:
+name: conflicting
+pattern: ^[0-9]+$
+
+Induced slot conflicting in MimsSoil
+
+name: conflicting
+description: intentionally set to incompatible states between a Checklist and an Extension
+from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
+alias: conflicting
+owner: MimsSoil
+domain_of:
+- Mims
+- Soil
+range: string
+pattern: ^[a-zA-Z]+$
+
+depth slot's usage in Mims:
+name: depth
+examples:
+- value: 10 meter
+recommended: true
+
+depth slot's usage in Soil:
+name: depth
+examples:
+- value: 10 meter
+required: true
+
+Induced slot depth in MimsSoil
+
+name: depth
+annotations:
+  Preferred_unit:
+    tag: Preferred_unit
+    value: meter
+description: The vertical distance below local surface. For sediment or soil samples
+  depth is measured from sediment or soil surface, respectively. Depth can be reported
+  as an interval for subsurface samples
+title: depth
+examples:
+- value: 10 meter
+in_subset:
+- environment
+from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
+keywords:
+- depth
+slot_uri: MIXS:0000018
+alias: depth
+owner: MimsSoil
+domain_of:
+- Mims
+- Soil
+range: string
+required: true
+recommended: true
+pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
+  *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
+structured_pattern:
+  syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
+  interpolated: true
+  partial_match: true
+
+elev slot's usage in Mims:
+name: elev
+recommended: true
+
+elev slot's usage in Soil:
+name: elev
+required: true
+
+Induced slot elev in MimsSoil
+
+name: elev
+annotations:
+  Preferred_unit:
+    tag: Preferred_unit
+    value: meter
+description: Elevation of the sampling site is its height above a fixed reference
+  point, most commonly the mean sea level. Elevation is mainly used when referring
+  to points on the earth's surface, while altitude is used for points above the surface,
+  such as an aircraft in flight or a spacecraft in orbit
+title: elevation
+examples:
+- value: 100 meter
+in_subset:
+- environment
+from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
+keywords:
+- elevation
+slot_uri: MIXS:0000093
+alias: elev
+owner: MimsSoil
+domain_of:
+- Mims
+- Soil
+range: string
+required: true
+recommended: true
+pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
+  *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
+structured_pattern:
+  syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
+  interpolated: true
+  partial_match: true
+
+project_name not modified by Mims or Soil
+
+----
+samp_name not modified by Mims or Soil
+
+----
+samp_vol_we_dna_ext not modified by Mims or Soil
+
+----
+temp slot's usage in Mims:
+name: temp
+recommended: true
+
+Soil uses the global definition for temp
+Induced slot temp in MimsSoil
+
+name: temp
+annotations:
+  Preferred_unit:
+    tag: Preferred_unit
+    value: degree Celsius
+description: Temperature of the sample at the time of sampling
+title: temperature
+examples:
+- value: 25 degree Celsius
+in_subset:
+- environment
+from_schema: https://w3id.org/GenomicsStandardsConsortium/mixs-missing-value-sandbox
+keywords:
+- temperature
+slot_uri: MIXS:0000113
+alias: temp
+owner: MimsSoil
+domain_of:
+- Mims
+- Soil
+range: string
+recommended: true
+pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
+  *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
+structured_pattern:
+  syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
+  interpolated: true
+  partial_match: true
+

assets/ranges_of_requireds_of_combination.txt

@@ -0,0 +1,52 @@
+Slot collection_date is required in MimsSoil
+datetime
+----
+Slot depth is required in MimsSoil
+string
+^{scientific_float}( *- *{scientific_float})? *{text}$
+^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
+----
+Slot elev is required in MimsSoil
+string
+^{scientific_float}( *- *{scientific_float})? *{text}$
+^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)? *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
+----
+Slot env_broad_scale is required in MimsSoil
+string
+^{termLabel} \[{termID}\]$
+^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
+----
+Slot env_local_scale is required in MimsSoil
+string
+----
+Slot env_medium is required in MimsSoil
+string
+^{termLabel} \[{termID}\]$
+^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
+----
+Slot geo_loc_name is required in MimsSoil
+string
+^{text}: {text}, {text}$
+^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
+----
+Slot lat_lon is required in MimsSoil
+string
+^{lat} {lon}$
+^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
+----
+Slot project_name is required in MimsSoil
+string
+----
+Slot samp_name is required in MimsSoil
+string
+----
+Slot samp_taxon_id is required in MimsSoil
+string
+^{text} \[{NCBItaxon_id}\]$
+^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
+----
+Slot seq_meth is required in MimsSoil
+string
+^{text}|({termLabel} \[{termID}\])$
+^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
+----

project.Makefile

@@ -12,3 +12,9 @@ src/mixs_missing_value_sandbox/schema/mixs_missing_value_sandbox.yaml
 	$(RUN) linkml-convert --schema $(word 2,$^) \
 		--output $@ \
 		--index-slot mims_soil_data $(word 1,$^)
+
+assets/compare_mims_and_soil_slots.txt:
+	poetry run python src/scripts/compare_mims_and_soil_slots.py > $@
+
+assets/ranges_of_requireds_of_combination.txt:
+	poetry run python src/scripts/ranges_of_requireds_of_combination.py > $@