Merge branch 'investigate-failing-pytest-cherrypick' into 'main'

Cherry-picked fixes to main for pytests

See merge request MoNET/analysis-api-schema!58

Author: mkapur-pnnl

config.yaml

@@ -7,6 +7,7 @@
 excludes:
   - markdown
   - shacl
+  - shex
   # excelgen re-saves the whole workbook once per class AND once per slot
   # (~2900 full writes for this schema), which is ~97% of gen-project's runtime
   # (507s of 520s) and the source of the "permissible values with total length

docs/elements/Method.md

@@ -17,8 +17,8 @@ Alias: method
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-| [KuoMethod](KuoMethod.md) |  |  no  |
 | [TextureMethod](TextureMethod.md) |  |  no  |
+| [KuoMethod](KuoMethod.md) |  |  no  |
 
 
 

docs/elements/acquisition_end_time.md

@@ -17,16 +17,16 @@ Alias: acquisition_end_time
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-| [XRDDataGenerationActivity](XRDDataGenerationActivity.md) | X-ray Diffraction (XRD) mineralogical analysis activity |  no  |
+| [RespirationDataGenerationActivity](RespirationDataGenerationActivity.md) | Data generation activity for soil respiration analysis |  no  |
+| [NucleotideSequencing](NucleotideSequencing.md) | A lab activity in which DNA or RNA that was extracted from a sample is sequen... |  no  |
 | [PlateDataGenerationActivity](PlateDataGenerationActivity.md) | Abstract base for plate measurement activities |  no  |
+| [AMP2DataGenerationActivity](AMP2DataGenerationActivity.md) | AMP2 plate measurement (OD, fluorescence, flow cytometry) |  no  |
+| [EcoplateDataGenerationActivity](EcoplateDataGenerationActivity.md) | Ecoplate absorbance measurement at a single timepoint |  no  |
+| [XRDDataGenerationActivity](XRDDataGenerationActivity.md) | X-ray Diffraction (XRD) mineralogical analysis activity |  no  |
 | [DataGenerationActivity](DataGenerationActivity.md) | Abstract base for any data generation activity (physical to digital) |  no  |
 | [XRayDataGenerationActivity](XRayDataGenerationActivity.md) | Abstract base class for X-ray analytical methods including XRF (elemental) |  no  |
-| [AMP2DataGenerationActivity](AMP2DataGenerationActivity.md) | AMP2 plate measurement (OD, fluorescence, flow cytometry) |  no  |
 | [XRFDataGenerationActivity](XRFDataGenerationActivity.md) | X-ray Fluorescence (XRF) elemental analysis activity |  no  |
-| [NucleotideSequencing](NucleotideSequencing.md) | A lab activity in which DNA or RNA that was extracted from a sample is sequen... |  no  |
 | [MassSpectrometryDataGenerationActivity](MassSpectrometryDataGenerationActivity.md) | A record of the mass spectrometry run that generates a raw data product |  no  |
-| [EcoplateDataGenerationActivity](EcoplateDataGenerationActivity.md) | Ecoplate absorbance measurement at a single timepoint |  no  |
-| [RespirationDataGenerationActivity](RespirationDataGenerationActivity.md) | Data generation activity for soil respiration analysis |  no  |
 
 
 

docs/elements/acquisition_start_time.md

@@ -17,16 +17,16 @@ Alias: acquisition_start_time
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-| [XRDDataGenerationActivity](XRDDataGenerationActivity.md) | X-ray Diffraction (XRD) mineralogical analysis activity |  no  |
+| [RespirationDataGenerationActivity](RespirationDataGenerationActivity.md) | Data generation activity for soil respiration analysis |  no  |
+| [NucleotideSequencing](NucleotideSequencing.md) | A lab activity in which DNA or RNA that was extracted from a sample is sequen... |  no  |
 | [PlateDataGenerationActivity](PlateDataGenerationActivity.md) | Abstract base for plate measurement activities |  no  |
+| [AMP2DataGenerationActivity](AMP2DataGenerationActivity.md) | AMP2 plate measurement (OD, fluorescence, flow cytometry) |  no  |
+| [EcoplateDataGenerationActivity](EcoplateDataGenerationActivity.md) | Ecoplate absorbance measurement at a single timepoint |  no  |
+| [XRDDataGenerationActivity](XRDDataGenerationActivity.md) | X-ray Diffraction (XRD) mineralogical analysis activity |  no  |
 | [DataGenerationActivity](DataGenerationActivity.md) | Abstract base for any data generation activity (physical to digital) |  no  |
 | [XRayDataGenerationActivity](XRayDataGenerationActivity.md) | Abstract base class for X-ray analytical methods including XRF (elemental) |  no  |
-| [AMP2DataGenerationActivity](AMP2DataGenerationActivity.md) | AMP2 plate measurement (OD, fluorescence, flow cytometry) |  no  |
 | [XRFDataGenerationActivity](XRFDataGenerationActivity.md) | X-ray Fluorescence (XRF) elemental analysis activity |  no  |
-| [NucleotideSequencing](NucleotideSequencing.md) | A lab activity in which DNA or RNA that was extracted from a sample is sequen... |  no  |
 | [MassSpectrometryDataGenerationActivity](MassSpectrometryDataGenerationActivity.md) | A record of the mass spectrometry run that generates a raw data product |  no  |
-| [EcoplateDataGenerationActivity](EcoplateDataGenerationActivity.md) | Ecoplate absorbance measurement at a single timepoint |  no  |
-| [RespirationDataGenerationActivity](RespirationDataGenerationActivity.md) | Data generation activity for soil respiration analysis |  no  |
 
 
 

docs/elements/additional_information.md

@@ -22,10 +22,10 @@ Alias: additional_information
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
+| [MetagenomicsGenePhylogenyProduct](MetagenomicsGenePhylogenyProduct.md) | Top-level archive for gene-based phylogeny outputs (zip/tar stored in MinIO) |  no  |
+| [MetagenomicsProduct](MetagenomicsProduct.md) | Abstract base for all metagenomics data products |  no  |
 | [MetagenomicsAnnotationProduct](MetagenomicsAnnotationProduct.md) | Top-level archive for functional annotation outputs (zip/tar stored in MinIO) |  no  |
 | [MetagenomicsBinningProduct](MetagenomicsBinningProduct.md) | Top-level archive (zip/tar) for binning results stored in MinIO |  no  |
-| [MetagenomicsProduct](MetagenomicsProduct.md) | Abstract base for all metagenomics data products |  no  |
-| [MetagenomicsGenePhylogenyProduct](MetagenomicsGenePhylogenyProduct.md) | Top-level archive for gene-based phylogeny outputs (zip/tar stored in MinIO) |  no  |
 
 
 

docs/elements/agitation_speed_rpm.md

@@ -22,15 +22,15 @@ Alias: agitation_speed_rpm
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-| [EcoplatePlateSetupActivity](EcoplatePlateSetupActivity.md) | Ecoplate-specific plate setup |  no  |
+| [HasIncubationConditions](HasIncubationConditions.md) | Mixin for activities/setups that involve controlled incubation |  no  |
 | [PlateSetupActivity](PlateSetupActivity.md) | Abstract base for 96-well plate setup activities |  no  |
-| [AMP2PlateSetupActivity](AMP2PlateSetupActivity.md) | AMP2-specific plate setup |  no  |
-| [StockCulturePreparation](StockCulturePreparation.md) | Preparation of a stock culture from user samples for long-term storage |  no  |
+| [CultureGrowth](CultureGrowth.md) | Abstract activity for growing cultures from samples or other cultures |  no  |
 | [ExperimentalCulture](ExperimentalCulture.md) | Growth of an experimental culture for downstream analysis |  no  |
 | [PreCultureGrowth](PreCultureGrowth.md) | Growth of a pre-culture to establish viable inoculum before |  no  |
 | [StrainPurity](StrainPurity.md) | Purity check of a strain culture |  no  |
-| [HasIncubationConditions](HasIncubationConditions.md) | Mixin for activities/setups that involve controlled incubation |  no  |
-| [CultureGrowth](CultureGrowth.md) | Abstract activity for growing cultures from samples or other cultures |  no  |
+| [AMP2PlateSetupActivity](AMP2PlateSetupActivity.md) | AMP2-specific plate setup |  no  |
+| [StockCulturePreparation](StockCulturePreparation.md) | Preparation of a stock culture from user samples for long-term storage |  no  |
+| [EcoplatePlateSetupActivity](EcoplatePlateSetupActivity.md) | Ecoplate-specific plate setup |  no  |
 
 
 

docs/elements/agrochem_addition.md

@@ -22,9 +22,9 @@ Alias: agrochem_addition
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-| [MonetSoilSample](MonetSoilSample.md) | A soil sample that has been collected according to the MONet soil sampling pr... |  no  |
 | [SoilSample](SoilSample.md) | A sample of soil collected from the environment |  no  |
 | [OtherUndescribedSample](OtherUndescribedSample.md) | A sample that does not fit into any of the other described sample types |  no  |
+| [MonetSoilSample](MonetSoilSample.md) | A soil sample that has been collected according to the MONet soil sampling pr... |  no  |
 
 
 

docs/elements/air_temp_regm.md

@@ -22,18 +22,18 @@ Alias: air_temp_regm
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
-| [PlantSample](PlantSample.md) | A sample containing plant material |  no  |
-| [SoilSample](SoilSample.md) | A sample of soil collected from the environment |  no  |
+| [WaterSample](WaterSample.md) | A sample of water collected from the environment |  no  |
 | [SedimentSample](SedimentSample.md) | A sample of sediment collected from the environment |  no  |
-| [CultureEnvironmentalSample](CultureEnvironmentalSample.md) | A sample containing organisms cultured from an environmental sample |  no  |
+| [FieldDeployedTerraformSample](FieldDeployedTerraformSample.md) | A sample collected from a field-deployed Terraform experiment |  no  |
 | [MixedCultureSample](MixedCultureSample.md) | A sample containing multiple cultured organisms |  no  |
 | [PureCultureSample](PureCultureSample.md) | A sample of a culture containing a single organism |  no  |
-| [AerosolArmSample](AerosolArmSample.md) | An aerosol sample collected by the ARM facility |  no  |
+| [SoilSample](SoilSample.md) | A sample of soil collected from the environment |  no  |
+| [PlantSample](PlantSample.md) | A sample containing plant material |  no  |
+| [TerraformSample](TerraformSample.md) | A sample collected from a Terraform experiment |  no  |
+| [CultureEnvironmentalSample](CultureEnvironmentalSample.md) | A sample containing organisms cultured from an environmental sample |  no  |
 | [AerosolSample](AerosolSample.md) | An aerosol sample collected from the environment |  no  |
+| [AerosolArmSample](AerosolArmSample.md) | An aerosol sample collected by the ARM facility |  no  |
 | [OtherUndescribedSample](OtherUndescribedSample.md) | A sample that does not fit into any of the other described sample types |  no  |
-| [FieldDeployedTerraformSample](FieldDeployedTerraformSample.md) | A sample collected from a field-deployed Terraform experiment |  no  |
-| [TerraformSample](TerraformSample.md) | A sample collected from a Terraform experiment |  no  |
-| [WaterSample](WaterSample.md) | A sample of water collected from the environment |  no  |
 
 
 

docs/elements/alkalinity.md

@@ -22,9 +22,9 @@ Alias: alkalinity
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
+| [WaterSample](WaterSample.md) | A sample of water collected from the environment |  no  |
 | [SedimentSample](SedimentSample.md) | A sample of sediment collected from the environment |  no  |
 | [OtherUndescribedSample](OtherUndescribedSample.md) | A sample that does not fit into any of the other described sample types |  no  |
-| [WaterSample](WaterSample.md) | A sample of water collected from the environment |  no  |
 
 
 

docs/elements/alkalinity_method.md

@@ -22,9 +22,9 @@ Alias: alkalinity_method
 
 | Name | Description | Modifies Slot |
 | --- | --- | --- |
+| [WaterSample](WaterSample.md) | A sample of water collected from the environment |  no  |
 | [SedimentSample](SedimentSample.md) | A sample of sediment collected from the environment |  no  |
 | [OtherUndescribedSample](OtherUndescribedSample.md) | A sample that does not fit into any of the other described sample types |  no  |
-| [WaterSample](WaterSample.md) | A sample of water collected from the environment |  no  |