docs: re-build, removes extra Person, adds CalibrationObject, new Connection pattern (#1509)

Author: dbirman

docs/source/acquisition.md

@@ -77,7 +77,7 @@ while the StimulusEpoch represents all stimuli being presented.
 | `specimen_id` | `Optional[str]` | Specimen ID is required for in vitro imaging modalities |
 | `acquisition_start_time` | `datetime (timezone-aware)` |  |
 | `acquisition_end_time` | `datetime (timezone-aware)` |  |
-| `experimenters` | List[[Person](components/identifiers.md#person)] |  |
+| `experimenters` | `List[str]` |  |
 | `protocol_id` | `Optional[List[str]]` | DOI for protocols.io |
 | `ethics_review_id` | `Optional[List[str]]` |  |
 | `instrument_id` | `str` | Should match the Instrument.instrument_id |

docs/source/components/connections.md

@@ -8,28 +8,10 @@ Description of a connection between devices in an instrument
 
 | Field | Type | Description |
 |-------|------|-------------|
-| `device_names` | `List[str]` |  |
-| `connection_data` | Dict[str, [ConnectionData](#connectiondata)] |  |
-
-
-### ConnectionData
-
-Configuration data for a device connection including direction and port information
-
-| Field | Type | Description |
-|-------|------|-------------|
-| `direction` | Optional[[ConnectionDirection](#connectiondirection)] |  |
-| `port` | `Optional[str]` |  |
-
-
-### ConnectionDirection
-
-Direction of a connection
-
-| Name | Value |
-|------|-------|
-| `SEND` | `Send` |
-| `RECEIVE` | `Receive` |
-| `SEND_AND_RECEIVE` | `Send and receive` |
+| `source_device` | `str` |  |
+| `source_port` | `Optional[str]` |  |
+| `target_device` | `str` |  |
+| `target_port` | `Optional[str]` |  |
+| `send_and_receive` | `bool` | Whether the connection is bidirectional (send and receive data) |
 
 

docs/source/components/specimen_procedures.md

@@ -78,7 +78,7 @@ Description of surgical or other procedure performed on a specimen
 | `specimen_id` | `str` |  |
 | `start_date` | `datetime.date` |  |
 | `end_date` | `datetime.date` |  |
-| `experimenters` | List[[Person](identifiers.md#person)] |  |
+| `experimenters` | `List[str]` |  |
 | `protocol_id` | `Optional[List[str]]` | DOI for protocols.io |
 | `protocol_parameters` | `Optional[Dict[str, str]]` | Parameters defined in the protocol and their value during this procedure |
 | `procedure_details` | List[[HCRSeries](#hcrseries) or [FluorescentStain](reagent.md#fluorescentstain) or [PlanarSectioning](#planarsectioning) or [ProbeReagent](reagent.md#probereagent) or [Reagent](reagent.md#reagent) or [GeneProbeSet](reagent.md#geneprobeset)] | Details of the procedures, including reagents and sectioning information. |

docs/source/components/subject_procedures.md

@@ -9,7 +9,7 @@ Description of a non-surgical procedure performed on a subject
 | Field | Type | Description |
 |-------|------|-------------|
 | `start_date` | `datetime.date` |  |
-| `experimenters` | Optional[List[[Person](identifiers.md#person)]] |  |
+| `experimenters` | `Optional[List[str]]` |  |
 | `ethics_review_id` | `str` |  |
 | `protocol_id` | `Optional[str]` | DOI for protocols.io |
 | `description` | `str` |  |
@@ -24,7 +24,7 @@ Description of subject procedures performed at one time
 |-------|------|-------------|
 | `protocol_id` | `Optional[str]` | DOI for protocols.io |
 | `start_date` | `datetime.date` |  |
-| `experimenters` | Optional[List[[Person](identifiers.md#person)]] |  |
+| `experimenters` | `Optional[List[str]]` |  |
 | `ethics_review_id` | `Optional[str]` |  |
 | `animal_weight_prior` | `Optional[float]` | Animal weight before procedure |
 | `animal_weight_post` | `Optional[float]` | Animal weight after procedure |

docs/source/components/subjects.md

@@ -15,6 +15,17 @@ Description of breeding info for subject
 | `paternal_genotype` | `str` |  |
 
 
+### CalibrationObject
+
+Description of a calibration object
+
+| Field | Type | Description |
+|-------|------|-------------|
+| `empty` | `bool` | Set to true if the calibration was performed with no object. |
+| `description` | `str` |  |
+| `objects` | Optional[List[[Device](devices.md#device)]] | For calibration objects that are built up from one or more devices. |
+
+
 ### HomeCageEnrichment
 
 Materials provided in animal home cage

docs/source/model.md

@@ -40,7 +40,7 @@ Description of model evaluation
 | `name` | `str` | ('Unique name of the processing step.', ' If not provided, the type will be used as the name.') |
 | `stage` | [ProcessStage](processing.md#processstage) |  |
 | `code` | [Code](components/identifiers.md#code) | Code used for processing |
-| `experimenters` | List[[Person](components/identifiers.md#person)] | People responsible for processing |
+| `experimenters` | `List[str]` | People responsible for processing |
 | `pipeline_name` | `Optional[str]` | Pipeline names must exist in Processing.pipelines |
 | `start_date_time` | `datetime (timezone-aware)` |  |
 | `end_date_time` | `datetime (timezone-aware)` |  |
@@ -72,7 +72,7 @@ Description of model training
 | `name` | `str` | ('Unique name of the processing step.', ' If not provided, the type will be used as the name.') |
 | `stage` | [ProcessStage](processing.md#processstage) |  |
 | `code` | [Code](components/identifiers.md#code) | Code used for processing |
-| `experimenters` | List[[Person](components/identifiers.md#person)] | People responsible for processing |
+| `experimenters` | `List[str]` | People responsible for processing |
 | `pipeline_name` | `Optional[str]` | Pipeline names must exist in Processing.pipelines |
 | `start_date_time` | `datetime (timezone-aware)` |  |
 | `end_date_time` | `datetime (timezone-aware)` |  |

docs/source/processing.md

@@ -39,7 +39,7 @@ Description of a single processing step
 | `name` | `str` | ('Unique name of the processing step.', ' If not provided, the type will be used as the name.') |
 | `stage` | [ProcessStage](processing.md#processstage) |  |
 | `code` | [Code](components/identifiers.md#code) | Code used for processing |
-| `experimenters` | List[[Person](components/identifiers.md#person)] | People responsible for processing |
+| `experimenters` | `List[str]` | People responsible for processing |
 | `pipeline_name` | `Optional[str]` | Pipeline names must exist in Processing.pipelines |
 | `start_date_time` | `datetime (timezone-aware)` |  |
 | `end_date_time` | `datetime (timezone-aware)` |  |

docs/source/quality_control.md

@@ -70,7 +70,7 @@ Collection of quality control metrics evaluated on a data asset to determine pas
 | Field | Type | Description |
 |-------|------|-------------|
 | `metrics` | List[[QCMetric](quality_control.md#qcmetric) or [CurationMetric](quality_control.md#curationmetric)] |  |
-| `key_experimenters` | Optional[List[[Person](components/identifiers.md#person)]] | Experimenters who are responsible for quality control of this data asset |
+| `key_experimenters` | `Optional[List[str]]` | Experimenters who are responsible for quality control of this data asset |
 | `notes` | `Optional[str]` |  |
 | `default_grouping` | `List[str]` | Default tag grouping for this QualityControl object, used in visualizations |
 | `allow_tag_failures` | `List[str or tuple]` | List of tags that are allowed to fail without failing the overall QC |
@@ -85,7 +85,7 @@ Schema to track curator name and timestamp for curation events
 
 | Field | Type | Description |
 |-------|------|-------------|
-| `curator` | [Person](components/identifiers.md#person) |  |
+| `curator` | `str` |  |
 | `timestamp` | `datetime (timezone-aware)` |  |
 
 

docs/source/subject.md

@@ -21,5 +21,5 @@ Description of a subject of data collection
 | Field | Type | Description |
 |-------|------|-------------|
 | `subject_id` | `str` | Unique identifier for the subject of data acquisition |
-| `subject_details` | [MouseSubject](components/subjects.md#mousesubject) or [HumanSubject](components/subjects.md#humansubject) |  |
+| `subject_details` | [MouseSubject](components/subjects.md#mousesubject) or [HumanSubject](components/subjects.md#humansubject) or [CalibrationObject](components/subjects.md#calibrationobject) |  |
 | `notes` | `Optional[str]` |  |