Updates per sync meeting.

apiv2/schema/schema.yaml

@@ -726,18 +726,10 @@ classes:
       https_alignment_metadata:
         description: HTTPS url to the metadata file for this alignment
         range: string
-      s3_alignment_file:
-        description: Path to the alignment file
-        range: string
-      https_alignment_file:
-        description: HTTPS url for the alignment file
-        range: string
-      s3_tilt_file:
-        description: S3 path to the tilt file
-        range: string
-      https_tilt_file:
-        description: HTTPS url for the tilt file
-        range: string
+      is_portal_standard:
+        description: Whether this alignment is the portal standard
+        range: boolean
+        ifabsent: false
   AnnotationAuthor:
     name: AnnotationAuthor
     annotations:
@@ -1516,13 +1508,6 @@ classes:
         from_schema: cdp-dataset-config
         inverse: Deposition.frames
         range: Deposition
-      per_section_parameters:
-        name: per_section_parameters
-        description: Record how frames get mapped to TiltSeries
-        from_schema: cdp-dataset-config
-        multivalued: true
-        inverse: PerSectionParameters.frame
-        range: PerSectionParameters
       run:
         name: run
         from_schema: cdp-dataset-config
@@ -1596,69 +1581,6 @@ classes:
         - api_https_prefix
         range: string
         required: true
-  PerSectionParameters:
-    name: PerSectionParameters
-    annotations:
-      plural:
-        tag: plural
-        value: PerSectionParameters
-    description: Record how frames get mapped to TiltSeries
-    from_schema: cdp-dataset-config
-    mixins:
-    - IDMixin
-    attributes:
-      frame:
-        name: frame
-        from_schema: cdp-dataset-config
-        inverse: Frame.per_section_parameters
-        range: Frame
-        required: true
-      tiltseries:
-        name: tiltseries
-        from_schema: cdp-dataset-config
-        inverse: Tiltseries.per_section_parameters
-        range: Tiltseries
-        required: true
-      z_index:
-        name: z_index
-        description: z-index of the frame in the tiltseries
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - per_section_z_index
-        range: integer
-        required: true
-        minimum_value: 0
-      defocus:
-        name: defocus
-        description: defocus amount
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - per_section_defocus
-        range: float
-        minimum_value: 100
-        maximum_value: 100
-        unit:
-          symbol: µm
-          descriptive_name: microns
-      astigmatism:
-        name: astigmatism
-        description: Astigmatism amount for this frame
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - per_section_astigmatism
-        range: float
-      astigmatic_angle:
-        name: astigmatic_angle
-        description: Angle of ast
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - per_section_astigmatic_angle
-        range: float
-        minimum_value: -180
-        maximum_value: 180
-        unit:
-          symbol: °
-          descriptive_name: degrees
   PerSectionAlignmentParameters:
     name: PerSectionAlignmentParameters
     annotations:
@@ -1844,13 +1766,6 @@ classes:
         inverse: Alignment.tiltseries
         range: Alignment
         multivalued: true
-      per_section_parameters:
-        name: per_section_parameters
-        description: Record how frames get mapped to TiltSeries
-        from_schema: cdp-dataset-config
-        multivalued: true
-        inverse: PerSectionParameters.tiltseries
-        range: PerSectionParameters
       run:
         name: run
         from_schema: cdp-dataset-config
@@ -2346,11 +2261,14 @@ classes:
         range: string
         required: true
         description: Name of software used for reconstruction
-      is_canonical:
-        name: is_canonical
-        description: whether this tomogram is canonical for the run
-        from_schema: cdp-dataset-config
+      is_portal_standard:
+        description: whether this tomogram adheres to portal standards
         range: boolean
+        ifabsent: false
+      is_author_submitted:
+        description: whether this tomogram was submitted by the author of the dataset it belongs to.
+        range: boolean
+        ifabsent: false
       s3_omezarr_dir:
         name: s3_omezarr_dir
         description: S3 path to this tomogram in multiscale OME-Zarr format