feat: track gain and mdoc files alongside runs

apiv2/schema/schema.yaml

@@ -365,7 +365,7 @@ enums:
         description: JEOL Ltd.
       SIMULATED:
         text: SIMULATED
-        description: JEOL Ltd.
+        description: Simulated microscope
   fiducial_alignment_status_enum:
     name: fiducial_alignment_status_enum
     description: Fiducial Alignment method
@@ -541,6 +541,46 @@ classes:
         - author_primary_author_status
         ifabsent: false
         range: boolean
+  GainFile:
+    annotations:
+      plural:
+        tag: plural
+        value: GainFiles
+    description: Gain values for frames in this run
+    mixins:
+    - IDMixin
+    attributes:
+      run:
+        inverse: Run.gain_files
+        range: Run
+      s3_file_path:
+        description: Path to the file in s3
+        range: string
+        required: true
+      https_file_path:
+        description: Path to the file as an https url
+        range: string
+        required: true
+  FrameAcquisitionFile:
+    annotations:
+      plural:
+        tag: plural
+        value: FrameAcquisitionFiles
+    description: References to files containing more information about frame acquisition
+    mixins:
+    - IDMixin
+    attributes:
+      run:
+        inverse: Run.frame_acquisition_files
+        range: Run
+      s3_mdoc_path:
+        description: Path to the frame acquisition mdoc file in s3
+        range: string
+        required: true
+      https_mdoc_path:
+        description: Path to the frame acquisition mdoc file as an https url
+        range: string
+        required: true
   Alignment:
     name: Alignment
     annotations:
@@ -682,13 +722,6 @@ classes:
         unit:
           symbol: °
           descriptive_name: degrees
-      local_alignment_file:
-        name: local_alignment_file
-        description: Path to the local alignment file
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - alignment_local_alignment_file
-        range: string
       affine_transformation_matrix:
         name: affine_transformation_matrix
         description: A placeholder for the affine transformation matrix.
@@ -699,6 +732,16 @@ classes:
           - exact_cardinality: 4
           - exact_cardinality: 4
         range: string
+      s3_alignment_metadata:
+        description: S3 path to the metadata file for this alignment
+        range: string
+      https_alignment_metadata:
+        description: HTTPS url to the metadata file for this alignment
+        range: string
+      is_portal_standard:
+        description: Whether this is the portal standard alignment
+        range: boolean
+        ifabsent: false
   AnnotationAuthor:
     name: AnnotationAuthor
     annotations:
@@ -1534,15 +1577,6 @@ 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
-        annotations:
-          cascade_delete: true
       run:
         name: run
         from_schema: cdp-dataset-config
@@ -1616,69 +1650,6 @@ 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:
@@ -1726,22 +1697,14 @@ classes:
         unit:
           symbol: Å
           descriptive_name: Angstrom
-      in_plane_rotation:
-        name: in_plane_rotation
-        description: In-plane rotation of the projection in degrees
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - per_section_alignment_in_plane_rotation
+      volume_x_rotation:
+        description: X-axis rotation in degrees
         range: float
         unit:
           symbol: °
           descriptive_name: degrees
-      beam_tilt:
-        name: beam_tilt
-        description: Beam tilt during projection in degrees
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - per_section_alignment_beam_tilt
+      in_plane_rotation:
+        description: In-plane rotation of the projection in degrees
         range: float
         unit:
           symbol: °
@@ -1800,6 +1763,18 @@ classes:
         range: Frame
         annotations:
           cascade_delete: true
+      gain_files:
+        multivalued: true
+        inverse: GainFile.run
+        range: GainFile
+        annotations:
+          cascade_delete: true
+      frame_acquisition_files:
+        multivalued: true
+        inverse: FrameAcquisitionFile.run
+        range: FrameAcquisitionFile
+        annotations:
+          cascade_delete: true
       tiltseries:
         name: tiltseries
         from_schema: cdp-dataset-config
@@ -1869,15 +1844,6 @@ classes:
         multivalued: true
         annotations:
           cascade_delete: 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
-        annotations:
-          cascade_delete: true
       run:
         name: run
         from_schema: cdp-dataset-config
@@ -1918,20 +1884,6 @@ classes:
         exact_mappings:
         - tiltseries_https_mrc_file
         range: string
-      s3_collection_metadata:
-        name: s3_collection_metadata
-        description: S3 path to the collection metadata file for this tiltseries
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - tiltseries_s3_collection_metadata
-        range: string
-      https_collection_metadata:
-        name: https_collection_metadata
-        description: HTTPS path to the collection metadata file for this tiltseries
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - tiltseries_https_collection_metadata
-        range: string
       s3_angle_list:
         name: s3_angle_list
         description: S3 path to the angle list file for this tiltseries
@@ -1946,20 +1898,6 @@ classes:
         exact_mappings:
         - tiltseries_https_angle_list
         range: string
-      s3_gain_file:
-        name: s3_gain_file
-        description: S3 path to the gain file for this tiltseries
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - tiltseries_s3_gain_file
-        range: string
-      https_gain_file:
-        name: https_gain_file
-        description: HTTPS path to the gain file for this tiltseries
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - tiltseries_https_gain_file
-        range: string
       acceleration_voltage:
         name: acceleration_voltage
         description: Electron Microscope Accelerator voltage in volts
@@ -2193,13 +2131,6 @@ classes:
         - tiltseries_aligned_tiltseries_binning
         range: integer
         minimum_value: 0
-      frames_count:
-        name: frames_count
-        description: Number of frames associated with this tiltseries
-        from_schema: cdp-dataset-config
-        exact_mappings:
-        - frames_count
-        range: integer
   TomogramAuthor:
     name: TomogramAuthor
     annotations:
@@ -2295,6 +2226,7 @@ classes:
     from_schema: cdp-dataset-config
     mixins:
     - IDMixin
+    - DateStampedEntityMixin
     attributes:
       alignment:
         name: alignment
@@ -2417,11 +2349,18 @@ classes:
         range: string
         required: true
         description: Name of software used for reconstruction
-      is_canonical:
-        name: is_canonical
-        description: Is this tomogram considered the canonical tomogram for the run experiment? True=Yes
-        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
+      is_visualization_default:
+        description: Data curator’s subjective choice of default tomogram to display in visualization for a run
+        range: boolean
+        ifabsent: false
       s3_omezarr_dir:
         name: s3_omezarr_dir
         description: S3 path to this tomogram in multiscale OME-Zarr format
@@ -2533,6 +2472,16 @@ classes:
         required: true
         # TODO - is this reasonable?
         ifabsent: false
+      publications:
+        description: Comma-separated list of DOIs for publications associated with the tomogram.
+        range: string
+        recommended: true
+        pattern: (^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)|(^(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+(\s*,\s*(doi:)?10\.[0-9]{4,9}/[-._;()/:a-zA-Z0-9]+)*$)
+      related_database_entries:
+        description: If a CryoET tomogram is also deposited into another database, enter the database identifier here (e.g. EMPIAR-11445). Use a comma to separate multiple identifiers.
+        range: string
+        recommended: true
+        pattern: (^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)|(^(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8})(\s*,\s*(EMPIAR-[0-9]{5}|EMD-[0-9]{4,5}|pdb[0-9a-zA-Z]{4,8}))*$)
   DateStampedEntityMixin:
     name: DateStampedEntityMixin
     description: A set of dates at which a data item was deposited, published and