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Method to validate the relationship between elements #218

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Method to validate the relationship between elements#218

Description

@LucaMarconato
LucaMarconato
opened on Apr 5, 2023

I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp

I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).

Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().

Things that would be checked:

  • The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
  • The column with name table.uns['spatialdata_attrs']['region_key'] exists
  • The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
  • The column with name table.uns['spatialdata_attrs']['instance_key'] exists
  • The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}
  • In a points object, the column with name INSTANCE_KEY exists.
  • In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217

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Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
      Skip to content
      Method to validate the relationship between elements #218
      Open
      Open
      Method to validate the relationship between elements#218
      Description
      @LucaMarconato
      LucaMarconato
      opened on Apr 5, 2023
      I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
      I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
      
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
      Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
      Things that would be checked:
      •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
      •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
      •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
      •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
      •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
      2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

      •  In a points object, the column with name INSTANCE_KEY exists.
      •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
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Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
          Skip to content
          Method to validate the relationship between elements #218
          Open
          Open
          Method to validate the relationship between elements#218
          Description
          @LucaMarconato
          LucaMarconato
          opened on Apr 5, 2023
          I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
          I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
          
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
          Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
          Things that would be checked:
          •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
          •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
          •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
          •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
          •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
          2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

          •  In a points object, the column with name INSTANCE_KEY exists.
          •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
              Skip to content
              Method to validate the relationship between elements #218
              Open
              Open
              Method to validate the relationship between elements#218
              Description
              @LucaMarconato
              LucaMarconato
              opened on Apr 5, 2023
              I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
              I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
              
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
              Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
              Things that would be checked:
              •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
              •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
              •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
              •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
              •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
              2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

              •  In a points object, the column with name INSTANCE_KEY exists.
              •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
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Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
                  Skip to content
                  Method to validate the relationship between elements #218
                  Open
                  Open
                  Method to validate the relationship between elements#218
                  Description
                  @LucaMarconato
                  LucaMarconato
                  opened on Apr 5, 2023
                  I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
                  I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
                  
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
                  Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
                  Things that would be checked:
                  •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
                  •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
                  •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
                  •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
                  •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
                  2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

                  •  In a points object, the column with name INSTANCE_KEY exists.
                  •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
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var __m = "*";
var __re = new RegExp('^' + ".*" + '
Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
                      Skip to content
                      Method to validate the relationship between elements #218
                      Open
                      Open
                      Method to validate the relationship between elements#218
                      Description
                      @LucaMarconato
                      LucaMarconato
                      opened on Apr 5, 2023
                      I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
                      I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
                      
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
                      Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
                      Things that would be checked:
                      •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
                      •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
                      •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
                      •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
                      •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
                      2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

                      •  In a points object, the column with name INSTANCE_KEY exists.
                      •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
                      Metadata
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Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
                          Skip to content
                          Method to validate the relationship between elements #218
                          Open
                          Open
                          Method to validate the relationship between elements#218
                          Description
                          @LucaMarconato
                          LucaMarconato
                          opened on Apr 5, 2023
                          I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
                          I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
                          
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
                          Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
                          Things that would be checked:
                          •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
                          •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
                          •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
                          •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
                          •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
                          2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

                          •  In a points object, the column with name INSTANCE_KEY exists.
                          •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
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Method to validate the relationship between elements · Issue #218 · scverse/spatialdata · GitHub
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                              Method to validate the relationship between elements #218
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                              Method to validate the relationship between elements#218
                              Description
                              @LucaMarconato
                              LucaMarconato
                              opened on Apr 5, 2023
                              I discussed this with @melonora today. Relevant also to @timtreis and @sagar87. CC @giovp
                              I would add a method to check the consistency of the table and the elements. This function would not throw errors, but check relationships are missing/invalid.
                              
This is useful because sometimes we catch bugs only downstream (when trying to plot or aggregate something).
                              Not sure when we should call this method, maybe after the constructor, after reading and before saving. Or just let the user call it. The name could be validate_data_relationships().
                              Things that would be checked:
                              •  The regions in table.uns['spatialdata_attrs']['region'] are present in the sdata object.
                              •  The column with name table.uns['spatialdata_attrs']['region_key'] exists
                              •  The values of the rows in the column table.uns['spatialdata_attrs']['region_key'] are exactly the one in table.uns['spatialdata_attrs']['region'].
                              •  The column with name table.uns['spatialdata_attrs']['instance_key'] exists
                              •  The values of the rows in the column table.uns['spatialdata_attrs']['instance_key'] correspond to the value in the index of the corresponding regions. This check is done in napari_spatialdata when creating a shapes layer and or a labels layer. For instance this warning is given when some of the labels values and the table instance_key values don't match:
                              2023-04-05 15:12:39.751 | WARNING | napari_spatialdata.interactive:_find_annotation_for_labels:435 - 11050/11051 labels not annotated: {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86}

                              •  In a points object, the column with name INSTANCE_KEY exists.
                              •  In a points object, the values of the INSTANCE_KEY column actually refer to real regions. I have just realized that there may be a bug around this, I discuss this in this issue: Bug with INSTANCE_KEY for points? #217
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