Implement Multi-Z communication with chaise

[RFSH]

This is part of #57 epic. I wanted to have a pointer so I can document what we decided during our meetings so it might be a little hard to read and follow.

The following are the summary of interactions and what needs to be done for each one:

On load (chaise):

• The main image:

  • (implemented) Use the default_Z value to fetch the main image (/entity/Gene_Expression:Processed_image/Z_Index=val)
  • (assumption) We can assume that the channel color information are consistent across images with different z_index and same channel number. This means that the channel number 1 in an image with z_index=0 has the same color information with channel number 1 in image with z_index=10. So we can fetch the channel info once and use it for all the images.

• The list of images (based on page size) to be displayed below the main image as carrousel:

  • We should be able to use the same request with different parameter for different pages of images.

On load (OSD viewer):

• Display the main image.
• Show thumbnail of the list of images
  • For iiif: We can just do {i@d}/full/150,150/0/default.jpg for the first channel where 150,150 is the size of thumbnails that we want to show.
  • For other images: We could just show a default image (just a placeholder)

On change page in carrousel:

• (OSD viewer) Ask chaise to give a list of new images.
• (Chaise) send the same request that was done in load with different parameters.

On click on a thumbnail:

• (OSD viewer) switch to that image and display it.
• (OSD viewer) send the event to chaise, so it can update the annotations

[RFSH]

@rastogi-bhavya and I had a call where I explained the new model and how he can modify the records. The recording can be found here. In the following I will just summarize the main points and URLs that we discussed during the meeting:

• Look at the structure of Processed_Image: https://dev.rebuildingakidney.org/ermrest/catalog/2/schema/Gene_Expression/table/Processed_Image

• The image with multiple Z_Index: https://dev.rebuildingakidney.org/ermrest/catalog/2/entity/Gene_Expression:Image/RID=16-2GJM

• The channels of the image with multiple Z_Index: https://dev.rebuildingakidney.org/ermrest/catalog/2/entity/Gene_Expression:Image_Channel/Image=16-2GJM

• The main image of the image with multiple Z_Index: https://dev.rebuildingakidney.org/ermrest/catalog/2/entity/Gene_Expression:Processed_Image/Reference_Image=16-2GJM&Z_Index=81

• The pagination request for getting the Z_Index images: https://dev.rebuildingakidney.org/ermrest/catalog/2/attributegroup/Gene_Expression:Processed_Image/Reference_Image=16-2GJM/Z_Index;a:=array(*)@sort(Z_Index)@after(50)?limit=25

• How to fake the Processed_Image data to add more Z_Index records:

1. Make sure the value of uri column in the Image table is saved somewhere.

2. Send a PUT request to remove the uri value:

   PUT https://dev.rebuildingakidney.org/ermrest/catalog/2/attributegroup/Gene_Expression:Image/RID;uri
   Content-Type: application/json
   
   [
     {
        "RID": "16-2E4P",
        "uri": null
     }
   ]

3. Find the existing Processed_Image records and make sure existing Z_Index values are not-null

   GET https://dev.rebuildingakidney.org/ermrest/catalog/2/entity/Gene_Expression:Processed_Image/Reference_Image=16-2E4P

   If you need change the Z_Index you would sent a PUT request with the proper value

    PUT https://dev.rebuildingakidney.org/ermrest/catalog/2/attributegroup/Gene_Expression:Processed_Image/RID;Z_Index
    Content-Type: application/json
   
    [
      {
         "RID": "<the rid of processed_image record>",
         "Z_Index": 0
      }
    ]

4. Send a POST request to add the new entries. Make sure Reference_Image, Channel_Number, and Z_Index values are correct. Also copy the File_URL, File_Bytes, and File_MD5 of one of the existing records. Make sure you've noted the RID of records that you created. So later we won't be confused by this fake data. These are the RID of records that I created during the call for this table: 18-MKVY, 18-MKW0

   POST https://dev.rebuildingakidney.org/ermrest/catalog/2/entity/Gene_Expression:Processed_Image
   [
       {
           "Reference_Image": "16-2E4P",
           "Channel_Number": 0,
           "Z_Index": 1,
           "File_URL": "/hatrac/resources/gene_expression/pyramidal_tiff/2018/3b10e1732b0e5013bf2ec228803fcce2:YVG4QOQ7PR2GRUSJYAIKJ5G4FI",
            "File_Bytes": 225153692,
            "File_MD5": "3b10e1732b0e5013bf2ec228803fcce2"
       },
       {
           "Reference_Image": "16-2E4P",
           "Channel_Number": 0,
           "Z_Index": 2,
           "File_URL": "/hatrac/resources/gene_expression/pyramidal_tiff/2018/3b10e1732b0e5013bf2ec228803fcce2:YVG4QOQ7PR2GRUSJYAIKJ5G4FI",
           "File_Bytes": 225153692,
           "File_MD5": "3b10e1732b0e5013bf2ec228803fcce2"
       }
   ]