Map Annotation: For the iconify() function that previously recognised URLs, I added a regex to recognise chromosome regions in the form chr17:13450000-234323323. These are turned into an Icon that when clicked dispatches a 'update' event to the nb_bridge to show that region.
Long Annotations: In order to support the reverse interaction, we listen for 'update' events from the nb_bridge and when received, we query OMERO for Images that are annotated with that region. This is done using 3 LongAnnotations on each image for chromosome number, start and end, each with different namespace. When we have the images, we browse to /webclient/?show=image-1|image-2 to show them.
In the script, I also added chromosome, start and end as individual Key-Value pairs. This allows us to filter a Dataset by these values as in https://github.com/ome/omero-web/pull/22
As an alternative to using LongAnnotations and Key-Values for chromosome, start and end values, we could use an OMERO tables. That would be trickier to update when adding more images, but could work once we have a stable set of images. Filtering via tables needs parade (not built-in to webclient).
This is a prototype / draft for how to connect Nucleosome Browser events to Mapr. See demo at https://www.youtube.com/watch?v=6sHkjBTKQr0&feature=youtu.be
Follows instructions at https://docs.google.com/document/d/1PEYqxZQEY9yZpxGY_mvlgQy3EpPvGbTq3iFBHdepPs8/edit
It relies on Chromosome Region annotations on Images in OMERO, added using script at https://gist.github.com/will-moore/79e4e18c1e8ba632773f8fd9fdce05c1
iconify()function that previously recognised URLs, I added a regex to recognise chromosome regions in the formchr17:13450000-234323323. These are turned into an Icon that when clicked dispatches a 'update' event to the nb_bridge to show that region.LongAnnotationson each image for chromosomenumber,startandend, each with different namespace. When we have the images, we browse to /webclient/?show=image-1|image-2 to show them.