mapr - browse data by custom attributes

[atarkowska]

Goal of this effort is to produce a prototype (or perhaps experimental) plugin which will outline how to take a particular map-annotation instance (e.g. genetic information) and "elevate" (or "reify") it into the UI.

https://github.com/ome/omero-mapr

[atarkowska]

MAPR URLs

---

URL	METHOD	URL PARAMS	QUERY STRING	Success Response	Error Response:	Sample Call:
/webclient/	GET		show=<type>-<value>	302 redirect		/webclient/?show=gene-CDC20
/mapr/<type>/	GET	type=(gene|phenotype|sirna|compound|organism)	value=<value> query=(true|false) default:false	200 HTML		/mapr/organism/?value=Homo%20Sapiens /mapr/organism/?value=Homo%20Sapiens&query=true

Attribute URL

Attribute URL, Attributes are preconfigured in application settings https://github.com/ome/omero-mapr/blob/master/mapr/mapr_settings.py or can be altered by changing omero configomeroweb.mapr.config

• URL

  /mapr/<type>/

• Method:

  GET

• URL Params

  Required:

  type=[gene|phenotype|sirna|compound|organism]

• QUERY STRING

  Required:

  value=[string]

  Optional:

  query=[boolean] default:false

• Success Response:
  • Code: 200
    
  • Content: HTML

• Sample Call:

  /mapr/organism/?value=Homo%20Sapiens /mapr/organism/?value=Homo%20Sapiens&query=true

[atarkowska]

MAPR JSON API

---

URL	METHOD	URL PARAMS	QUERY STRING	Success Response	Error Response:	Sample Call:
/mapr/api/<type>/count/	GET	type=(gene|phenotype|sirna|compound|organism)	value=<value> query=(true|false) default:false	200 JSON	400 Invalid parameter value 400 ApiUsageException	/api/gene/count/?value=CDC20 /api/gene/count/?value=CDC20query=true
/mapr/api/<type>/	GET	type=(gene|phenotype|sirna|compound|organism)	id=<value|id> orphaned=(true|false) value=<value>	200 JSON	400 Invalid parameter value 400 ApiUsageException	/api/gene/?value=CDC20&orphaned=true get value and children count /api/gene/?value=CDC20&query=true&orphaned=true get value matching %value% pattern and children count and image count /api/gene/?id=CDC20 returns list of screens and/or projects for given gene ID /api/gene/?value=CDC20&query=true returns list of screens and/or projects for matching %value% pattern with exact value
/mapr/api/<type>/<containers>/	GET	type=(gene|phenotype|sirna|compound|organism) containers=(plates|datasets|images)	value=<value> id=<parent_id> if containers=images then node=(plate|dataset)	200 JSON	400 Invalid parameter value 400 ApiUsageException	api/gene/plates/?value=CDC20&query=true&id=1202 return list of plates/datasets in screen/project for given parent_idand value /api/gene/images/?value=991&query=true&node=plate&id=1692 return list of images (Fileset IDs) for a give parent_id and matching %value% pattern with exact value
/mapr/api/annotations/<type>/	GET	type=(gene|phenotype|sirna|compound|organism)	type=map map=<value> or (screen|plate|project|dataset|image)=<id>	200 JSON	400 Invalid parameter value400 ApiUsageException	return map annotations containing given value (case sensitive)
/mapr/api/gene/paths_to_object/	GET		map.value=	200 JSON		find hierarchies for a given value (case sensitive) - in case we will provide multiple users or groups
/mapr/autocomplete/<type>/	GET	type=(gene|phenotype|sirna|compound|organism)	value=<value> query=true	200 JSON		find keywords for matching %value% pattern

[joshmoore]

This has been migrated to the repo itself, correct?

[atarkowska]

yes https://github.com/ome/omero-mapr/tree/master/docs

[atarkowska]

once you are happy with https://github.com/IDR/idr-demo.openmicroscopy.org/pull/10 I will open a PR against doc and link to the website and https://github.com/IDR/idr-notebooks/pull/8

[joshmoore]

for IDR/idr-demo.openmicroscopy.org#10, I'd like to strip out the results for readability. Haven't had a chance to do that yet.