Should use permalink chainlink icon

URL should be rolled in TermInfo query:

For everything not DataSet or Site:

http://virtualflybrain.org/reports/{some short form}

For DataSet

http://virtualflybrain.org/data/{some short form}

Site currently unsupported

BG template query:

MATCH (i:Individual)-[:INSTANCEOF]-(:Class { short_form: 'image' }),(a:Individual:VFB {short_form:'VFB_00000001'})<-[r1:Related { short_form : 'depicts' }]-(sc:Individual)-[r2]-(i:Individual)-[r3]-(bc:Individual) RETURN bc.short_form as id, bc.label as label limit 1;

http://vfbsandbox.inf.ed.ac.uk:8180/org.geppetto.frontend/geppetto?load_project_from_url=http://vfbsandbox.inf.ed.ac.uk/do/geppettoJson.json?i=VFB_00016207,VFB_00020020,VFB_00020062,VFBd_00100003%26t=VFBt_001%26d=

lobula is not visible through the brain even with opacity of brain set to 0.2

• see VirtualFlyBrain/VFB_json_schema#49

The addSOLRCache branch is broken when doing mvn install.

The variable alignment in line 1599 is out of scope, only visible inside the 'for loop' that ends before this 'if statement'.

Also line 1345 is missing import of exception and 1347 is using python print statement.

It would be very useful if queries could access template identity - this would allow only images on current template to be displayed.

superior AMMC commissure [FBbt_00100357] failing to initialize

Choosing a term to add to query should prompt display of query type choices, instead the user just sees the canvas without any pop-up. Choosing a query type requires going back to query icon or menu.

Check mesh

The second of the two images queries should end with (clustered), as in TermInfo

URL is 'annotation-source_data_link'

Need to find data source name?

Here's a full laptop screen of results:

I can't scroll down (either for the whole canvas or in the pop-up), so the only way I can reveal the controls under the table is to zoom out:

I suspect users would not think to do this and instead conclude the controls are missing (assuming they know to expect them in the first place).

See label from VirtualFlyBrain/VFB_neo4j#137

Show individuals with expression for Alleles (FBal), genes (FBgn), transposons (FBtp) or insertions (FBti).

Simple queries

The query widget must be synced with the focus term.
The initial implementation should only allow single leg queries - the first leg should not be searchable.

Need to think about how easily discoverable queries are for users. Having menus on term info could work if formatted like this:

compound queries.

Compound queries should work by logically refining existing query result sets. At least one major way to do this will be to select new query legs whilst browsing. Further discussion is probably needed to decide on whether we allow other mechanisms and what they should be.

Queries that return list of the same gross type can be combined. e.g. any queries that return only neuron classes can be combined with other queries that return only neuron classes. We can drive this by encoding return type in the metadata with query results and in metadata associated with each query.

We need documentation of multi-leg queries as a decision tree.

Also add launch from or menus from term info?

Adding
"statement": " and ", "parameters" : { "ARRAY_ID_RESULTS" : $ARRAY_ID_RESULTS, "ID" : "$ID" }around neo4j query string

and swapping:
'$ID' -> {ID}
$ARRAY_ID_RESULTS -> {ARRAY_ID_RESULTS}

Move to simply pulling the results headers from the results header to allow varying data to be displayed.

The initial config seems largely redundant as could be configured by the types returned in the results.

Wrong thumbnails showing up for neuropils

e.g.

Should be showing thumbnails of LAL - instead is showing thumbnails of neurons (in LAL?)

(Tested on http://vfbsandbox.inf.ed.ac.uk/)

AIM: approximately replicate the tree browsing functionality available on VFB 1

• Cypher to generate JSON for a tree. This returns the tree/graph of classes as JSON + a separate mapping from classes to anatomical and image individuals.
• Like VFB 1.0 this should allow selection of domains for term info and for addition to Canvas / stack viewer. In VFB 1.0 these two features are separable. This allows a compound image to be gradually assembled by a users.

Attempted launch of VFB 2.0 from sandbox3 via 3D=> the following error:

org.geppetto.core.common.GeppettoInitializationException: Unable to unmarshall simulation with url: http://vfbsandbox3.inf.ed.ac.uk/do/geppettoXml.xml?t=VFBt_001&i=VFB_00011319,VFB_00009437,VFB_00009455,VFB_00009456,VFB_00009457,VFB_00009461,VFB_00011205,VFB_00011207,VFB_00001756,VFB_00001747,VFB_00015975,VFB_00015994,VFB_00016138,VFB_00012942,VFB_00007950,VFB_00015379,VFB_00008537