If I have a chain with a root and a leaf that are housed in the same lyph what happens?

For example

When I try to load the following file I get a repeated stream of TypeErrors.
Keast_Flatmap_051420(25).xlsx. This also happens when I try to load the latest models for export and validation, so am stuck on that.

errorHandler.js:16 TypeError: Cannot read property 'version' of undefined
    at Object.eval [as updateDirectives] (ResourceEditor.html:15)
    at Object.debugUpdateDirectives [as updateDirectives] (core.js:30043)
    at checkAndUpdateView (core.js:29439)
    at callViewAction (core.js:29680)
    at execEmbeddedViewsAction (core.js:29643)
    at checkAndUpdateView (core.js:29440)
    at callViewAction (core.js:29680)
    at execComponentViewsAction (core.js:29622)
    at checkAndUpdateView (core.js:29445)
    at callViewAction (core.js:29680)

With the new behavior for dealing with branches implemented in issue #12 we need to make sure that we can traverse multiple chains. I suggest that we add a relationship nextChain between the leaf node of one chain and the root of the next chain so that the query can be kept as simple as possible, requiring the addition of only a single new edge type (i.e., apinatomy:nextChain).

Advance lyph sizing methods to make sure internal lyphs always fit into housing lyphs or layers.

When trying to access https://open-physiology-viewer.surge.sh/ lately it times out 9/10 times.

@albatros13 can you update my permissions so I can manage the issues tags?

A -> internalIn -> B and B -> internalLyphs -> [A] where A or B are templates results into a warning that A cannot be internal in 2 lyphs. This is due to the template replacement procedure - each reference to template is replaced to a unique instance - this works fine for most cases but leads to an unjustified warning for the case when both sides of the relationship are specified.

When 2 or more chain links are bundled by a hosting lyph, align them so that their axes are parallel to the lyph's axes (currently they are reversed). This can be fixed by processing hostedNodes on opposite borders in reversed order

The new layout requirements (https://docs.google.com/document/d/1Aub84B5vRVgQmXvZ7hkJEpW2c9MNxYRhjS3kBB7So1I/edit) imply that connectivity models are placed into scaffolds that trigger automated layout. We should define a schema to describe scaffolds, implement support for 2 types of models in the ApiNATOMY viewer (e.g., open, merge, convert from Excel templates etc.), associate scaffolds with connectivity models, refer to scaffold elements from connectivity models, etc.

Use force-directed algorithm to position nodes on a grid aligned alone their host (container) lyph. See http://moritzstefaner.github.io/gridexperiments/ for example.

There should be a possibility to open external links for resources that have references to externals and publications

Currently we can create templates using specific lyphs as layers, e.g., in the definition
{"id": "K-129",
"name": "Segment of Spinal Cord",
"isTemplate": true,
"layers": ["104","105","K-86","KM-27","K-85","K-84","K-83","K-82","K-81","K-80","K-79",...]}
layers here are either materials (abstract) or lyphs (not templates in this example).
Should this be banned? Should we automatically set property isTemplate for such layers in the generated model?
The problem manifests when we auto-generate links for all lyphs which are not templates - these lyphs become visible free flowating lyphs in the model...

As ApiNATOMY models are rich in concepts connected by many relationships, it becomes increasingly harder to maintain ongoing code with the introduction of new rules and scenarios.
We need to ensure that the data input for the viewer is as expected: all entity types are recognized, required fields present, expected data types are correct (i.e., it is a common mistake while coding to confuse what the content of a field is: an id or an object reference) get warning about unspecified/unprocessed properties in the model. Possibly two schemas are neede: 1) for pure data input, 2) for extended JSON objects operated by the viewer.

Add filters to skip information messages and show fatal errors or warnings in the dialog showing model conversion results
Add "Download" button to store the logging messages and stats in a file

When creating materials, the polygonOffsetFactor parameter is used to define which objects with the same z-coordinate are located closer to the camera/viewer - smaller values mean the object appears on top of other surfaces. We set this parameter in the model to work for our ongoing scenario (Kidney model).
Refactor code to remove ad-hoc polygonOffsetFactor assignments from the visualization models and introduce a method to derive polygonOffsetFactor for each modeling primitive from the input data (ApiNATOMY model of an organ).

To model scaffold components F1, F2, F3, F4 etc., we need to be able to define area between two straight edges and an elliptic curve. Existing templates model layout of TOO map as a combination of axes and semicircle links, but this method does not allow us to define 4 regions and retain graphical content within their contours.
This can be addressed by extending the schema for defining regions by allowing regions to be composed of links (similarly to the levels in chains, but with common start and end node)

The viewer currently grinds to a near halt when working on large models. This happens even when most of the model is not visible.

While testing ApiNATOMY viewer Angular components, I discovered that our SciGraph query dialog (which should assist modelers in annotating resources with ontology terms) fails with message:
Http failure response for https://scigraph.olympiangods.org/scigraph/vocabulary/search/liver?prefix=UBERON: 0 Unknown Error
We should fix the feature and discuss the way we can support this feature, perhaps, via configurable URI to the SciGraph server instance.

I accidentally put the ids for chains in as source and target for links and ApiNATOMY did not complain.

Google sheets provides a direct link to download the xlsx version of a spreadsheet. The viewer should be able to accept the document id or google sheets url and construct the xlsx link from that. There should be a button to reimport the same doc id without having to enter it again so that the author can set the document they are working for their whole authoring session.
The format of the output is https://docs.google.com/spreadsheets/d/{spreadsheet-id}/export?format=xlsx and the interface box should accept https://docs.google.com/spreadsheets/d/{spreadsheet-id}.+ and {spreadsheet-id} as values. The internal api should require only the spreadsheet-id, and will need to handle cases where the spreadsheet id is not actually for a spreadsheet, and cases where the spreadsheet is not accessible. Advice to users is if they are concerned about sharing the document with edit permissions then they can set link sharing to view only and the viewer will still be able to download the document without having to do the api key dance.

Adding this feature will entirely remove the need to manually download the xlsx sheets from google sheets, which is massively time consuming during the authoring workflow.

Suggest a branch per model for development, and a folder per model. Will need to come up with a naming/numbering scheme.

The surfaces of regions need to have a polygon priority ordering to keep regions from z-fighting. Sometimes this could be inferred from the order in which scaffolds are loaded, but other times we would always want the F component to be below the D component because F is larger than D.

The ApiNATOMY schema allows users to define group templates within nested groups. Users may also refer to group templates defined in other groups. Model generator currently does not process correctly references to templates (in particular, chains), defined in other groups.

We should:

1. in a group, skip references to templates (trying to expand a chain defined in another group currently throws an exception as the reference is a string and not an object).
2. include resources generated from the template into all groups that refer to the template.
   Without this functionality, it is impossible to create groups that combine several external chains

When loading the attached file a red error message appears briefly and then disappears and the model is only partially loaded. I think the only thing that needs to be done is to keep the error visible and maybe add a note that the model may not have loaded correctly. Keast_Flatmap_051420.xlsx

This is needed so that we can add a label (abbrev) suffix to all generated labels during export to jsonld to make it quick to identify the source of an entity.

Chains provide a way to directly query from link to link and across chains. The link node structure requires traversing links, nodes, and clones. Both types of queries cannot be run at the same time, we need to settle on a single representation that we will query. Preferably this would be a direct relationship between links that deals specifically with the anatomical connectivity rather than the structure needed to render the anatomy in the viewer.

In older models, links that we generate for all lyphs without axes may be flying around and obstruct the visual inspection of other constructs. We can prevent them from showing by default by creating a special group which user can toggle on and off in the viewer.

When converting ApiNATOMY models to JSON-LD external ontology identifiers and references are currently conflated. To avoid this it would be helpful to have a Reference type that was a subclass of the External type that would make it possible to distinguish between external ontology ids and literature references since the semantics are significantly different.

Writing this I also realize that it might make sense to create another subclass of external ids that are OntologyId or OntologyTerm which would provide a way to differentiate ontology ids from other external ids rather than making them the default interpretation (if they continue to be of type External).

As the publication key has already been split from the external key in the model, it might make sense to have an edge that is ontologyTerm with specific semantics as well which could be used to unambiguously translate to rdf:type using the json-ld @context. This would (for example) make it possible to automatically include axon segments as the type of the named individual links/lyphs from the model.

Work on the borderModel and borderLinkModel to enable

• creation of overall border and individual side borders (axis, two radial borders and outer longitudinal border), and process relationships among borders and other entities (e.g., boundary nodes)
• drawing and highlighting of lyph borders
• possibility to use a border as a rotational axis for an internal lyph

Separate connectivity model from scaffold model, define relationship for applying a scaffold to a model.
Using the new schema part, model scaffold examples from the requirement document
https://docs.google.com/document/d/1Aub84B5vRVgQmXvZ7hkJEpW2c9MNxYRhjS3kBB7So1I/edit

The earlier version of graph.json (before commit 030d687) contains an example of a coalescence between lyph 78 and lyph 24. However these two lyphs are only adjacent in the viewer when the Coalescences box is unchecked:

The lyphs drift apart when the box is checked:

When the attached file is first loaded the viewer displays it as:

Each time the Update layout button is clicked the lyphs move and change position, eventually disappearing off the screen:

apinatomy:nodes and apinatomy:links do not have "@type": "@id" apparently?

For some reason the @context entries derived from graphScheme.json are no longer being extracted when I run on the json-ld branch branch or on master. @albatros13 was there some change to graphScheme.json that would cause this? Does the viewer pull the schema from github directly? I'm very confused right now.

Maybe take the "$id" field from graphScheme and embed it under "schema_version"? This means that "$id" would need to include the version number in its uri.

Please, please, add the ability to move around a zoomed diagram!

A series of tests are needed to check that nested objects are processed correctly.
For example, a user may define a chain by specifying some properties of levels (links) using nested objects
{
"id": "t1", "lyphTemplate": "template1",
"root": "n1", "leaf" : "n2,
"levels": [{"source": {"layout":{"x": -100}}}, {}, {}, {}, {"target": {"layout": {"x": 100}}}]
}
Here property {"layout":{"x": -100}} should be applied to the first node of the chain which is its root "n1". Similarly, {"layout": {"x": 100}} applies to the last node in the chain, or its leaf "n2".
While the definitions
{
"id": "t1", "lyphTemplate": "template1",
"levels": [{"source": "n1"}, {}, {}, {}, {"target": "n2"}]
},
{ "id": "n1", "layout":{"x": -100} },
{ "id": "n2", "layout":{"x": 100} }
are processed correctly, nested objects are often not expected by the model generator (but they are validated by the schema and hence should be processed).

'An unexpected error occurred: Error: TypeError: Cannot create property 'conveys' on string 'sn_drg-s1_12'.
Lyph sn_drg-s1_12 did not exist, it must have been sn-drg-s1_12
Yet we should avoid exception, generate a fake lyph, process the model, and issue a warning in logs.

It looks like these are in the list Generated links for internal lyphs in the logs.

After switching off and on visualization of layers, layers in the lyph on border do not reappear

Implement a function that sends query requests to SciGraph-based service and shows returned results as a dynamic group in the model viewer.

The viewer can toggle connectivity model groups. When we try to visualize scaffold models, the viewer fails as the new model has no methods for group processing. We should either make group-related functionality conditionally available for connectivity models only or support groups in scaffolds too.

Container lyphs represent organs with inner structure (e.g., Kidney lobus with two omega trees). The viewer should keep dependent entities (omega tree nodes and edges with conveying lyphs) within the boundaries of the host lyph.

The updateViewObjects of the lyphModel.js needs updating: currently 'boundToRectangle' method only pushes link source and target nodes to the straight rectangle while in practice the host lyph can be tilted, so we need to force these links to be within the lyph shape (for simplicity, we can do it for the rectangle shape, but accounting for its transformation/rotation).

In the case of 3d lyph icons, the host lyph is a tube/cyst/bag and the dependent entities are free to float in the whole its volume (this is what happens conceptually and should be implemented ideally, but 3d visualization is of low priority, 'nice to have' feature).

Some changes between the current live version (49) and the backup copy from Aug 31st have induced a stack overflow to occur when trying to export the flattened json-ld. I'm loading the version from the 31st, because I can't track down the issue right now, but it basically entails dumping the standard resourcemaps and comparing the diff to see what is causing the issue. @MCSZ if you know what you changed this morning you might be able to figure it out faster than I can without having to save and compare the resource maps (though fixing the code so that this can't happen will require that).

Copy of Keast_Flatmap_051420 - August 31, 1 53 PM.xlsx
Keast_Flatmap_051420(49).xlsx

errorHandler.js:16 Error: Uncaught (in promise): RangeError: Maximum call stack size exceeded
RangeError: Maximum call stack size exceeded
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:36)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:44)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:62)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:44)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:62)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:44)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:62)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:44)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:62)
    at Object.../node_modules/jsonld/dist/node6/lib/util.js.api.clone (util.js:44)
    at resolvePromise (zone.js:831)
    at resolvePromise (zone.js:788)
    at zone.js:892
    at ZoneDelegate.../node_modules/zone.js/dist/zone.js.ZoneDelegate.invokeTask (zone.js:423)
    at Object.onInvokeTask (core.js:26247)
    at ZoneDelegate.../node_modules/zone.js/dist/zone.js.ZoneDelegate.invokeTask (zone.js:422)
    at Zone.../node_modules/zone.js/dist/zone.js.Zone.runTask (zone.js:195)
    at drainMicroTaskQueue (zone.js:601)
    at ZoneTask.../node_modules/zone.js/dist/zone.js.ZoneTask.invokeTask [as invoke] (zone.js:502)
    at invokeTask (zone.js:1744)

Significant model manipulations may happen on input data change or when UI operations are called. We need regression tests for all major commands (create a new model, load, merge, save, edit resources, etc.)

To complete issue #12, I added a property to the Link class to point to the chain in which this link is a level. Theoretically, one link can be used in several chains, so this relationship may need to be revised.
Alternatively, we need a check to issue a warning if the modeller creates chains that share a link.
We also need to add unit tests to make sure the relationship auto-completes.
Also, we do not assemble chains by collecting links with set-up property levelIn as their order is unclear, this has to be reflected in the documentation and via logging.

When a chain is generated to stretch alone housing lyphs, its end points (root and leaf) are placed to the first and the last housing lyphs. This is achieved by setting the node's property "internalIn". The problem arises when a user tries to join several chains by sharing their end nodes - the same node is forced to be internal in two different lyphs causing model inconsistency. When this happens with border nodes, we clone the nodes, but no actions are taken for internal nodes.

Find the cause of issues:
Remaining references to undefined resources:
{"s_lnk-snl16":[["lnk-snl16","source"]],"t_lnk-snl16":[["lnk-snl16","target"]],"s_lnk-snl26":[["lnk-snl26","source"]],"t_lnk-snl26":[["lnk-snl26","target"]],"s_ns255":[["ns255","source"]],"t_ns255":[["ns255","target"]]}
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-img_11","name":"Axon of FOS to IMG from DRG","class":"Lyph","external":["GO:0030424"],"color":"#ff7f00","border":"b_an-img_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-img_11","layers":["ref_mat_54_229_an-img_11_1","ref_mat_56_229_an-img_11_2","ref_mat_116_229_an-img_11_3"],"internalIn":"K101","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-hypo_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-hypo_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-img_3","name":"Soma to SPOG neuron 3 in IMG","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-img_3","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-img_3","layers":["ref_mat_54_229_sn-img_3_1","ref_mat_56_229_sn-img_3_2","ref_mat_116_229_sn-img_3_3"],"internalIn":"K102","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-hypo_3"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_3","name":"Axon to SPOG neuron 3 in PG","class":"Lyph","external":["GO:0030424"],"color":"#1f78b4","border":"b_an-pg_3","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_3","layers":["ref_mat_54_229_an-pg_3_1","ref_mat_56_229_an-pg_3_2","ref_mat_116_229_an-pg_3_3"],"internalIn":"sn-hypo_3","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad_3"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_3","name":"Axon to SPOG neuron 3 in PG","class":"Lyph","external":["GO:0030424"],"color":"#1f78b4","border":"b_an-pg_3","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_3","layers":["ref_mat_54_229_an-pg_3_1","ref_mat_56_229_an-pg_3_2","ref_mat_116_229_an-pg_3_3"],"internalIn":"sn-hypo_3","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad2_3"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-blad-bn_11","name":"Neuron segment from PG to bladder neck_neuron 11","class":"Lyph","external":["GO:0030424"],"color":"#33a02c","border":"b_sn-blad-bn_11","internalLyphColumns":1,"internalLyphs":["an-pg_11","sn-blad-bn_11"],"thickness":{},"length":{},"conveys":"lnk-sn-blad-bn_11","internalIn":"n-blad","inCoalescences":[],"scale":{"width":40,"height":80}}
"sn-blad-bn_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn2_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn3_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd2_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_11","name":"Axon of POS through PG","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an-pg_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_11","layers":["ref_mat_54_229_an-pg_11_1","ref_mat_56_229_an-pg_11_2","ref_mat_116_229_an-pg_11_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd3_11"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_4","name":"Axon through pelvic ganglia axon_4","class":"Lyph","external":["GO:0030424"],"color":"#ff7f00","border":"b_an-pg_4","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_4","layers":["ref_mat_54_229_an-pg_4_1","ref_mat_56_229_an-pg_4_2","ref_mat_116_229_an-pg_4_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad_4"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-pg_4","name":"Axon through pelvic ganglia axon_4","class":"Lyph","external":["GO:0030424"],"color":"#ff7f00","border":"b_an-pg_4","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-pg_4","layers":["ref_mat_54_229_an-pg_4_1","ref_mat_56_229_an-pg_4_2","ref_mat_116_229_an-pg_4_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad2_4"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-PG_10","name":"Axon to FOS neuron 10 in pelvic ganglia","class":"Lyph","external":["GO:0030424"],"color":"#7570b3","border":"b_an-PG_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-PG_10","layers":["ref_mat_54_229_an-PG_10_1","ref_mat_56_229_an-PG_10_2","ref_mat_116_229_an-PG_10_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn_10"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-PG_10","name":"Axon to FOS neuron 10 in pelvic ganglia","class":"Lyph","external":["GO:0030424"],"color":"#7570b3","border":"b_an-PG_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-PG_10","layers":["ref_mat_54_229_an-PG_10_1","ref_mat_56_229_an-PG_10_2","ref_mat_116_229_an-PG_10_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn2_10"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-PG_10","name":"Axon to FOS neuron 10 in pelvic ganglia","class":"Lyph","external":["GO:0030424"],"color":"#7570b3","border":"b_an-PG_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-PG_10","layers":["ref_mat_54_229_an-PG_10_1","ref_mat_56_229_an-PG_10_2","ref_mat_116_229_an-PG_10_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn3_10"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-PG_10","name":"Axon to FOS neuron 10 in pelvic ganglia","class":"Lyph","external":["GO:0030424"],"color":"#7570b3","border":"b_an-PG_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-PG_10","layers":["ref_mat_54_229_an-PG_10_1","ref_mat_56_229_an-PG_10_2","ref_mat_116_229_an-PG_10_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd_10"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-PG_10","name":"Axon to FOS neuron 10 in pelvic ganglia","class":"Lyph","external":["GO:0030424"],"color":"#7570b3","border":"b_an-PG_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-PG_10","layers":["ref_mat_54_229_an-PG_10_1","ref_mat_56_229_an-PG_10_2","ref_mat_116_229_an-PG_10_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd2_10"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-PG_10","name":"Axon to FOS neuron 10 in pelvic ganglia","class":"Lyph","external":["GO:0030424"],"color":"#7570b3","border":"b_an-PG_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-PG_10","layers":["ref_mat_54_229_an-PG_10_1","ref_mat_56_229_an-PG_10_2","ref_mat_116_229_an-PG_10_3"],"internalIn":"K104","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd3_10"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-pg_1","name":"Soma to PPOG neuron 1 in pelvic ganglia","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-pg_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-pg_1","layers":["ref_mat_54_229_sn-pg_1_1","ref_mat_56_229_sn-pg_1_2","ref_mat_116_229_sn-pg_1_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn_1"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-pg_1","name":"Soma to PPOG neuron 1 in pelvic ganglia","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-pg_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-pg_1","layers":["ref_mat_54_229_sn-pg_1_1","ref_mat_56_229_sn-pg_1_2","ref_mat_116_229_sn-pg_1_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bn2_1"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-pg_1","name":"Soma to PPOG neuron 1 in pelvic ganglia","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-pg_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-pg_1","layers":["ref_mat_54_229_sn-pg_1_1","ref_mat_56_229_sn-pg_1_2","ref_mat_116_229_sn-pg_1_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd_1"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-pg_1","name":"Soma to PPOG neuron 1 in pelvic ganglia","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-pg_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-pg_1","layers":["ref_mat_54_229_sn-pg_1_1","ref_mat_56_229_sn-pg_1_2","ref_mat_116_229_sn-pg_1_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"sn-blad-bd2_1"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-pg_2","name":"Soma to SPOG neuron 2 in pelvic ganglia","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-pg_2","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-pg_2","layers":["ref_mat_54_229_sn-pg_2_1","ref_mat_56_229_sn-pg_2_2","ref_mat_116_229_sn-pg_2_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80}}
"sn-blad_2"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"sn-pg_2","name":"Soma to SPOG neuron 2 in pelvic ganglia","class":"Lyph","external":["ILX:0110736"],"color":"#a6cee3","border":"b_sn-pg_2","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-sn-pg_2","layers":["ref_mat_54_229_sn-pg_2_1","ref_mat_56_229_sn-pg_2_2","ref_mat_116_229_sn-pg_2_3"],"internalIn":"K103","inCoalescences":[],"scale":{"width":40,"height":80}}
"sn-blad2_2"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bd0tobd1_1","name":"Axon to PPOG neuron 1 in bladder dome layer 0","class":"Lyph","external":["GO:0030424"],"color":"#fdbf6f","border":"b_an-bd0tobd1_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bd0tobd1_1","layers":["ref_mat_54_229_an-bd0tobd1_1_1","ref_mat_56_229_an-bd0tobd1_1_2","ref_mat_116_229_an-bd0tobd1_1_3"],"internalIn":"sn-blad-bd_1","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bd0forbd2_1","name":"Axon to PPOG neuron 1 in bladder dome layer 0 for layer 2","class":"Lyph","external":["GO:0030424"],"color":"#cab2d6","border":"b_an-bd0forbd2_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bd0forbd2_1","layers":["ref_mat_54_229_an-bd0forbd2_1_1","ref_mat_56_229_an-bd0forbd2_1_2","ref_mat_116_229_an-bd0forbd2_1_3"],"internalIn":"sn-blad-bd2_1","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bd0_2","class":"Lyph","generated":true,"border":"b_an-bd0_2","internalLyphColumns":1,"thickness":{},"length":{},"conveys":"lnk_an-bd0_2","internalIn":"sn-blad2_2","inCoalescences":[],"width":20.480000000000004,"height":40.96000000000001,"scale":{"width":40,"height":80}}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bd0_3","name":"Axon to SPOG neuron 3 in Bladder dome layer 0","class":"Lyph","external":["GO:0030424"],"color":"#fb9a99","border":"b_an-bd0_3","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bd0_3","layers":["ref_mat_54_229_an-bd0_3_1","ref_mat_56_229_an-bd0_3_2","ref_mat_116_229_an-bd0_3_3"],"internalIn":"sn-blad2_3","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an_bd0-bv_10","name":"Axon to FOS neuron 10 bladder dome 0 to blood vessel","class":"Lyph","external":["GO:0030424"],"color":"#b2df8a","border":"b_an_bd0-bv_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an_bd0-bv_10","layers":["ref_mat_54_229_an_bd0-bv_10_1","ref_mat_56_229_an_bd0-bv_10_2","ref_mat_116_229_an_bd0-bv_10_3"],"internalIn":"sn-blad-bd_10","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an_bd0-bd1_10","name":"Axon to FOS neuron 10 bladder dome 0 to bladder dome 1","class":"Lyph","external":["GO:0030424"],"color":"#33a02c","border":"b_an_bd0-bd1_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an_bd0-bd1_10","layers":["ref_mat_54_229_an_bd0-bd1_10_1","ref_mat_56_229_an_bd0-bd1_10_2","ref_mat_116_229_an_bd0-bd1_10_3"],"internalIn":"sn-blad-bd2_10","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an_bd0-bd3_10","name":"Axon to FOS neuron 10 bladder dome 0 to bladder dome 3","class":"Lyph","external":["GO:0030424"],"color":"#e31a1c","border":"b_an_bd0-bd3_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an_bd0-bd3_10","layers":["ref_mat_54_229_an_bd0-bd3_10_1","ref_mat_56_229_an_bd0-bd3_10_2","ref_mat_116_229_an_bd0-bd3_10_3"],"internalIn":"sn-blad-bd3_10","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bd_4","name":"Axon through bladder dome_4","class":"Lyph","external":["GO:0030424"],"color":"#ffff99","border":"b_an-bd_4","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bd_4","layers":["ref_mat_54_229_an-bd_4_1","ref_mat_56_229_an-bd_4_2","ref_mat_116_229_an-bd_4_3"],"internalIn":"sn-blad2_4","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_11_K99"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bn0tobn1_1","name":"Axon to PPOG neuron 1 in bladder neck layer 0","class":"Lyph","external":["GO:0030424"],"color":"#1f78b4","border":"b_an-bn0tobn1_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bn0tobn1_1","layers":["ref_mat_54_229_an-bn0tobn1_1_1","ref_mat_56_229_an-bn0tobn1_1_2","ref_mat_116_229_an-bn0tobn1_1_3"],"internalIn":"sn-blad-bn_1","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an_bn0-bv_10","name":"Axon to FOS neuron 10 bladder neck 0 to blood vessel","class":"Lyph","external":["GO:0030424"],"color":"#e7298a","border":"b_an_bn0-bv_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an_bn0-bv_10","layers":["ref_mat_54_229_an_bn0-bv_10_1","ref_mat_56_229_an_bn0-bv_10_2","ref_mat_116_229_an_bn0-bv_10_3"],"internalIn":"sn-blad-bn_10","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_1_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bn0forbn2_1","name":"Axon to PPOG neuron 1 in bladder neck layer 0 for layer 2","class":"Lyph","external":["GO:0030424"],"color":"#33a02c","border":"b_an-bn0forbn2_1","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bn0forbn2_1","layers":["ref_mat_54_229_an-bn0forbn2_1_1","ref_mat_56_229_an-bn0forbn2_1_2","ref_mat_116_229_an-bn0forbn2_1_3"],"internalIn":"sn-blad-bn2_1","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_87_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bn0_2","name":"Axon to SPOG neuron 2 in bladder neck layer 0","class":"Lyph","external":["GO:0030424"],"color":"#a6cee3","border":"b_an-bn0_2","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bn0_2","layers":["ref_mat_54_229_an-bn0_2_1","ref_mat_56_229_an-bn0_2_2","ref_mat_116_229_an-bn0_2_3"],"internalIn":"sn-blad_2","inCoalescences":[],"scale":{"width":40,"height":80}}
"ref_mat_KM_87_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an_bn0-bn1_10","name":"Axon to FOS neuron 10 bladder neck 0 to bladder neck 1","class":"Lyph","external":["GO:0030424"],"color":"#e6ab02","border":"b_an_bn0-bn1_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an_bn0-bn1_10","layers":["ref_mat_54_229_an_bn0-bn1_10_1","ref_mat_56_229_an_bn0-bn1_10_2","ref_mat_116_229_an_bn0-bn1_10_3"],"internalIn":"sn-blad-bn2_10","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_87_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an_bn0-bn3_10","name":"Axon to FOS neuron 10 bladder neck 0 to bladder neck 3","class":"Lyph","external":["GO:0030424"],"color":"#666666","border":"b_an_bn0-bn3_10","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an_bn0-bn3_10","layers":["ref_mat_54_229_an_bn0-bn3_10_1","ref_mat_56_229_an_bn0-bn3_10_2","ref_mat_116_229_an_bn0-bn3_10_3"],"internalIn":"sn-blad-bn3_10","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_87_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bn_4","name":"Axon through bladder neck_4","class":"Lyph","external":["GO:0030424"],"color":"#cab2d6","border":"b_an-bn_4","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bn_4","layers":["ref_mat_54_229_an-bn_4_1","ref_mat_56_229_an-bn_4_2","ref_mat_116_229_an-bn_4_3"],"internalIn":"sn-blad_4","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_11_K100"
Property "internalIn" of the first resource (Lyph) should match the second resource:
{"id":"an-bn3-3_11","name":"Axon to bladder neck layer 3 for layer 1","class":"Lyph","external":["GO:0030424"],"color":"#a6cee3","border":"b_an-bn3-3_11","internalLyphColumns":1,"thickness":{},"length":{},"supertype":"229","inheritedExternal":["CL:0000540"],"conveys":"lnk-an-bn3-3_11","layers":["ref_mat_54_229_an-bn3-3_11_1","ref_mat_56_229_an-bn3-3_11_2","ref_mat_116_229_an-bn3-3_11_3"],"internalIn":"sn-blad-bn3_11","inCoalescences":[],"scale":{"width":40,"height":80},"hidden":true}
"ref_mat_KM_11_K100"
Property "fasciculatesIn" of the first resource (Link) should match the second resource:
{"id":"dn_drg-l6_10_lnk_1","class":"Link","generated":true,"color":"#000","source":"dn_drg-l6_10_node_0_join_0","target":"ns160_join_0","conveyingLyph":"dn_drg-l6_10_lyph_1","levelIn":"dn_drg-l6_10","fasciculatesIn":"ref_mat_KM_9_K_129_K27_1","length":64,"geometry":"link","lineWidth":"0.003","hidden":true}
"ref_mat_KM_9_K_129_K28_1"

When rendering wires for the scaffolds the aliasing of the borders/arcs/lines becomes quite apparent. It would be nice to have those anti-aliased.

While working out the issues with connectivity queries today we ran into a major point of confusion that should not be allowed to happen. All the dendrite chains had been specified as being "leafed" that is, they had a leaf but no root. For sake of sanity chains with only a single explicit root/leaf should have that be the root. This helps with the follow-your-nose approach to exploring apinatomy models and provides unambiguous behavior when only a single named (not generated) node is associated with a chain. Otherwise you have to query all chains in both directions.