Extend Knox's RESTful API with an endpoint for exporting combinatorial SBOL ("/sbol/exportCombinatorial"). The input parameters for this endpoint should be the spaceID of the design space graph to be exported as SBOL and a namespace (for example, "http://example.org") to prefix the URIs of all SBOL objects generated during the export process. The generated objects should include CombinatorialDerivations and their template ComponentDefinitions. The variants properties of a CombinatorialDerivation's VariableComponents should contain the component IDs labeling the edges of the exported design space graph. These component IDs are ideally SBOL compliant URIs consisting of a namespace followed by a displayId and a version (for example, "http://examples.org/pTet/1").

To replicate, checkout the version_control branch

1. Join two design spaces (each with a small amount of version history)
2. Checkout a different branch from the new design space

Error is thrown when calling the/branch/commitTo endpoint. This can be reproduced on the current version_control branch

2019-03-01 15:28:20.025  WARN 26182 --- [nio-8080-exec-7] o.n.o.drivers.http.request.HttpRequest   : Thread: 54, response: Unrecognized transaction id. Transaction may have timed out and been rolled back.
2019-03-01 15:28:20.027  WARN 26182 --- [nio-8080-exec-7] o.n.ogm.drivers.http.driver.HttpDriver   : http://localhost:7474/db/data/transaction/87
2019-03-01 15:28:20.046 ERROR 26182 --- [nio-8080-exec-7] o.a.c.c.C.[.[.[/].[dispatcherServlet]    : Servlet.service() for servlet [dispatcherServlet] in context with path [] threw exception [Request processing failed; nested exception is org.springframework.dao.DataAccessResourceFailureException: Error executing Cypher "Neo.TransientError.Network.CommunicationError"; Code: Neo.TransientError.Network.CommunicationError; Description: Can not start an object, expecting field name; nested exception is org.neo4j.ogm.exception.CypherException: Error executing Cypher "Neo.TransientError.Network.CommunicationError"; Code: Neo.TransientError.Network.CommunicationError; Description: Can not start an object, expecting field name] with root cause

org.neo4j.ogm.exception.CypherException: Error executing Cypher "Neo.TransientError.Network.CommunicationError"; Code: Neo.TransientError.Network.CommunicationError; Description: Can not start an object, expecting field name

Flip the orientation of all edges on the graph that the operator is being applied to

Once a new endpoint for exporting combinatorial SBOL has been added to Knox's RESTful API (see #3), its web GUI should also be extended with an Export tab that includes appropriate input controls linked to the new endpoint.

The method getEdges() from the Node class returns a set of edges, so it removes duplicate edges that are important. For example, the "option" case (dotted line) uses two edges with the same source and destination to represent it, but only one is returned in the edge set.

Adding a contributing file to the repository.

Importing the attached file (hierarchical_ordering.xml) on the combinatorial_sbol branch produces the design space pictured in hierarchical_ordering.png, when it should produce the design space pictured in hierarchical_ordering_fixed.png.
hierarchical_ordering.zip

Enhance Knox's visualization of edges with the same source and sink nodes. Any ordered pair of nodes can have up to three edges from the first node to the second: an edge with an orientation of "inline", an edge with an orientation of "reverseComplement", and a blank edge (which would have orientation "none"). The link below shows some examples of how one might condense the visualization of design space graphs as they are stored by Knox. These include:

1. Replacing a labeled edge and blank edge that have the same sink and source with a dashed edge.
2. Replacing labeled edges with different orientations but the same sink and source with an edge that is labeled with two symbols having different orientations (instead of just one symbol as usual).

This would entail modifying the d3GraphDesignSpace endpoint ("designSpace/graph/d3") of Knox's RESTful API so that it returns the appropriate D3 representation. In addition, there may need to be modifications to how Knox's web GUI uses the D3 representation returned by a call to d3GraphDesignSpace.

https://docs.google.com/presentation/d/1BBF3KeHLVOipeEAWHTSoSlFU6eVy-r4n_Y6oT1DF7Nc/edit?usp=sharing

The file blunt_end_restriction_enzyme_clevage_site.svg is misspelt and therefore shows a user_defined.svg symbol instead.
File is at knox/src/main/resources/static/img/sbol/blunt_end_restriction_enzyme_clevage_site.svg

Instead of specifying commitPath, change the API so that both endpoints automatically roll back one commit before current

I tried to replicate this on the UI by applying the operators manually and Knox became unresponsive, but I didn't get any error logs.

The missing accept node bug can be replicated with this SBOL on the combinatorial_sbol branch

oneormore_zeroormore.txt

Importing either of the attached files (inline_or_rcomplement_explicit.xml or inline_or_rcomplement_implicit.xml) should produce the design space pictured in inline_or_rcomplement.png.
inline_or_rcomplement.zip

Windows 10
Steps to reproduce

1. Download & Install Neo4j Browser
2. Follow the same steps in README - Quickstart (except running KnoxApplication.java from IntelliJ)
3. Run step 10 in Quickstart and it fails on joining test 1 with test 2, outputting the following errors in the console

`2019-07-05 13:59:50.619 ERROR 21664 --- [nio-8080-exec-6] o.a.c.c.C.[.[.[/].[dispatcherServlet] : Servlet.service() for servlet [dispatcherServlet] in context with path [] threw exception [Request processing failed; nested exception is org.springframework.dao.InvalidDataAccessApiUsageException: Error mapping GraphModel to instance of knox.spring.data.neo4j.domain.DesignSpace; nested exception is org.neo4j.ogm.exception.MappingException: Error mapping GraphModel to instance of knox.spring.data.neo4j.domain.DesignSpace] with root cause

java.lang.IllegalArgumentException: No enum constant knox.spring.data.neo4j.domain.Edge.Orientation.inline`

On the webpage:

Add a Boolean argument "isCommit" to the JoinDesignSpace, orDesignSpaces, repeatDesignSpaces, andDesignSpaces, and mergeDesignSpaces methods in DesignSpaceService with a default value of true.

If "isCommit" is true, then a merge commit should be created by calling the mergeVersionHistories method as normal. If "isCommit" is false and the arguments of the operator are such that the output design space is also one of the input design spaces, then no merge commit should be created (do not call mergeVersionHistories).

Expected: two edges between two nodes
Actual: one edge

This can be reproduced on the current combinatorial_sbol branch

constellation_optional_one.txt