cytoscape / cxio

CX serialization and de-serialization

WARNING: This library is deprecated. The CX library has been moved into ndex-object-model

cxio

Old Java Library for reading/writing CX JSON streams

Docuemnts

• CX Specification
• CX Wiki

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© UC, San Diego Trey Ideker Lab

cxio's Issues

Edge Table is empty/bogus for some networks

When cx is loaded that does not have edgeAttributes, the edge table seems to be completely incorrect. Example case can be seen with network on NDex with uuid:633d141d-0e39-11e5-ac0f-000c29cb28fb where there are no edgeAttributes. Only the shared interaction column is filled in, but the name and interaction and shared name columns are all empty.

Serialize/deserialize function for NodeAttributesElement value is not symmetrical

The "value" field in a NodeAttributesElement object can be a single value or a list of numbers or strings. In order to store the value and make our code independent from the implementation of NodeAttributesElement. We use CxioUtil.getAttributeValuesAsString() to serialize and NodeAttributesElement.createInstanceWithMultipleValues() function to de-serialize the value. We found out that CxioUtil.getAttributeValuesAsString() converts a list of long, for example [5,8] into string '["5","8"]', but when we pass this stringified value to NodeAttributesElement.createInstanceWithMultipleValues(), it will construct a list of string rather than a list of long. The roundtrip of this kind of CX attributes will fail.

Could take a look of this issue?