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Bipartite network api update #347

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merged 5 commits into from
Jan 30, 2024
Merged

Bipartite network api update #347

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13c0972
draft kpartite network api
d-callan Jan 29, 2024
eb30f80
leave bipartite network but update it
d-callan Jan 29, 2024
c396a25
update correlations plugin java to new api
d-callan Jan 29, 2024
fddea44
update docs
d-callan Jan 29, 2024
024392b
remove all referenes to cols from bipartite network
d-callan Jan 30, 2024
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8 changes: 4 additions & 4 deletions docs/api.html
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53 changes: 49 additions & 4 deletions schema/library.raml
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Original file line number Diff line number Diff line change
Expand Up @@ -646,10 +646,18 @@ types:
type: object
properties:
pcoaVariance: number[]
FeaturePrefilterThresholds:
type: object
additionalProperties: false
properties:
proportionNonZero?: number
variance?: number
standardDeviation?: number
CorrelationComputeConfig:
type: object
properties:
correlationMethod: CorrelationMethod
prefilterThresholds?: FeaturePrefilterThresholds
CorrelationMethod:
type: string
enum:
Expand Down Expand Up @@ -778,6 +786,15 @@ types:
additionalProperties: false
properties:
isCutoff: boolean
InternalJob:
type: object
properties:
jobId: JobID
status: JobStatus
owned: boolean
created: datetime
grabbed: datetime
finished: datetime
PluginOverview:
displayName: Plugin Overview
type: object
Expand Down Expand Up @@ -939,16 +956,44 @@ types:
variables:
type: VariableMapping[]
required: false
KPartiteNetworkConfig:
type: NetworkConfig
properties:
partitionsMetadata: string[]
NodeIdList:
type: object
additionalProperties: false
properties:
nodeIds: string[]
KPartiteNetworkData:
type: NetworkData
properties:
partitions: NodeIdList[]
KPartiteNetwork:
type: object
additionalProperties: false
properties:
data: KPartiteNetworkData
config: KPartiteNetworkConfig
KPartiteNetworkPostResponse:
type: object
additionalProperties: false
properties:
kpartitenetwork: KPartiteNetwork
BipartiteNetworkConfig:
type: NetworkConfig
properties:
column1Metadata: string
column2Metadata: string
partitionsMetadata:
type: string[]
minItems: 2
maxItems: 2
BipartiteNetworkData:
type: NetworkData
properties:
column1NodeIDs: string[]
column2NodeIDs: string[]
partitions:
type: NodeIdList[]
maxItems: 2
minItems: 2
BipartiteNetwork:
type: object
additionalProperties: false
Expand Down
40 changes: 35 additions & 5 deletions schema/url/networks.raml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,18 +28,48 @@ types:
type: VariableMapping[]
required: false

KPartiteNetworkConfig:
type: NetworkConfig
properties:
partitionsMetadata: string[]

NodeIdList:
additionalProperties: false
properties:
nodeIds: string[]

KPartiteNetworkData:
type: NetworkData
properties:
partitions: NodeIdList[]

KPartiteNetwork:
additionalProperties: false
properties:
data: KPartiteNetworkData
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Remind me what do we have planned for the partitions metadata?

config: KPartiteNetworkConfig

KPartiteNetworkPostResponse:
additionalProperties: false
properties:
kpartitenetwork: KPartiteNetwork

# a specific case of a KPartiteNetwork w two partitions
BipartiteNetworkConfig:
type: NetworkConfig
properties:
column1Metadata: string
column2Metadata: string
partitionsMetadata:
type: string[]
minItems: 2
maxItems: 2

BipartiteNetworkData:
type: NetworkData
properties:
column1NodeIDs: string[]
column2NodeIDs: string[]

partitions:
type: NodeIdList[]
maxItems: 2
minItems: 2

BipartiteNetwork:
additionalProperties: false
Expand Down
16 changes: 12 additions & 4 deletions .../org/veupathdb/service/eda/ds/plugin/correlation/AbstractCorrelationBipartiteNetwork.java
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Expand Up @@ -120,12 +120,20 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
BipartiteNetworkData bipartiteNetworkData = new BipartiteNetworkDataImpl();
bipartiteNetworkData.setLinks(links);
bipartiteNetworkData.setNodes(nodes);
bipartiteNetworkData.setColumn1NodeIDs(uniqueColumn1IDs);
bipartiteNetworkData.setColumn2NodeIDs(uniqueColumn2IDs);
NodeIdList col1NodeIdList = new NodeIdListImpl();
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I think it's worth removing references to columns everywhere. There's no reason we need to even show the bp net in two columns (could be two rows, two blobs of nodes, or even nodes placed based on some layout algorithm but with two different colors), i just didn't have good words for it back in the day (4 months ago).
All that to say, i'd recommend "col1NodIdList" -> "partition1NodeIdList"

col1NodeIdList.setNodeIds(uniqueColumn1IDs);
NodeIdList col2NodeIdList = new NodeIdListImpl();
col2NodeIdList.setNodeIds(uniqueColumn2IDs);
List<NodeIdList> partitions = new ArrayList<NodeIdList>();
partitions.add(col1NodeIdList);
partitions.add(col2NodeIdList);
bipartiteNetworkData.setPartitions(partitions);

BipartiteNetworkConfig bipartiteNetworkConfig = new BipartiteNetworkConfigImpl();
bipartiteNetworkConfig.setColumn1Metadata(stats.getData1Metadata());
bipartiteNetworkConfig.setColumn2Metadata(stats.getData2Metadata());
List<String> partitionsMetadata = new ArrayList<String>();
partitionsMetadata.add(stats.getData1Metadata());
partitionsMetadata.add(stats.getData2Metadata());
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ahhh i remmber. that's what the metadata is

bipartiteNetworkConfig.setPartitionsMetadata(partitionsMetadata);

BipartiteNetwork bipartiteNetwork = new BipartiteNetworkImpl();
bipartiteNetwork.setData(bipartiteNetworkData);
Expand Down
8 changes: 4 additions & 4 deletions src/main/resources/api.html
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