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Implement reverse operator #20

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Implement reverse operator #20

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8c942fc
Fix demo bug that no operators work
Zackhardtoname Jul 26, 2019
bc4f342
Enable automated build through the devtools dependency
Zackhardtoname Jul 26, 2019
0e3ca78
Implement reverse operator
Zackhardtoname Jul 29, 2019
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12 changes: 7 additions & 5 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -82,6 +82,13 @@
<version>2.4.0</version>
</dependency>

<!-- hot swapping, enable live reload -->
<!-- It would be automatically disabled in production environments -->
<dependency>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-devtools</artifactId>
<optional>true</optional>
</dependency>
</dependencies>

<build>
Expand All @@ -91,11 +98,8 @@
<artifactId>spring-boot-maven-plugin</artifactId>
</plugin>
</plugins>


</build>


<repositories>
<repository>
<id>spring-snapshots</id>
Expand All @@ -118,6 +122,4 @@
</pluginRepository>
</pluginRepositories>



</project>
40 changes: 20 additions & 20 deletions src/main/examples/transcriptional_unit.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -16,12 +16,12 @@ CREATE (d1)-[:CONTAINS]->(n8)
CREATE (d1)-[:CONTAINS]->(n10)
CREATE (d1)-[:CONTAINS]->(n13)

CREATE (n1)-[:PRECEDES {componentIDs: ["p1"], componentRoles: ["promoter"], orientation: "inline"}]->(n2)
CREATE (n2)-[:PRECEDES {componentIDs: ["p2"], componentRoles: ["promoter"], orientation: "inline"}]->(n4)
CREATE (n4)-[:PRECEDES {componentIDs: ["rz1"], componentRoles: ["ribozyme"], orientation: "inline"}]->(n6)
CREATE (n6)-[:PRECEDES {componentIDs: ["rb1"], componentRoles: ["ribosome_entry_site"], orientation: "inline"}]->(n8)
CREATE (n8)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "inline"}]->(n10)
CREATE (n10)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "inline"}]->(n13)
CREATE (n1)-[:PRECEDES {componentIDs: ["p1"], componentRoles: ["promoter"], orientation: "INLINE"}]->(n2)
CREATE (n2)-[:PRECEDES {componentIDs: ["p2"], componentRoles: ["promoter"], orientation: "INLINE"}]->(n4)
CREATE (n4)-[:PRECEDES {componentIDs: ["rz1"], componentRoles: ["ribozyme"], orientation: "INLINE"}]->(n6)
CREATE (n6)-[:PRECEDES {componentIDs: ["rb1"], componentRoles: ["ribosome_entry_site"], orientation: "INLINE"}]->(n8)
CREATE (n8)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "INLINE"}]->(n10)
CREATE (n10)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "INLINE"}]->(n13)

CREATE (d1)-[:ARCHIVES]->(b0:Branch {branchID: "test1"})-[:CONTAINS]->(c0:Commit {commitID: "c0"})-[:CONTAINS]->(s1:Snapshot {nodeIndex: 7})
CREATE (d1)-[:SELECTS]->(b0)-[:LATEST]->(c0)
Expand All @@ -42,12 +42,12 @@ CREATE (s1)-[:CONTAINS]->(n31)
CREATE (s1)-[:CONTAINS]->(n33)
CREATE (s1)-[:CONTAINS]->(n36)

CREATE (n23)-[:PRECEDES {componentIDs: ["p1"], componentRoles: ["promoter"], orientation: "inline"}]->(n25)
CREATE (n25)-[:PRECEDES {componentIDs: ["p2"], componentRoles: ["promoter"], orientation: "inline"}]->(n27)
CREATE (n27)-[:PRECEDES {componentIDs: ["rz1"], componentRoles: ["ribozyme"], orientation: "inline"}]->(n29)
CREATE (n29)-[:PRECEDES {componentIDs: ["rb1"], componentRoles: ["ribosome_entry_site"], orientation: "inline"}]->(n31)
CREATE (n31)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "inline"}]->(n33)
CREATE (n33)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "inline"}]->(n36)
CREATE (n23)-[:PRECEDES {componentIDs: ["p1"], componentRoles: ["promoter"], orientation: "INLINE"}]->(n25)
CREATE (n25)-[:PRECEDES {componentIDs: ["p2"], componentRoles: ["promoter"], orientation: "INLINE"}]->(n27)
CREATE (n27)-[:PRECEDES {componentIDs: ["rz1"], componentRoles: ["ribozyme"], orientation: "INLINE"}]->(n29)
CREATE (n29)-[:PRECEDES {componentIDs: ["rb1"], componentRoles: ["ribosome_entry_site"], orientation: "INLINE"}]->(n31)
CREATE (n31)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "INLINE"}]->(n33)
CREATE (n33)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "INLINE"}]->(n36)

CREATE (d2:DesignSpace {spaceID: "test2", nodeIndex: 5, commitIndex: 1})

Expand All @@ -63,10 +63,10 @@ CREATE (d2)-[:CONTAINS]->(n17)
CREATE (d2)-[:CONTAINS]->(n19)
CREATE (d2)-[:CONTAINS]->(n22)

CREATE (n13b)-[:PRECEDES {componentIDs: ["p1","p2"], componentRoles: ["promoter"], orientation: "inline"}]->(n15)
CREATE (n15)-[:PRECEDES {componentIDs: ["rb1","rb2"], componentRoles: ["ribosome_entry_site"], orientation: "inline"}]->(n17)
CREATE (n17)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "inline"}]->(n19)
CREATE (n19)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "inline"}]->(n22)
CREATE (n13b)-[:PRECEDES {componentIDs: ["p1","p2"], componentRoles: ["promoter"], orientation: "INLINE"}]->(n15)
CREATE (n15)-[:PRECEDES {componentIDs: ["rb1","rb2"], componentRoles: ["ribosome_entry_site"], orientation: "INLINE"}]->(n17)
CREATE (n17)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "INLINE"}]->(n19)
CREATE (n19)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "INLINE"}]->(n22)

CREATE (d2)-[:ARCHIVES]->(b1:Branch {branchID: "test2"})-[:CONTAINS]->(c1:Commit {commitID: "c0"})-[:CONTAINS]->(s2:Snapshot {nodeIndex: 5})
CREATE (d2)-[:SELECTS]->(b1)-[:LATEST]->(c1)
Expand All @@ -83,9 +83,9 @@ CREATE (s2)-[:CONTAINS]->(n41)
CREATE (s2)-[:CONTAINS]->(n43)
CREATE (s2)-[:CONTAINS]->(n46)

CREATE (n37)-[:PRECEDES {componentIDs: ["p1","p2"], componentRoles: ["promoter"], orientation: "inline"}]->(n39)
CREATE (n39)-[:PRECEDES {componentIDs: ["rb1","rb2"], componentRoles: ["ribosome_entry_site"], orientation: "inline"}]->(n41)
CREATE (n41)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "inline"}]->(n43)
CREATE (n43)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "inline"}]->(n46)
CREATE (n37)-[:PRECEDES {componentIDs: ["p1","p2"], componentRoles: ["promoter"], orientation: "INLINE"}]->(n39)
CREATE (n39)-[:PRECEDES {componentIDs: ["rb1","rb2"], componentRoles: ["ribosome_entry_site"], orientation: "INLINE"}]->(n41)
CREATE (n41)-[:PRECEDES {componentIDs: ["c1"], componentRoles: ["CDS"], orientation: "INLINE"}]->(n43)
CREATE (n43)-[:PRECEDES {componentIDs: ["t1"], componentRoles: ["terminator"], orientation: "INLINE"}]->(n46)

;
34 changes: 32 additions & 2 deletions src/main/java/knox/spring/data/neo4j/controller/KnoxController.java
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Expand Up @@ -4,10 +4,8 @@
import java.io.InputStream;
import java.util.*;

import knox.spring.data.neo4j.domain.DesignSpace;
import knox.spring.data.neo4j.exception.*;
import knox.spring.data.neo4j.sample.DesignSampler.EnumerateType;
import knox.spring.data.neo4j.sbol.SBOLConversion;
import knox.spring.data.neo4j.services.DesignSpaceService;

import org.sbolstandard.core2.SBOLConversionException;
Expand Down Expand Up @@ -522,6 +520,38 @@ public ResponseEntity<String> mergeDesignSpaces(@RequestParam(value = "inputSpac
}
}

/**
* @api {post} /designSpace/reverse Reverse
* @apiName reverseDesignSpace
* @apiGroup DesignSpace
*
* @apiParam {String} inputSpaceID ID for the input design space to be reversed.
* @apiParam {String} outputSpaceID ID for the output design space resulting from reverse. If omitted, then the result is
* stored in the input design space.
*
* @apiDescription Reverse the edges from the input design space.
*/
@RequestMapping(value = "/designSpace/reverse", method = RequestMethod.POST)
public ResponseEntity<String> reverseDesignSpace(@RequestParam(value = "inputSpaceID", required = true) String inputSpaceID,
@RequestParam(value = "outputSpaceID", required = false) String outputSpaceID) {
try {
long startTime = System.nanoTime();

if (outputSpaceID == null) {
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@dany-fu dany-fu Jul 31, 2019 •
edited
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We should follow the conventions set by the other functions and throw error if outputSpaceID is null.

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If the output space is null, in the file DesignSpaceService.java, the functions usually choose the first element in the inputBranches as the output space. I think my charges here are consistent?

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@dany-fu dany-fu Aug 2, 2019 •
edited
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I see that in the DesignSpaceService.java, but when you test on the UI, it will throw an error if the outputBranch is empty. But the change you made, where you put get .get(0) in knox.js, is inconsistent with the rest of the repo.

designSpaceService.reverseDesignSpace(inputSpaceID);
} else {
designSpaceService.reverseDesignSpace(inputSpaceID, outputSpaceID);
}

return new ResponseEntity<String>("{\"message\": \"Design space was successfully reversed after " +
(System.nanoTime() - startTime) + " ns.\"}", HttpStatus.NO_CONTENT);
} catch (ParameterEmptyException | DesignSpaceNotFoundException |
DesignSpaceConflictException | DesignSpaceBranchesConflictException ex) {
return new ResponseEntity<String>("{\"message\": \"" + ex.getMessage() + "\"}",
HttpStatus.BAD_REQUEST);
}
}

/**
* @api {post} /designSpace/or OR
* @apiName orDesignSpaces
Expand Down
1 change: 0 additions & 1 deletion src/main/java/knox/spring/data/neo4j/domain/Edge.java
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Expand Up @@ -555,7 +555,6 @@ public boolean hasOrientation() {
return isInline() || isReverseComplement();
}


public boolean hasOrientation(Orientation orientation) {
return hasOrientation() && this.orientation.equals(orientation);
}
Expand Down
22 changes: 22 additions & 0 deletions src/main/java/knox/spring/data/neo4j/operations/ReverseOperator.java
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@@ -0,0 +1,22 @@
package knox.spring.data.neo4j.operations;

import knox.spring.data.neo4j.domain.Edge;
import knox.spring.data.neo4j.domain.NodeSpace;

import java.util.ArrayList;
import java.util.List;
import java.util.Set;

public class ReverseOperator {
public static void apply(NodeSpace inputSpace, NodeSpace outputSpace) {
//copy input space to a new output space
outputSpace.copyNodeSpace(inputSpace);

Set<Edge> allEdges = outputSpace.getEdges();

//traverse all edges of input space and flip the orientation attribute
for(Edge edge: allEdges){
edge.reverseOrientation();
}
}
}
34 changes: 28 additions & 6 deletions src/main/java/knox/spring/data/neo4j/services/DesignSpaceService.java
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Expand Up @@ -9,14 +9,11 @@
import knox.spring.data.neo4j.domain.Snapshot;
import knox.spring.data.neo4j.exception.*;
import knox.spring.data.neo4j.operations.ANDOperator;
import knox.spring.data.neo4j.operations.Concatenation;
import knox.spring.data.neo4j.operations.JoinOperator;
import knox.spring.data.neo4j.operations.MergeOperator;
import knox.spring.data.neo4j.operations.OROperator;
import knox.spring.data.neo4j.operations.Product;
import knox.spring.data.neo4j.operations.ReverseOperator;
import knox.spring.data.neo4j.operations.RepeatOperator;
import knox.spring.data.neo4j.operations.Star;
import knox.spring.data.neo4j.operations.Union;
import knox.spring.data.neo4j.repositories.BranchRepository;
import knox.spring.data.neo4j.repositories.CommitRepository;
import knox.spring.data.neo4j.repositories.DesignSpaceRepository;
Expand Down Expand Up @@ -325,7 +322,31 @@ public void mergeBranches(String targetSpaceID, List<String> inputBranchIDs,

saveDesignSpace(targetSpace);
}


public void reverseDesignSpace(String inputSpaceID) {
reverseDesignSpace(inputSpaceID, inputSpaceID);
}

public void reverseDesignSpace(String inputSpaceID, String outputSpaceID) {
List<String> inputSpaceIDs = new ArrayList<>();
inputSpaceIDs.add(inputSpaceID);
List<NodeSpace> inputSpaces = new ArrayList<NodeSpace>(inputSpaceIDs.size());

DesignSpace outputSpace = loadIOSpaces(inputSpaceIDs, outputSpaceID, inputSpaces);

ReverseOperator.apply(inputSpaces.get(0), outputSpace);


List<NodeSpace> inputSnaps = new ArrayList<NodeSpace>(inputSpaces.size());

NodeSpace outputSnap = mergeVersionHistories(castNodeSpacesToDesignSpaces(inputSpaces),
outputSpace, inputSnaps);

ReverseOperator.apply(inputSnaps.get(0), outputSnap);

saveDesignSpace(outputSpace);
}

private DesignSpace loadIOSpaces(List<String> inputSpaceIDs, String outputSpaceID,
List<NodeSpace> inputSpaces) {
for (String inputSpaceID : inputSpaceIDs) {
Expand Down Expand Up @@ -863,7 +884,8 @@ private DesignSpace findDesignSpace(String targetSpaceID) {
}

private DesignSpace loadDesignSpace(String targetSpaceID) {
DesignSpace targetSpace = designSpaceRepository.findOne(getDesignSpaceGraphID(targetSpaceID), 3);
Long keyID = getDesignSpaceGraphID(targetSpaceID);
DesignSpace targetSpace = designSpaceRepository.findOne(keyID, 3);

for (Commit commit : targetSpace.getCommits()) {
commit.setSnapshot(reloadSnapshot(commit.getSnapshot()));
Expand Down
18 changes: 17 additions & 1 deletion src/main/resources/static/js/endpoints.js
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Expand Up @@ -30,7 +30,8 @@ export const operators = {
OR: 'or',
AND: 'and',
MERGE: 'merge',
REPEAT: 'repeat'
REPEAT: 'repeat',
REVERSE: 'reverse'
};


Expand Down Expand Up @@ -288,4 +289,19 @@ export function designSpaceMerge(inputSpaces, outputSpace, tolerance){
} else {
swalError(request.response);
}
}

export function designSpaceReverse(inputSpace, outputSpace){
let query = "?";
query += encodeQueryParameter("inputSpaceID", inputSpace, query);
query += encodeQueryParameter("outputSpaceID", outputSpace, query);

let request = new XMLHttpRequest();
request.open("POST", endpoints.DESIGN + "/" + operators.REVERSE + query, false);
request.send(null);
if (request.status >= 200 && request.status < 300) {
swalSuccess();
} else {
swalError(request.response);
}
}
14 changes: 14 additions & 0 deletions src/main/resources/static/js/knox.js
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Expand Up @@ -517,6 +517,15 @@ $('#apply-operators-tooltip').click(() => {
}
div.appendChild(tolDiv);
}
if(this.value === endpoint.operators.REVERSE){
if(div.contains(inputDiv)){
div.removeChild(inputDiv);
}
const guidance = document.createElement("P");
const text = document.createTextNode("The current designSpace will be reversed.");
guidance.appendChild(text);
div.appendChild(guidance);
}
});

swal({
Expand Down Expand Up @@ -557,6 +566,11 @@ $('#apply-operators-tooltip').click(() => {
case endpoint.operators.MERGE:
endpoint.designSpaceMerge(inputSpaces, outputSpace, tolerance);
break;

case endpoint.operators.REVERSE:
// the reverse operator would only reverse one inputSpace
endpoint.designSpaceReverse(inputSpaces[0], outputSpace);
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Zack, you missed my other comment that this is inconsistent with the other functions. This code should be in the Java file, not here. Please squash these commits when you've fixed them.

break;
}
}
});
Expand Down