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Some more documents have been added to table API.
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@keiono
keiono committed Aug 13, 2014
1 parent 58ac96b commit 1fb7600
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Showing 2 changed files with 130 additions and 51 deletions.
3 changes: 2 additions & 1 deletion src/main/java/org/cytoscape/rest/internal/datamapper/TableMapper.java
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Expand Up @@ -10,6 +10,7 @@
import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
import org.cytoscape.rest.internal.service.JsonTags;

import com.fasterxml.jackson.databind.JsonNode;

Expand Down Expand Up @@ -41,7 +42,7 @@ public void createNewColumn(final JsonNode rootNode, final CyTable table) {

// Optional: mutability
boolean isImmutable = false;
final JsonNode immutable = rootNode.get("immutable");
final JsonNode immutable = rootNode.get(JsonTags.COLUMN_IMMUTABLE);
if(immutable != null) {
isImmutable = immutable.asBoolean();
}
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178 changes: 128 additions & 50 deletions src/main/java/org/cytoscape/rest/internal/service/TableDataService.java
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Expand Up @@ -10,6 +10,7 @@
import javax.ws.rs.Consumes;
import javax.ws.rs.DELETE;
import javax.ws.rs.GET;
import javax.ws.rs.NotFoundException;
import javax.ws.rs.POST;
import javax.ws.rs.PUT;
import javax.ws.rs.Path;
Expand All @@ -27,15 +28,25 @@
import org.cytoscape.rest.internal.datamapper.TableMapper;
import org.cytoscape.rest.internal.serializer.CyTableSerializer;
import org.cytoscape.rest.internal.serializer.TableModule;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;

/**
* REST API for CyTable objects. This is for assigned table only.
*
* @author kono
*
*/
@Singleton
@Path("/v1/networks/{networkId}/tables")
public class TableDataService extends AbstractDataService {

private final static Logger logger = LoggerFactory.getLogger(TableDataService.class);

private static enum TableType {
DEFAULT_NODE("defaultnode"), DEFAULT_EDGE("defaultedge"), DEFAULT_NETWORK("defaultnetwork");

Expand All @@ -50,145 +61,186 @@ private String getType() {
}
}


private final TableMapper tableMapper;
private final ObjectMapper tableObjectMapper;


public TableDataService() {
super();
this.tableMapper = new TableMapper();
this.tableObjectMapper = new ObjectMapper();
this.tableObjectMapper.registerModule(new TableModule());
}


/**
* Create new column to the target table.
*
* @param id
* @title Create new column in the target table.
*
* This method creates a new, empty column in the specified table.
*
* @param networkId
* Network ID
* @param tableType
* @param is
* Table type (defaultnode, defaultedge or defaultnetwork)
*
*/
@POST
@Path("/{tableType}/columns")
@Consumes(MediaType.APPLICATION_JSON)
public void createColumn(@PathParam("networkId") Long id, @PathParam("tableType") String tableType, final InputStream is) {
final CyNetwork network = getCyNetwork(id);
public void createColumn(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
final InputStream is) {
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
final ObjectMapper objMapper = new ObjectMapper();
try {
final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);
tableMapper.createNewColumn(rootNode, table);
} catch (IOException e) {
e.printStackTrace();
logger.error("Failed to create column.", e);
throw new WebApplicationException("Could not create column.", e, 500);
}
}



/**
* Delete a column from a table.
* Delete a column from a table
*
* @param id
* @param networkId
* Network SUID
* @param tableType
* Table type (defaultnode, defaultedge or defaultnetwork)
* @param columnName
* Name of the column to be deleted
*
*/
@DELETE
@Path("/{tableType}/columns/{columnName}")
public void deleteColumn(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public void deleteColumn(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@PathParam("columnName") String columnName) {
final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
if (table != null) {
table.deleteColumn(columnName);
} else {
logger.error("Failed to delete a column. (Missing table?)");
throw new NotFoundException("Could not find the table. (This should not happen!)");
}
}

/**
* This if for update existing column name to a new one.
* @title Update a column name
*
* @param id
* @param networkId
* Network SUID
* @param tableType
* Table type (defaultnode, defaultedge or defaultnetwork)
* @param columnName
* @param is
* Original name of the column to be updated.
*
*/
@PUT
@Path("/{tableType}/columns")
@Consumes(MediaType.APPLICATION_JSON)
public void updateColumnName(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public void updateColumnName(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@PathParam("columnName") String columnName, final InputStream is) {
final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
final ObjectMapper objMapper = new ObjectMapper();
try {
final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);
tableMapper.updateColumnName(rootNode, table);
} catch (IOException e) {
throw new WebApplicationException(e, 500);
logger.error("Could not parse the input JSON (new column name)", e);
throw new WebApplicationException("Could not parse the input JSON.", e, 412);
}
}


/**
* @title Update a values in a column
*
* @param networkId
* Network SUID
* @param tableType
* Table type (defaultnode, defaultedge or defaultnetwork)
* @param columnName
* Target column name.
*
*/
@PUT
@Path("/{tableType}/columns/{columnName}")
@Consumes(MediaType.APPLICATION_JSON)
public void createColumnValues(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public void updateColumnValues(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@PathParam("columnName") String columnName, final InputStream is) {
final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);

final ObjectMapper objMapper = new ObjectMapper();
try {
final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);
tableMapper.updateColumnValues(rootNode, table, columnName);
} catch (IOException e) {
e.printStackTrace();
throw new WebApplicationException(e, 500);
logger.error("Could not read JSON for new column values.", e);
throw new WebApplicationException("Could not parse the input JSON.", e, 412);
}
}


/**
* @title Update table data
*
* @param networkId
* Network SUID
* @param tableType
* Table type (defaultnode, defaultedge or defaultnetwork)
*/
@PUT
@Path("/{tableType}")
@Consumes(MediaType.APPLICATION_JSON)
public void updateTable(@PathParam("networkId") Long id, @PathParam("tableType") String tableType, final InputStream is) {
final CyNetwork network = getCyNetwork(id);
public void updateTable(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
final InputStream is) {
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);

final ObjectMapper objMapper = new ObjectMapper();
try {
final JsonNode rootNode = objMapper.readValue(is, JsonNode.class);
tableMapper.updateTableValues(rootNode, table);
} catch (IOException e) {
e.printStackTrace();
throw new WebApplicationException(e, 500);
logger.error("Could not parse JSON for new table entries.", e);
throw new WebApplicationException("Could not parse new table data JSON.", e, 412);
}
}


/**
* @title Get a row in a table
*
* @param networkId
* Network SUID
* @param tableType
* Table type (defaultnode, defaultedge or defaultnetwork)
* @param primaryKey
* Name of primary key column
*
* @return Row in the table
*/
@GET
@Path("/{tableType}/rows/{primaryKey}")
@Produces(MediaType.APPLICATION_JSON)
public String getRow(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public String getRow(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@PathParam("primaryKey") Long primaryKey) {
final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
final CyRow row = table.getRow(primaryKey);
try {
return this.serializer.serializeRow(row);
} catch (IOException e) {
throw new WebApplicationException(e, 500);
logger.error("Copuld not serialize a table.");
throw new WebApplicationException("Could not serialize the table.", e, 500);
}
}

@GET
@Path("/{tableType}/rows/{primaryKey}/{columnName}")
@Produces(MediaType.APPLICATION_JSON)
public String getCell(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public String getCell(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@PathParam("primaryKey") Long primaryKey, @PathParam("columnName") String columnName) {
final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
final CyRow row = table.getRow(primaryKey);
try {
Expand All @@ -201,8 +253,8 @@ public String getCell(@PathParam("networkId") Long id, @PathParam("tableType") S
@GET
@Path("/{tableType}/rows")
@Produces(MediaType.APPLICATION_JSON)
public String getRows(@PathParam("networkId") Long id, @PathParam("tableType") String tableType) {
final CyNetwork network = getCyNetwork(id);
public String getRows(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType) {
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
try {
return this.serializer.serializeAllRows(table.getAllRows());
Expand All @@ -214,8 +266,8 @@ public String getRows(@PathParam("networkId") Long id, @PathParam("tableType") S
@GET
@Path("/{tableType}/columns")
@Produces(MediaType.APPLICATION_JSON)
public String getColumnNames(@PathParam("networkId") Long id, @PathParam("tableType") String tableType) {
final CyNetwork network = getCyNetwork(id);
public String getColumnNames(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType) {
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
try {
return this.serializer.serializeColumns(table.getColumns());
Expand All @@ -224,13 +276,12 @@ public String getColumnNames(@PathParam("networkId") Long id, @PathParam("tableT
}
}


@GET
@Path("/{tableType}/columns/{columnName}")
@Produces(MediaType.APPLICATION_JSON)
public String getColumnValues(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public String getColumnValues(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@PathParam("columnName") String columnName) {
final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
final CyColumn column = table.getColumn(columnName);
final List<Object> values = column.getValues(column.getType());
Expand All @@ -251,7 +302,7 @@ public String getColumnValues(@PathParam("networkId") Long id, @PathParam("table
@GET
@Path("/")
@Produces(MediaType.APPLICATION_JSON)
public String getTables(@PathParam("networkId") Long id) {
public String getTables(@PathParam("networkId") Long networkId) {
final Set<CyTable> tables = this.tableManager.getAllTables(true);

try {
Expand Down Expand Up @@ -294,14 +345,13 @@ private final List<? extends CyIdentifiable> getGraphObjectsByType(final CyNetwo
return objects;
}


@GET
@Path("/{tableType}")
@Produces(MediaType.APPLICATION_JSON)
public String getTable(@PathParam("networkId") Long id, @PathParam("tableType") String tableType,
public String getTable(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@QueryParam(JsonTags.TABLE_FORMAT) String format) {

final CyNetwork network = getCyNetwork(id);
final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);

if (format != null && format.equals("csv")) {
Expand All @@ -321,4 +371,32 @@ public String getTable(@PathParam("networkId") Long id, @PathParam("tableType")
}
}
}

/**
* @title Get a table as CSV
*
* @param networkId
* Network SUID
* @param tableType
* Table type (defaultnode, defaultedge or defaultnetwork)
*
* @return Entire table as CSV
*
*/
@GET
@Path("/{tableType}.csv")
@Produces(MediaType.APPLICATION_JSON)
public String getTableAsCsv(@PathParam("networkId") Long networkId, @PathParam("tableType") String tableType,
@QueryParam(JsonTags.TABLE_FORMAT) String format) {

final CyNetwork network = getCyNetwork(networkId);
final CyTable table = getTableByType(network, tableType);
final CyTableSerializer tableSerializer = new CyTableSerializer();
try {
final String result = tableSerializer.toCSV(table);
return result;
} catch (Exception e) {
throw new WebApplicationException("Could not serialize table to CSV.", e, 500);
}
}
}

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