csip-erosion Displaying differences for changeset

Displaying differences for changeset

display as Allow wrapping

nbproject/build-impl.xml~

@@ -1007,8 +1007,8 @@

+ <copyfiles files="${file.reference.Lmod2Rusle2.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>

- <copyfiles files="${file.reference.Lmod2Rusle2.jar}" iftldtodir="${build.web.dir}/WEB-INF" todir="${dist.ear.dir}/lib"/>

@@ -1115,8 +1115,8 @@

</target>

+ <copyfiles files="${file.reference.Lmod2Rusle2.jar}" todir="${build.web.dir}/WEB-INF/lib"/>

- <copyfiles files="${file.reference.Lmod2Rusle2.jar}" todir="${build.web.dir}/WEB-INF/lib"/>

nbproject/project.xml

@@ -16,11 +16,11 @@

<path-in-war>WEB-INF/lib</path-in-war>

</library>

- <file>${file.reference.Lmod2Rusle2.jar}</file>

+ <file>${reference.csip-core.jar}</file>

<path-in-war>WEB-INF/lib</path-in-war>

</library>

- <file>${reference.csip-core.jar}</file>

+ <file>${file.reference.Lmod2Rusle2.jar}</file>

<path-in-war>WEB-INF/lib</path-in-war>

</library>

src/java/c/MsSQLGIS.java

@@ -2,7 +2,7 @@

import csip.ModelDataService;

import csip.ServiceException;

-import csip.annotations.Resource;

+import csip.annotations.*;

import static csip.annotations.ResourceType.JDBC;

import java.sql.Connection;

import java.sql.ResultSet;

@@ -16,9 +16,6 @@

import java.util.logging.Level;

import java.util.logging.Logger;

import javax.ws.rs.Path;

-import oms3.annotations.Description;

-import oms3.annotations.Name;

-import oms3.annotations.VersionInfo;

src/java/d/rusle2/Climate1_1.java

@@ -9,11 +9,9 @@

import csip.Config;

import java.util.Date;

import javax.ws.rs.Path;

-import oms3.annotations.Description;

-import oms3.annotations.Name;

-import oms3.annotations.VersionInfo;

import csip.ModelDataService;

import csip.ServiceException;

+import csip.annotations.*;

import csip.annotations.Resource;

import static csip.annotations.ResourceType.JDBC;

import static d.rusle2.Climate1_1.DB;

src/java/d/soils/V1_21.java

@@ -12,11 +12,11 @@

import csip.ServiceException;

import java.io.IOException;

import javax.ws.rs.*;

-import oms3.annotations.*;

import org.apache.commons.io.IOUtils;

import org.codehaus.jettison.json.JSONArray;

import org.codehaus.jettison.json.JSONObject;

import csip.ModelDataService;

+import csip.annotations.*;

import csip.annotations.Resource;

import static csip.annotations.ResourceType.JDBC;

import csip.utils.JSONUtils;

src/java/m/ApplicationConfig.java

@@ -38,25 +38,9 @@

resources.add(csip.QueryService.class);

resources.add(csip.ReportService.class);

resources.add(csip.UIService.class);

- resources.add(d.rusle2.CMZ1_0.class);

- resources.add(d.rusle2.CMZ1_1.class);

- resources.add(d.rusle2.Climate1_0.class);

resources.add(d.rusle2.Climate1_1.class);

- resources.add(d.rusle2.IsCoord.class);

- resources.add(d.rusle2.LanduseManagement.class);

- resources.add(d.rusle2.LanduseManagementFilter.class);

- resources.add(d.rusle2.SoilMappingCheck.class);

- resources.add(d.rusle2.StateCounty1_0.class);

- resources.add(d.rusle2.StateCounty2_0.class);

- resources.add(d.soils.V1_1.class);

resources.add(d.soils.V1_21.class);

resources.add(m.rusle2.V1_31.class);

- resources.add(m.rusle2.V2_0.class);

- resources.add(m.rusle2.V2_1.class);

- resources.add(m.rusle2.rusle2check.class);

- resources.add(m.sci.V1_3.class);

- resources.add(m.stir.V1_2.class);

resources.add(m.weps.V1_3.class);

- resources.add(m.weps.V1_4.class);

}

src/java/m/rusle2/V1_31.java

@@ -27,7 +27,6 @@

import java.io.FileOutputStream;

import java.util.*;

import javax.ws.rs.*;

-import oms3.annotations.*;

import org.apache.commons.io.FileUtils;

import org.apache.commons.lang.StringEscapeUtils;

import org.codehaus.jettison.json.JSONArray;

@@ -40,8 +39,8 @@

import static csip.ModelDataService.REPORT_DIM;

import static csip.ModelDataService.REPORT_NAME;

import static csip.ModelDataService.REPORT_TYPE;

-import static csip.ModelDataService.REPORT_VALUE;

import static csip.ModelDataService.VALUE;

+import csip.annotations.*;

import static util.ErosionConst.*;

import csip.utils.JSONUtils;

@@ -189,33 +188,32 @@

@Override

- protected JSONArray createResults() throws Exception {

- JSONArray results = new JSONArray();

+ protected void postProcess() throws Exception {

int errors = 0;

for (int i = 0; i < operations.size(); i++) {

String op = operations.get(i);

if (isUrlReachable(op)) {

- results.put(JSONUtils.dataDesc("OPERATION_" + (i + 1), op, "operation is valid"));

+ putResult("OPERATION_" + (i + 1), op, "operation is valid");

} else {

- results.put(JSONUtils.dataDesc("OPERATION_INVALID_" + (i + 1), op, "OPERATION IS MISSING!"));

+ putResult("OPERATION_INVALID_" + (i + 1), op, "OPERATION IS MISSING!");

errors++;

}

for (int i = 0; i < vegetations.size(); i++) {

String vege = vegetations.get(i);

if (isUrlReachable(vege)) {

- results.put(JSONUtils.dataDesc("VEGETATION_" + (i + 1), vege, "vegetation is valid"));

+ putResult("VEGETATION_" + (i + 1),vege,"vegetation is valid");

} else {

- results.put(JSONUtils.dataDesc("VEGETATION_INVALID_" + (i + 1), vege, "VEGETATION IS MISSING"));

+ putResult("VEGETATION_INVALID_" + (i + 1), vege, "VEGETATION IS MISSING");

errors++;

}

for (int i = 0; i < residues.size(); i++) {

String res = residues.get(i);

if (isUrlReachable(res)) {

- results.put(JSONUtils.dataDesc("RESIDUE_" + (i + 1), res, "residue is valid"));

+ putResult("RESIDUE_" + (i + 1), res, "residue is valid");

} else {

- results.put(JSONUtils.dataDesc("RESIDUE_INVALID_" + (i + 1), res, "RESIDUE IS MISSING"));

+ putResult("RESIDUE_INVALID_" + (i + 1), res, "RESIDUE IS MISSING");

errors++;

}

@@ -224,20 +222,19 @@

String sout = FileUtils.readFileToString(stdout);

for (String r : JSONUtils.getRequestedResults(getMetainfo())) {

if ((errors > 0) && (r.equals(RES_SLOPE_DEGRAD))) {

- results.put(JSONUtils.dataDesc(r, getResult(sout, r), R2_MISSING_XML_FILES_WARNING_MSG));

+ putResult(r, getResult(sout, r), R2_MISSING_XML_FILES_WARNING_MSG);

} else {

- results.put(JSONUtils.data(r, getResult(sout, r)));

+ putResult(r, getResult(sout, r));

}

if (errors > 0) {

appendMetainfoWarning(R2_MISSING_XML_FILES_WARNING_MSG);

}

- results.put(JSONUtils.data(KEY_CLIMATES, climate));

- results.put(JSONUtils.data(KEY_SOILS, soil));

- results.put(JSONUtils.data(KEY_MANAGEMENTS, mgmt));

+ putResult(KEY_CLIMATES, climate);

+ putResult(KEY_SOILS, soil);

+ putResult(KEY_MANAGEMENTS, mgmt);

// results.put(JSONUtils.data(KEY_ALT_R2DB, in_ALT_R2DB));

- return results;

}

@@ -653,62 +650,65 @@

@Override

- protected JSONArray createReport() throws Exception {

+ protected void doReport() throws Exception {

String sReportJSON = FileUtils.readFileToString(getResourceFile(REPORT_JSON));

JSONArray reportItemsFromTemplate = new JSONArray(sReportJSON);

- JSONArray reportItemsOutput = new JSONArray();

String sout = FileUtils.readFileToString(stdout);

for (int i = 0; i < reportItemsFromTemplate.length(); i++) {

JSONObject obj = (JSONObject) reportItemsFromTemplate.get(i);

String itemName = obj.getString(REPORT_NAME);

String dimension = JSONUtils.getJSONString(obj, REPORT_DIM, null);

String type = JSONUtils.getJSONString(obj, REPORT_TYPE, "");

+ String units = JSONUtils.getJSONString(obj, REPORT_UNITS, null);

+ String desc = JSONUtils.getJSONString(obj, REPORT_DESC, null);

//LOG.info("Attempting to fetch results for:" + itemName);

String value = getResult(sout, "\"" + itemName + "\"");

//LOG.info("the value='" + value + "'");

if ((value != null) && (value.equals("null"))) {

- obj.put(REPORT_VALUE, (String) null);

+ putReport(itemName, value, desc, units);

// if there is no value, then item should be removed from the array

} else {

if ((dimension != null) && (dimension.length() > 0) && (value != null) && (!value.equals("null"))) {

try {

- obj.put(REPORT_VALUE, new JSONArray(value));

- } catch (JSONException je) {

- obj = processReportElement(obj, type, value);

+ putReport(itemName, new JSONArray(value), desc, units);

+ } catch (JSONException je) {

+ processReportElement(itemName,dimension,units,desc, type, value);

}

} else {

- obj = processReportElement(obj, type, value);

+ processReportElement(itemName,dimension,units,desc, type, value);

}

- obj.remove(REPORT_TYPE);

- reportItemsOutput.put(obj);

}

+ if(dimension != null)

+ putReportMetaInfo(itemName,REPORT_DIM,new JSONArray(dimension));

}

- return reportItemsOutput;

}

- private JSONObject processReportElement(JSONObject obj, String type, String value) throws Exception {

+ // This is a gross signiture but due to csip report changes this is the easiest way to change it without losing Wes's logic.

+ private void processReportElement(String itemName, String dim, String units, String desc, String type, String value) throws Exception {

if ((type.equals("TEXT")) || (type.equals("FILENAME")) || (type.equals("DATE"))) {

// because the RomeShell returns escaped strings, and the JSONObject in Java re-escapes them

// we have to remove one level of "escaping" !!!

String newString = StringEscapeUtils.unescapeJava(value);

- obj.put(REPORT_VALUE, Services.removeFirstLastChar(newString));

+ putReport(itemName, Services.removeFirstLastChar(newString), desc, units);

}

if (type.equals("INTEGER") && (value != null) && (!value.equals("null")) && (!value.equals("\"\""))) {

- obj.put("value", new Double(value).intValue());

+ putReport(itemName, new Double(value).intValue(), desc, units);

}

if (type.equals("REAL") && (value != null)) {

if ((!value.equals("null")) && (!value.equals("\"\""))) {

- obj.put(REPORT_VALUE, new Double(value).doubleValue());

+ putReport(itemName, Double.parseDouble(value), desc, units);

}

if (value.equals("\"\"")) {

- obj.put(REPORT_VALUE, new Double(0).doubleValue());

+ putReport(itemName, new Double(0), desc, units);

}

if (type.equals("")) {

- obj.put(REPORT_VALUE, value);

+ putReport(itemName, value, desc, units);

}

- return obj;

}

src/java/m/weps/V1_3.java

 @@ -11,6 +11,7 @@
   import csip.Executable;
   import csip.ModelDataService;
   import csip.ServiceException;
++import csip.annotations.*;
   import csip.annotations.Polling;
   import csip.annotations.Resource;
   import static csip.annotations.ResourceType.*;
 @@ -28,9 +29,6 @@
   import javax.ws.rs.Path;
   import man2weps.WepsTranslator;
   import man2weps.mcrew.ManageData;
--import oms3.annotations.Description;
--import oms3.annotations.Name;
--import oms3.annotations.VersionInfo;
   import org.apache.commons.io.FileUtils;
   import org.apache.commons.io.IOUtils;
   import org.apache.http.HttpResponse;
 @@ -889,9 +887,8 @@
       @Override
--    public JSONArray createResults() throws Exception {
++    public void postProcess() throws Exception {
           LOG.info("Create the WEPS results...");
--        JSONArray results = new JSONArray();
           FileReader fr = new FileReader(sessionWorkDir + "/sci_energy.out");
           BufferedReader bfr = new BufferedReader(fr);
 @@ -915,20 +912,19 @@
           double windEros_tonAcreYear = Double.parseDouble(wo.windEros) * CONV_KGM2_TONACRE;
           double waterEros_tonAcreYear = Double.parseDouble(wo.waterEros) * CONV_KGM2_TONACRE;
--        results.put(JSONUtils.dataDesc(WEPS_RES_SOIL_COND_INDEX, wo.soilConditioningIndex, "total SCI (soil conditioning index)"));
--        results.put(JSONUtils.dataDesc(WEPS_RES_SCI_OM_FACTOR, wo.sciOmFactor, "SCI Organic Matter subfactor"));
--        results.put(JSONUtils.dataDesc(WEPS_RES_SCI_ER_FACTOR, wo.sciErFactor, "SCI Erosion Rate subfactor"));
--        results.put(JSONUtils.dataDesc(WEPS_RES_SCI_FO_FACTOR, wo.sciFoFactor, "SCI Field Operations subfactor"));
--        results.put(JSONUtils.dataUnitDesc(WEPS_RES_DIESEL_ENERGY, dieselEnergy_gallonsPerAcre, "gallon(Diesel)/acre", "energy used by management operations, expressed as fuel consumption equivalent"));
--        results.put(JSONUtils.dataUnitDesc(WEPS_RES_AVG_BIOMASS, averageBiomass_tonAcreYear, "ton/acre/year", "Average biomass"));
--        results.put(JSONUtils.dataUnitDesc(WEPS_RES_WIND_EROS, windEros_tonAcreYear, "ton/acre/year", "Wind erosion (computed by WEPS)"));
--        results.put(JSONUtils.dataUnitDesc(WEPS_RES_WATER_EROS, waterEros_tonAcreYear, "ton/acre/year", "Water erosion (external input)"));
--        results.put(JSONUtils.dataDesc(WEPS_RES_AVG_ALL_STIR, wo.avgAllStir, "Average STIR"));
--        results.put(JSONUtils.data(WEPS_SALTATION, wo.saltation));
--        results.put(JSONUtils.data(WEPS_SUSPENSION, wo.suspension));
--        results.put(JSONUtils.data(WEPS_PM10, wo.pm10));
++        putResult(WEPS_RES_SOIL_COND_INDEX, wo.soilConditioningIndex, "total SCI (soil conditioning index)");
++        putResult(WEPS_RES_SCI_OM_FACTOR, wo.sciOmFactor, "SCI Organic Matter subfactor");
++        putResult(WEPS_RES_SCI_ER_FACTOR, wo.sciErFactor, "SCI Erosion Rate subfactor");
++        putResult(WEPS_RES_SCI_FO_FACTOR, wo.sciFoFactor, "SCI Field Operations subfactor");
++        putResult(WEPS_RES_DIESEL_ENERGY, dieselEnergy_gallonsPerAcre, "SCI Field Operations subfactor");
++        putResult(WEPS_RES_AVG_BIOMASS, averageBiomass_tonAcreYear, "Average biomass", "ton/acre/year");
++        putResult(WEPS_RES_WIND_EROS, windEros_tonAcreYear, "Wind erosion (computed by WEPS)", "ton/acre/year");
++        putResult(WEPS_RES_WATER_EROS, waterEros_tonAcreYear, "Water erosion (external input)", "ton/acre/year");
++        putResult(WEPS_RES_AVG_ALL_STIR, wo.avgAllStir, "Average STIR");
++        putResult(WEPS_SALTATION, wo.saltation);
++        putResult(WEPS_SUSPENSION, wo.suspension);
++        putResult(WEPS_PM10, wo.pm10);
--        return results;
       }

src/java/m/weps/V1_3_1.java.orig

@@ -11,7 +11,6 @@

import csip.annotations.*;

import static csip.annotations.ResourceType.*;

import csip.utils.JSONUtils;

-import oms3.annotations.*;

import usda.weru.weps.reports.query.WepsConnection;

import wepsreportdata.WepsReportData;

import java.io.*;

src/java/m/weps/WeightsParser.java

 @@ -9,7 +9,8 @@
   import java.util.List;
   import java.util.logging.Level;
   import java.util.logging.Logger;
--import oms3.annotations.*;
++import oms3.annotations.Execute;
++import oms3.annotations.In;
   import org.apache.commons.io.FileUtils;
   /**

web/META-INF/csip-conf.json

@@ -1,5 +1,5 @@

{

- "csip-erosion.version": "$version: 2.0.88 d33ce9ed6382 2017-05-08 Jakob23, built at 2018-02-12 10:14 by brad$",

+ "csip-erosion.version": "$version: 2.0.90 ddd0216b86c9 2018-05-24 Jakob23, built at 2018-05-24 16:08 by Brad$",

"lmod.db": "jdbc:sqlserver:\/\/129.82.20.129:1433;databaseName=lmod_temp;user=lmod-rw;password=managements",

"conservation_resources.db": "jdbc:sqlserver://129.82.20.129:1433;databaseName=conservation_resources;user=sa;password=csurams#1",

"conservation_resources.database": "mssql",

web/WEB-INF/csip-conf.json

@@ -1,5 +1,5 @@

{

- "csip-erosion.version": "$version: 2.0.88 d33ce9ed6382 2017-05-08 Jakob23, built at 2018-02-12 10:14 by brad$",

+ "csip-erosion.version": "$version: 2.0.90 ddd0216b86c9 2018-05-24 Jakob23, built at 2018-05-24 16:08 by Brad$",

"weps.version" : "1.3.9",

"lmod.db": "jdbc:sqlserver:\/\/129.82.20.242:1433;databaseName=lmod_zedx;user=lmod-rw;password=managements",

"conservation_resources.db": "jdbc:sqlserver://129.82.20.241:1433;databaseName=conservation_resources;user=sa;password=csurams#1",