Merge pull request #267 from AtlasOfLivingAustralia/various

adam-collins · web-flow · commit c54e2696f50a · 2025-03-05T13:33:57.000+10:00
Various
diff --git a/grails-app/controllers/au/org/ala/spatial/ShapesController.groovy b/grails-app/controllers/au/org/ala/spatial/ShapesController.groovy
@@ -1034,6 +1034,9 @@ class ShapesController {
                 WKTReader wktReader = new WKTReader()
                 Geometry geom = wktReader.read(wkt.toString())
 
+                // union all the polygons in a MULTIPOLYGON, if any
+                geom = geom.union()
+
                 // Use CCW for exterior rings. Normalizing will use the JTS default (CW). Reverse makes it CCW.
                 Geometry validGeom = GeomMakeValid.makeValid(geom)
                 validGeom.normalize()
@@ -1059,27 +1062,8 @@ class ShapesController {
         return filename.replaceAll("[^a-zA-Z0-9\\(\\)\\[\\]\\-]", "_")
     }
 
-    private static cleanObjectId(String id) {
+    private static String cleanObjectId(String id) {
         String.valueOf(Long.valueOf(id))
     }
-
-    // requestBody schemas
-//    class UploadWkt {
-//        String wkt
-//        String name
-//        String description
-//        String user_id
-//    }
-//
-//    class UploadGeoJSON {
-//        String name
-//        String description
-//        String user_id
-//        Map geojson
-//    }
-//
-//    class UploadFeatures {
-//        List<String> featureIndex
-//    }
 }
 
diff --git a/grails-app/controllers/au/org/ala/spatial/WorkflowController.groovy b/grails-app/controllers/au/org/ala/spatial/WorkflowController.groovy
@@ -15,6 +15,7 @@
 
 package au.org.ala.spatial
 
+import au.ala.org.ws.security.RequireApiKey
 import au.org.ala.web.AuthService
 import grails.converters.JSON
 
@@ -41,6 +42,7 @@ class WorkflowController {
      * @param id
      * @return
      */
+    @RequireApiKey
     def save(Long id) {
         String user_id = authService.getUserId()
         def data = request.JSON
@@ -49,57 +51,25 @@ class WorkflowController {
         def description = data['description']?.toString()
         def metadata = data['metadata']?.toString()
 
-        def header
-
-        String errorMsg
-        if ("true".equalsIgnoreCase(data['doi']?.toString())) {
-            // test for minimum data for a DOI
-            errorMsg = getErrorForDoi(data)
-
-            if (!errorMsg) {
-                // analysis_id is used to hold the minted value. This makes it readonly.
-                header = userDataService.put(user_id, RECORD_TYPE, description, metadata, isPublic, null)
-                if (header?.ud_header_id) {
-                    userDataService.update(header.ud_header_id, user_id, RECORD_TYPE, description, metadata, isPublic, header.ud_header_id.toString())
-                }
-            }
-        } else {
-            header = userDataService.put(user_id, RECORD_TYPE, description, metadata, isPublic, null)
-        }
-
-        header = mapping(header)
+        def header = mapping(userDataService.put(user_id, RECORD_TYPE, description, metadata, isPublic, null))
 
         def result
-        if (errorMsg) {
-            result = false
-            def map = [successful: result, message: errorMsg]
-            render map as JSON
-        } else if (header) {
+        if (header) {
             result = true
             def map = [successful: result, data: header]
             render map as JSON
         } else {
             result = false
-            errorMsg = "Failed to save workflow"
-            def map = [successful: result, message: errorMsg]
+            def map = [successful: result, message: "Failed to save workflow"]
             render map as JSON
         }
     }
 
-    def doi(String id) {
-        List list = userDataService.searchDescAndTypeOr(null, RECORD_TYPE, null, null, id, 0, 1)
-
-        if (list.size() > 0) {
-            show(list.get(0).ud_header_id)
-        } else {
-            render status: HttpURLConnection.HTTP_NOT_FOUND
-        }
-    }
-
+    @RequireApiKey
     def show(Long id) {
         String user_id = authService.getUserId()
 
-        def item = userDataService.get(id)
+        def item = UDHeader.get(id)
 
         if (!item) {
             render status: 404
@@ -128,10 +98,11 @@ class WorkflowController {
         }
     }
 
+    @RequireApiKey
     def delete(Long id) {
         String user_id = authService.getUserId()
 
-        def metadata = userDataService.get(id)
+        def metadata = UDHeader.get(id)
 
         // check authorisation and that it is not minted (no analysis_id)
         if ((metadata.user_id == user_id ||
@@ -148,6 +119,7 @@ class WorkflowController {
         }
     }
 
+    @RequireApiKey
     def search() {
         String user_id = authService.getUserId()
 
@@ -161,10 +133,6 @@ class WorkflowController {
         render formattedList as JSON
     }
 
-    private def getErrorForDoi(data) {
-        return ""
-    }
-
     private def mapping(header) {
         return [id     : header.ud_header_id, mintId: header.analysis_id, name: header.description,
                 userId : header.user_id, isPrivate: !PUBLIC.equalsIgnoreCase(header.data_path),
diff --git a/grails-app/services/au/org/ala/spatial/TabulationService.groovy b/grails-app/services/au/org/ala/spatial/TabulationService.groovy
@@ -479,6 +479,10 @@ class TabulationService {
         //is it grid as contextual layer?
         IntersectionFile f = layerService.getIntersectionFile(fid)
 
+        if (f == null) {
+            return []
+        }
+
         if (f.getType().equalsIgnoreCase("c")) {
             if (wkt.length() > 0) {
                 String sql
diff --git a/grails-app/services/au/org/ala/spatial/UserDataService.groovy b/grails-app/services/au/org/ala/spatial/UserDataService.groovy
@@ -3,34 +3,85 @@ package au.org.ala.spatial
  * A small cache for data resource attribution.
  * This should be revisited if this cache grows or needs regular refreshing.
  */
-//@CompileStatic
 class UserDataService {
 
-    void put(String s1, String s2, String s3, String s4, String s5, String o) {
-
-
-
-
-
-
-
+    UDHeader put(String user_id, String record_type, String description, String metadata, String data_path, String analysis_id) {
+        Date upload_dt = new Date(System.currentTimeMillis())
+        UDHeader udHeader = new UDHeader(
+                user_id: user_id,
+                record_type: record_type,
+                description: description,
+                metadata: metadata,
+                data_path: data_path,
+                analysis_id: analysis_id,
+                upload_dt: upload_dt
+        )
+
+        UDHeader.withTransaction {
+            if (!udHeader.save(flush: true)) {
+                udHeader.errors.allErrors.each { error ->
+                    log.error("Error saving UDHeader: ${error}")
+                }
+                return null
+            }
+        }
+
+        return udHeader
     }
 
-
-    void update(Object o, String s1, String s2, String s3, String s4, String s5, String s6) {
-
-
-
-
+    UDHeader update(Long ud_header_id, String user_id, String record_type, String description, String metadata, String data_path, String analysis_id) {
+        UDHeader.withTransaction {
+            UDHeader udHeader = UDHeader.get(ud_header_id)
+            if (udHeader != null) {
+                udHeader.user_id = user_id
+                udHeader.record_type = record_type
+                udHeader.description = description
+                udHeader.metadata = metadata
+                udHeader.data_path = data_path
+                udHeader.analysis_id = analysis_id
+                udHeader.upload_dt = new Date(System.currentTimeMillis())
+
+                if (!udHeader.save(flush: true)) {
+                    udHeader.errors.allErrors.each { error ->
+                        log.error("Error saving UDHeader: ${error}")
+                    }
+                    return null
+                }
+            }
+
+            return udHeader
+        }
     }
 
-    Object searchDescAndTypeOr(String o1, String s1, String o2, String o3, String s2, int integer1, int integer2) {}
+    boolean delete(Long ud_header_id) {
+        UDHeader.withTransaction {
+            UDHeader.get(ud_header_id).delete()
+        }
 
-    Object get(long aLong) {
-        null
+        return true
     }
 
-    void delete(long aLong) {
-
+    List<UDHeader> searchDescAndTypeOr(String desc, String record_type, String user_id, String data_path, String analysis_id, int start, int limit) {
+        def criteria = UDHeader.createCriteria()
+        def results = criteria.list(max: limit, offset: start) {
+            if (desc) {
+                ilike('description', desc)
+            }
+            if (record_type) {
+                eq('record_type', record_type)
+            }
+            or {
+                if (user_id) {
+                    eq('user_id', user_id)
+                }
+                if (data_path) {
+                    eq('data_path', data_path)
+                }
+                if (analysis_id) {
+                    eq('analysis_id', analysis_id)
+                }
+            }
+        }
+        return results
     }
 }
diff --git a/src/main/groovy/au/org/ala/spatial/StreamGobbler.groovy b/src/main/groovy/au/org/ala/spatial/StreamGobbler.groovy
@@ -41,7 +41,17 @@ class StreamGobbler extends Thread {
             String line
             while ((line = br.readLine()) != null) {
                 if (taskWrapper != null) {
-                    taskWrapper.task.history.put(System.currentTimeMillis() as String, logPrefix + ": " + line)
+                    // surpress some JDK logging
+                    if (!line.startsWith('INFO:') && !line.startsWith('NOTE:') && !line.contains('java.')) {
+                        String str = logPrefix + ": " + line
+
+                        // trim str to max 250 characters
+                        if (str.length() > 250) {
+                            str = str.substring(0, 250)
+                        }
+
+                        taskWrapper.task.history.put(System.currentTimeMillis() as String, str)
+                    }
                 }
                 if (stringBuffer != null) {
                     stringBuffer.append(line).append('\n');
diff --git a/src/main/groovy/au/org/ala/spatial/Util.groovy b/src/main/groovy/au/org/ala/spatial/Util.groovy
@@ -249,6 +249,8 @@ class Util {
             s.q.addAll(json.fq)
         }
         s.wkt = json.wkt
+
+        return s;
     }
 
     static String[] getDistributionsOrChecklists(List<Distributions> ja) {
diff --git a/src/main/groovy/au/org/ala/spatial/process/Classification.groovy b/src/main/groovy/au/org/ala/spatial/process/Classification.groovy
@@ -52,8 +52,11 @@ class Classification extends SlaveProcess {
         taskLog("Cutting Grids")
         def cutDataPath = cutGrid(envnameslist, resolution as String, regionEnvelope.region, regionEnvelope.envelope, null)
 
+        File tmpDir = new File(getTaskPath() + "/tmp/")
+
         taskLog("Running aloc process")
         String[] cmd = ["java", "-Xmx" + String.valueOf(spatialConfig.aloc.xmx),
+                        "-Djava.util.prefs.userRoot=" + getTaskPath() + "/tmp/",
                         "-jar", spatialConfig.data.dir + '/modelling/aloc/aloc.jar',
                         cutDataPath, String.valueOf(groups), String.valueOf(spatialConfig.aloc.threads), getTaskPath()]
 
@@ -130,5 +133,7 @@ class Classification extends SlaveProcess {
             Util.replaceTextInFile(getTaskPath() + "classification.html", replaceMap)
             addOutput("metadata", "classification.html", true)
         }
+
+        tmpDir.delete()
     }
 }
diff --git a/src/main/groovy/au/org/ala/spatial/process/Maxent.groovy b/src/main/groovy/au/org/ala/spatial/process/Maxent.groovy
@@ -68,6 +68,7 @@ class Maxent extends SlaveProcess {
         }
         taskLog("Run Maxent model")
         def cmd = ["java", "-mx" + String.valueOf(spatialConfig.maxent.mx),
+                   "-Djava.util.prefs.userRoot=" + getTaskPath() + "/tmp/",
                    "-jar", spatialConfig.data.dir + '/modelling/maxent/maxent.jar',
                    "-e", cutDataPath, "-s", speciesPath.get(0), "-a", "tooltips=false",
                    "nowarnings", "noprefixes", "-z",
@@ -212,6 +213,9 @@ class Maxent extends SlaveProcess {
             FileUtils.moveFile(new File(getTaskPath() + "_species.gri"), target)
             addOutput("layers", "/layer/" + taskWrapper.id + "_species.gri")
         }
+
+        File tmpDir = new File(getTaskPath() + "/tmp/")
+        FileUtils.deleteDirectory(tmpDir)
     }
 
     static def writeMaxentsld(filename) {
diff --git a/src/main/groovy/au/org/ala/spatial/process/SlaveProcess.groovy b/src/main/groovy/au/org/ala/spatial/process/SlaveProcess.groovy
@@ -1082,7 +1082,7 @@ class SlaveProcess {
             runCmd(cmd.toArray(new String[cmd.size()]), false, spatialConfig.admin.timeout)
 
         } catch (Exception e) {
-            e.printStackTrace()
+            log.error("Failed to convert asc to grd: " + e.getMessage(), e)
         }
     }
 

Original file line number	Diff line number	Diff line change
`@@ -249,6 +249,8 @@ class Util {`
`249`	`249`	`s.q.addAll(json.fq)`
`250`	`250`	`}`
`251`	`251`	`s.wkt = json.wkt`
	`252`	`+`
	`253`	`+ return s;`
`252`	`254`	`}`
`253`	`255`
`254`	`256`	`static String[] getDistributionsOrChecklists(List<Distributions> ja) {`
Original file line number	Diff line number	Diff line change
`@@ -52,8 +52,11 @@ class Classification extends SlaveProcess {`
`52`	`52`	`taskLog("Cutting Grids")`
`53`	`53`	`def cutDataPath = cutGrid(envnameslist, resolution as String, regionEnvelope.region, regionEnvelope.envelope, null)`
`54`	`54`
	`55`	`+ File tmpDir = new File(getTaskPath() + "/tmp/")`
	`56`	`+`
`55`	`57`	`taskLog("Running aloc process")`
`56`	`58`	`String[] cmd = ["java", "-Xmx" + String.valueOf(spatialConfig.aloc.xmx),`
	`59`	`+ "-Djava.util.prefs.userRoot=" + getTaskPath() + "/tmp/",`
`57`	`60`	`"-jar", spatialConfig.data.dir + '/modelling/aloc/aloc.jar',`
`58`	`61`	`cutDataPath, String.valueOf(groups), String.valueOf(spatialConfig.aloc.threads), getTaskPath()]`
`59`	`62`
`@@ -130,5 +133,7 @@ class Classification extends SlaveProcess {`
`130`	`133`	`Util.replaceTextInFile(getTaskPath() + "classification.html", replaceMap)`
`131`	`134`	`addOutput("metadata", "classification.html", true)`
`132`	`135`	`}`
	`136`	`+`
	`137`	`+ tmpDir.delete()`
`133`	`138`	`}`
`134`	`139`	`}`
Original file line number	Diff line number	Diff line change
`@@ -68,6 +68,7 @@ class Maxent extends SlaveProcess {`
`68`	`68`	`}`
`69`	`69`	`taskLog("Run Maxent model")`
`70`	`70`	`def cmd = ["java", "-mx" + String.valueOf(spatialConfig.maxent.mx),`
	`71`	`+ "-Djava.util.prefs.userRoot=" + getTaskPath() + "/tmp/",`
`71`	`72`	`"-jar", spatialConfig.data.dir + '/modelling/maxent/maxent.jar',`
`72`	`73`	`"-e", cutDataPath, "-s", speciesPath.get(0), "-a", "tooltips=false",`
`73`	`74`	`"nowarnings", "noprefixes", "-z",`
`@@ -212,6 +213,9 @@ class Maxent extends SlaveProcess {`
`212`	`213`	`FileUtils.moveFile(new File(getTaskPath() + "_species.gri"), target)`
`213`	`214`	`addOutput("layers", "/layer/" + taskWrapper.id + "_species.gri")`
`214`	`215`	`}`
	`216`	`+`
	`217`	`+ File tmpDir = new File(getTaskPath() + "/tmp/")`
	`218`	`+ FileUtils.deleteDirectory(tmpDir)`
`215`	`219`	`}`
`216`	`220`
`217`	`221`	`static def writeMaxentsld(filename) {`
Original file line number	Diff line number	Diff line change
`@@ -1082,7 +1082,7 @@ class SlaveProcess {`
`1082`	`1082`	`runCmd(cmd.toArray(new String[cmd.size()]), false, spatialConfig.admin.timeout)`
`1083`	`1083`
`1084`	`1084`	`} catch (Exception e) {`
`1085`		`- e.printStackTrace()`
	`1085`	`+ log.error("Failed to convert asc to grd: " + e.getMessage(), e)`
`1086`	`1086`	`}`
`1087`	`1087`	`}`
`1088`	`1088`