Merge pull request #99 from bowring/geochron

Revised LAICPMS uploading to Geochron
CIRDLES · Aug 3, 2016 · c31c082 · c31c082
2 parents b9b68f4 + 911dd7e
commit c31c082
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Showing 17 changed files with 543 additions and 361 deletions.
diff --git a/.gitignore b/.gitignore
@@ -21,6 +21,8 @@ test_*
 *.ser
 *.zip
 *.log
+tempDataForAliquotUpload
+tempDataForAliquotUploadzip
 
 
 # Misc data files

diff --git a/pom.xml b/pom.xml
@@ -21,7 +21,7 @@
     <groupId>org.cirdles</groupId>
     <artifactId>ET_Redux</artifactId>
     <name>ET_Redux</name>
-    <version>3.6.0</version>
+    <version>3.6.1</version>
     <description>Successor to U-Pb_Redux</description>
     <url>https://cirdles.org</url>
     <inceptionYear>2006</inceptionYear>
@@ -236,7 +236,7 @@
         <dependency>
             <groupId>com.github.cirdles</groupId>
             <artifactId>GeoSamples</artifactId>
-            <version>v.2.0.0</version>
+            <version>-SNAPSHOT</version>
         </dependency>
         <dependency>
             <groupId>com.github.bowring</groupId>

diff --git a/src/main/java/org/earthtime/ETReduxFrame.java b/src/main/java/org/earthtime/ETReduxFrame.java
@@ -3784,7 +3784,7 @@ private void editAliquot(SampleInterface sample, AliquotInterface aliquot) {
 
         } else if (sample.isAnalysisTypeLAICPMS()) {
             if (sample.isSampleTypeAnalysis()) {
-                myEditor = new AliquotEditorForLAICPMS(this, true, theSample, aliquot);
+                myEditor = new AliquotEditorForLAICPMS(this, true, sample, aliquot);
             } else if (sample.isSampleTypeLegacy()) {
                 myEditor = new AliquotLegacyEditorForLAICPMS(this, true, theSample, aliquot);
             }

diff --git a/...va/org/earthtime/Tripoli/rawDataFiles/handlers/Thermo/UnivKansasElementIIFileHandler.java b/...va/org/earthtime/Tripoli/rawDataFiles/handlers/Thermo/UnivKansasElementIIFileHandler.java
@@ -299,6 +299,9 @@ protected SortedSet<TripoliFraction> loadRawDataFile(//
                 System.out.println("\n**** Element II FractionID  " + fractionID + "  " + fractionDateValue.toString() + "  is std: " + tripoliFraction.isStandard() + " >>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<");
 
                 myTripoliFractions.add(tripoliFraction);
+                if (tripoliFraction.getFractionID().compareToIgnoreCase("15YP12-018")==0){
+                    System.out.println("caution");
+                }
 
             } catch (ParseException parseException) {
                 // TODO: drop out here

diff --git a/src/main/java/org/earthtime/UPb_Redux/aliquots/UPbReduxAliquotXMLConverter.java b/src/main/java/org/earthtime/UPb_Redux/aliquots/UPbReduxAliquotXMLConverter.java
diff --git a/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/DateProbabilityDensityPanel.java b/src/main/java/org/earthtime/UPb_Redux/dateInterpretation/DateProbabilityDensityPanel.java
@@ -765,7 +765,10 @@ public void preparePanel(boolean doReScale, boolean inLiveMode) {
 
         // one row for each aliquot even though some may be dummy aliquots, based on count
         // row zero for sample totals and [0][size -+ 1] stores max for plotting scale
-        stackedAliquotKernels = new double[sample.getAliquots().size() + 1][pdfPoints.size() + 1];
+        //stackedAliquotKernels = new double[sample.getAliquots().size() + 1][pdfPoints.size() + 1];
+        // aug 2016 hack to fix project problem
+        stackedAliquotKernels = new double[Math.max(sample.getAliquots().size(), 9) + 1][pdfPoints.size() + 1];
+
 
         // June 2013 experiment with Vermeesch KDE
         ArrayList<Double> X = new ArrayList<>();

diff --git a/src/main/java/org/earthtime/UPb_Redux/dialogs/aliquotManagers/AliquotEditorDialog.java b/src/main/java/org/earthtime/UPb_Redux/dialogs/aliquotManagers/AliquotEditorDialog.java
@@ -855,8 +855,8 @@ protected void exportAliquotToXML() {
                 + getMyAliquot().getAliquotName()//
                 + "_" //
                 + getSample().getSampleIGSN()//
-                //                + "_"//
-                //                + getMyAliquot().getAliquotIGSN()//
+                                + "_"//
+                                + getMyAliquot().getAliquotIGSN()//
                 + fileExtension;
 
         File selectedFile = null;

diff --git a/...thtime/UPb_Redux/dialogs/projectManagers/exportManagers/GeochronProjectExportManager.form b/...thtime/UPb_Redux/dialogs/projectManagers/exportManagers/GeochronProjectExportManager.form
@@ -22,7 +22,7 @@
     <AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
     <AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
     <AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
-    <AuxValue name="designerSize" type="java.awt.Dimension" value="-84,-19,0,5,115,114,0,18,106,97,118,97,46,97,119,116,46,68,105,109,101,110,115,105,111,110,65,-114,-39,-41,-84,95,68,20,2,0,2,73,0,6,104,101,105,103,104,116,73,0,5,119,105,100,116,104,120,112,0,0,2,-62,0,0,4,-83"/>
+    <AuxValue name="designerSize" type="java.awt.Dimension" value="-84,-19,0,5,115,114,0,18,106,97,118,97,46,97,119,116,46,68,105,109,101,110,115,105,111,110,65,-114,-39,-41,-84,95,68,20,2,0,2,73,0,6,104,101,105,103,104,116,73,0,5,119,105,100,116,104,120,112,0,0,2,-35,0,0,4,-83"/>
   </AuxValues>
 
   <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
@@ -41,12 +41,12 @@
       </Properties>
       <Constraints>
         <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-          <AbsoluteConstraints x="0" y="0" width="1200" height="700"/>
+          <AbsoluteConstraints x="0" y="0" width="1200" height="730"/>
         </Constraint>
       </Constraints>
 
       <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
-        <Property name="useNullLayout" type="boolean" value="true"/>
+        <Property name="useNullLayout" type="boolean" value="false"/>
       </Layout>
       <SubComponents>
         <Component class="javax.swing.JPasswordField" name="geoPassPassword_passwordField">
@@ -58,7 +58,7 @@
           </Properties>
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-              <AbsoluteConstraints x="380" y="160" width="150" height="25"/>
+              <AbsoluteConstraints x="380" y="160" width="150" height="-1"/>
             </Constraint>
           </Constraints>
         </Component>
@@ -71,7 +71,7 @@
           </Properties>
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-              <AbsoluteConstraints x="380" y="130" width="150" height="25"/>
+              <AbsoluteConstraints x="380" y="130" width="150" height="-1"/>
             </Constraint>
           </Constraints>
         </Component>
@@ -188,11 +188,11 @@
             <Property name="font" type="java.awt.Font" editor="org.netbeans.beaninfo.editors.FontEditor">
               <Font name="SansSerif" size="14" style="1"/>
             </Property>
-            <Property name="text" type="java.lang.String" value="Step 2) Confirm Sample Details and upload to Geochron.org (Note - uploads overwrite previous uploads):"/>
+            <Property name="text" type="java.lang.String" value="Step 2) Confirm Sample Details and upload to Geochron.org with Public? and Update? options.  NOTE: Currently uses SESAR testbed for IGSNs (not real):"/>
           </Properties>
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-              <AbsoluteConstraints x="10" y="220" width="830" height="25"/>
+              <AbsoluteConstraints x="10" y="220" width="1130" height="25"/>
             </Constraint>
           </Constraints>
         </Component>
@@ -212,7 +212,7 @@
           </AuxValues>
           <Constraints>
             <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
-              <AbsoluteConstraints x="10" y="10" width="1180" height="110"/>
+              <AbsoluteConstraints x="10" y="10" width="1180" height="-1"/>
             </Constraint>
           </Constraints>
 
@@ -250,6 +250,27 @@
             </Container>
           </SubComponents>
         </Container>
+        <Container class="javax.swing.JPanel" name="buttonBar_panel">
+          <Properties>
+            <Property name="background" type="java.awt.Color" editor="org.netbeans.beaninfo.editors.ColorEditor">
+              <Color blue="ff" green="ff" red="eb" type="rgb"/>
+            </Property>
+            <Property name="border" type="javax.swing.border.Border" editor="org.netbeans.modules.form.editors2.BorderEditor">
+              <Border info="org.netbeans.modules.form.compat2.border.BevelBorderInfo">
+                <BevelBorder bevelType="1"/>
+              </Border>
+            </Property>
+          </Properties>
+          <Constraints>
+            <Constraint layoutClass="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout" value="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout$AbsoluteConstraintsDescription">
+              <AbsoluteConstraints x="0" y="700" width="1200" height="30"/>
+            </Constraint>
+          </Constraints>
+
+          <Layout class="org.netbeans.modules.form.compat2.layouts.DesignAbsoluteLayout">
+            <Property name="useNullLayout" type="boolean" value="false"/>
+          </Layout>
+        </Container>
       </SubComponents>
     </Container>
   </SubComponents>
-Original file line number
+Diff line change
@@ Expand Up / @@ -21,6 +21,8 @@ test_* @@
     *.ser
     *.zip
     *.log
+    tempDataForAliquotUpload
+    tempDataForAliquotUploadzip
     # Misc data files
@@ Expand Down @@