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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/java/org/openscience/nmrshiftdb/om Modified Files: BaseDBSample.java BaseDBSamplePeer.java TurbineUserAdapter.java TurbineUserPeerAdapter.java Log Message: this is the first part of the reports system for the lab system Index: BaseDBSample.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSample.java,v retrieving revision 1.9 retrieving revision 1.10 diff -C2 -r1.9 -r1.10 *** BaseDBSample.java 30 Oct 2006 15:45:32 -0000 1.9 --- BaseDBSample.java 17 Nov 2006 20:18:09 -0000 1.10 *************** *** 42,45 **** --- 42,46 ---- /** the value for the wished_spectrum field */ private String wished_spectrum; + private String other_wished_spectrum; /** the value for the finished field */ private String finished; *************** *** 424,428 **** ! /** * Get the Finished * @return String --- 425,455 ---- ! /** ! * Get the WishedSpectrum ! * @return String ! */ ! public String getOtherWishedSpectrum() ! { ! return other_wished_spectrum; ! } ! ! ! /** ! * Set the value of WishedSpectrum ! */ ! public void setOtherWishedSpectrum(String v ) ! { ! ! ! ! if ( !ObjectUtils.equals(this.wished_spectrum, v) ) ! { ! this.other_wished_spectrum = v; ! setModified(true); ! } ! } ! ! ! /** * Get the Finished * @return String *************** *** 876,879 **** --- 903,907 ---- fieldNames_.add("SpecialCare"); fieldNames_.add("WishedSpectrum"); + fieldNames_.add("OtherWishedSpectrum"); fieldNames_.add("Finished"); fieldNames_.add("Process"); *************** *** 934,937 **** --- 962,969 ---- return getWishedSpectrum(); } + if (name.equals("OtherWishedSpectrum")) + { + return getOtherWishedSpectrum(); + } if (name.equals("Finished")) { *************** *** 1003,1006 **** --- 1035,1042 ---- return getWishedSpectrum(); } + if (name.equals(DBSamplePeer.OTHER_WISHED_SPECTRUM )) + { + return getOtherWishedSpectrum(); + } if (name.equals(DBSamplePeer.FINISHED )) { *************** *** 1073,1088 **** } if ( pos == 11 ) { return getFinished(); } ! if ( pos == 12 ) { return getProcess(); } ! if ( pos == 13 ) { return getAttachment(); } ! if ( pos == 14 ) { return getAttachmentName(); --- 1109,1128 ---- } if ( pos == 11 ) + { + return getOtherWishedSpectrum(); + } + if ( pos == 12 ) { return getFinished(); } ! if ( pos == 13 ) { return getProcess(); } ! if ( pos == 14 ) { return getAttachment(); } ! if ( pos == 15 ) { return getAttachmentName(); *************** *** 1246,1249 **** --- 1286,1290 ---- copyObj.setSpecialCare(special_care); copyObj.setWishedSpectrum(wished_spectrum); + copyObj.setOtherWishedSpectrum(other_wished_spectrum); copyObj.setFinished(finished); copyObj.setProcess(process); Index: BaseDBSamplePeer.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/BaseDBSamplePeer.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** BaseDBSamplePeer.java 30 Oct 2006 15:45:32 -0000 1.8 --- BaseDBSamplePeer.java 17 Nov 2006 20:18:09 -0000 1.9 *************** *** 60,63 **** --- 60,64 ---- /** the column name for the WISHED_SPECTRUM field */ public static final String WISHED_SPECTRUM = mapBuilder.getDBSample_WishedSpectrum(); + public static final String OTHER_WISHED_SPECTRUM = mapBuilder.getDBSample_OtherWishedSpectrum(); /** the column name for the FINISHED field */ public static final String FINISHED = mapBuilder.getDBSample_Finished(); *************** *** 155,158 **** --- 156,160 ---- criteria.addSelectColumn( SPECIAL_CARE ); criteria.addSelectColumn( WISHED_SPECTRUM ); + criteria.addSelectColumn( OTHER_WISHED_SPECTRUM ); criteria.addSelectColumn( FINISHED ); criteria.addSelectColumn( PROCESS ); *************** *** 208,215 **** obj.setSpecialCare(row.getValue(offset+9).asString()); obj.setWishedSpectrum(row.getValue(offset+10).asString()); ! obj.setFinished(row.getValue(offset+11).asString()); ! obj.setProcess(row.getValue(offset+12).asString()); ! obj.setAttachment(row.getValue(offset+13).asBytes()); ! obj.setAttachmentName(row.getValue(offset+14).asString()); } --- 210,218 ---- obj.setSpecialCare(row.getValue(offset+9).asString()); obj.setWishedSpectrum(row.getValue(offset+10).asString()); ! obj.setOtherWishedSpectrum(row.getValue(offset+11).asString()); ! obj.setFinished(row.getValue(offset+12).asString()); ! obj.setProcess(row.getValue(offset+13).asString()); ! obj.setAttachment(row.getValue(offset+14).asBytes()); ! obj.setAttachmentName(row.getValue(offset+15).asString()); } *************** *** 426,429 **** --- 429,433 ---- criteria.add( SPECIAL_CARE, obj.getSpecialCare() ); criteria.add( WISHED_SPECTRUM, obj.getWishedSpectrum() ); + criteria.add( OTHER_WISHED_SPECTRUM, obj.getWishedSpectrum() ); criteria.add( FINISHED, obj.getFinished() ); criteria.add( PROCESS, obj.getProcess() ); Index: TurbineUserAdapter.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/TurbineUserAdapter.java,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 *** TurbineUserAdapter.java 7 Jun 2006 19:13:50 -0000 1.18 --- TurbineUserAdapter.java 17 Nov 2006 20:18:09 -0000 1.19 *************** *** 21,25 **** public static final String COUNTRY = "COUNTRY"; public static final String WEB_PAGE = "WEB_PAGE"; ! public static final String AFFILIATION = "AFFILIATION"; public static final String BROKENSUBMIT = "BROKENSUBMIT"; public static final String HALL_OF_FAME = "HALL_OF_FAME"; --- 21,26 ---- public static final String COUNTRY = "COUNTRY"; public static final String WEB_PAGE = "WEB_PAGE"; ! public static final String AFFILIATION_1 = "AFFILIATION_1"; ! public static final String AFFILIATION_2 = "AFFILIATION_2"; public static final String BROKENSUBMIT = "BROKENSUBMIT"; public static final String HALL_OF_FAME = "HALL_OF_FAME"; *************** *** 64,70 **** setPerm(WEB_PAGE, webPage); } ! public void setAffiliation(String affiliation) { ! setPerm(AFFILIATION, affiliation); } public void setBrokenSubmit(String brokensubmit) --- 65,75 ---- setPerm(WEB_PAGE, webPage); } ! public void setAffiliation1(String affiliation) { ! setPerm(AFFILIATION_1, affiliation); ! } ! public void setAffiliation2(String affiliation) ! { ! setPerm(AFFILIATION_2, affiliation); } public void setBrokenSubmit(String brokensubmit) Index: TurbineUserPeerAdapter.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/TurbineUserPeerAdapter.java,v retrieving revision 1.10 retrieving revision 1.11 diff -C2 -r1.10 -r1.11 *** TurbineUserPeerAdapter.java 11 Jan 2006 15:30:46 -0000 1.10 --- TurbineUserPeerAdapter.java 17 Nov 2006 20:18:09 -0000 1.11 *************** *** 18,22 **** public static final String COUNTRY = mapBuilder.getUser_Country(); public static final String WEB_PAGE = mapBuilder.getUser_WebPage(); ! public static final String AFFILIATION = mapBuilder.getUser_Affiliation(); public static final String BROKENSUBMIT = mapBuilder.getUser_BrokenSubmit(); public static final String HALL_OF_FAME = mapBuilder.getUser_HallOfFame(); --- 18,23 ---- public static final String COUNTRY = mapBuilder.getUser_Country(); public static final String WEB_PAGE = mapBuilder.getUser_WebPage(); ! public static final String AFFILIATION_1 = mapBuilder.getUser_Affiliation1(); ! public static final String AFFILIATION_2 = mapBuilder.getUser_Affiliation2(); public static final String BROKENSUBMIT = mapBuilder.getUser_BrokenSubmit(); public static final String HALL_OF_FAME = mapBuilder.getUser_HallOfFame(); *************** *** 56,60 **** user.setCountry(""); user.setWebPage(""); ! user.setAffiliation(""); user.setEmail(""); user.save(); --- 57,62 ---- user.setCountry(""); user.setWebPage(""); ! user.setAffiliation1(""); ! user.setAffiliation2(""); user.setEmail(""); user.save(); |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:18:57
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/reports In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/reports Added Files: yearly_report_1.jasper yearly_report_1.jrxml Log Message: this is the first part of the reports system for the lab system --- NEW FILE: yearly_report_1.jasper --- ¬í leftMarginB pageHeightI printOrderI backgroundt importsSett pageFooterq pageHeaderq parameterst Z expressiont expressionq resetGroupq sr expressionq leftBorderq reportFontq topPaddingq sr uq sq sr sq sq sq sq sq pq sq Frequency:sq GROUP_FREQt nmrshiftdbxsr PAGE_COUNTpq Variable_1pt loadFactorI field_YEAR field_50_D field_49_D initParams initFields PAGE_COUNT Variable_1 Exceptions SourceFile · "%03 > A#$()-¨.«2¶3¹7Ä8Ç<Ò=ÕAàBãFîGñKüS · · --- NEW FILE: yearly_report_1.jrxml --- <?xml version="1.0" encoding="UTF-8"?> <!-- Created using an evaluation version of JasperAssistant (http://www.jasperassistant.com) --> <!DOCTYPE jasperReport PUBLIC "-//JasperReports//DTD Report Design//EN" "http://jasperreports.sourceforge.net/dtds/jasperreport.dtd"> <jasperReport name="Unnamed" pageWidth="595" pageHeight="842" columnWidth="555" leftMargin="20" rightMargin="20" topMargin="30" bottomMargin="30"> <property name="com.jasperassistant.designer.Grid" value="false"/> <property name="com.jasperassistant.designer.SnapToGrid" value="false"/> <property name="com.jasperassistant.designer.GridWidth" value="12"/> <property name="com.jasperassistant.designer.GridHeight" value="12"/> <property name="com.jasperassistant.designer.DataSource" value="nmrshiftdb"/> <queryString> <![CDATA[select YEAR(DATE) as YEAR, AFFILITATION_1, AFFILIATION_2, (WISHED_SPECTRUM like "%13C%" or WISHED_SPECTRUM like "%variable temperature%" or WISHED_SPECTRUM like "%ID sel. NOE%" or WISHED_SPECTRUM like "%solvent suppression%" or WISHED_SPECTRUM like "%standard spectrum%") as 1_D, (WISHED_SPECTRUM like "%H,H-COSY%" or WISHED_SPECTRUM like "%NOESY%" or WISHED_SPECTRUM like "%HMQC%" or WISHED_SPECTRUM like "%HMBC%") as 2_D, OTHER_WISHED_SPECTRUM!="" as SPECIAL, OTHER_NUCLEI!="" as HETERO, VALUE from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE join CONDITION on MACHINE.FIELD_STRENGTH=CONDITION.CONDITION_ID order by YEAR, AFFILITATION_1, AFFILIATION_2, 1_D, 2_D, SPECIAL, HETERO, VALUE;]]> </queryString> <field name="1_D" class="java.lang.Long"/> <field name="2_D" class="java.lang.Long"/> <field name="AFFILIATION_2" class="java.lang.String"/> <field name="AFFILITATION_1" class="java.lang.String"/> <field name="HETERO" class="java.lang.Long"/> <field name="SPECIAL" class="java.lang.Long"/> <field name="VALUE" class="java.lang.String"/> <field name="YEAR" class="java.lang.Long"/> <variable name="is1D" class="java.lang.String"> <variableExpression><![CDATA[$F{1_D}.equals(new Long(1)) ? "1 D" : ""]]></variableExpression> </variable> <variable name="Variable_1" class="java.lang.String"/> <group name="GRP_YEAR"> <groupHeader> <band height="50"> <line> <reportElement x="3" y="1" width="551" height="1"/> <graphicElement pen="4Point"/> </line> <textField> <reportElement x="44" y="13" width="80" height="20"/> <textElement textAlignment="Left"/> <textFieldExpression class="java.lang.Long"><![CDATA[$F{YEAR}]]></textFieldExpression> </textField> <staticText> <reportElement x="5" y="13" width="30" height="20"/> <textElement/> <text><![CDATA[Year]]></text> </staticText> </band> </groupHeader> <groupFooter> <band height="50"> <textField> <reportElement x="157" y="16" width="80" height="20"/> <textElement/> <textFieldExpression class="java.lang.Integer"><![CDATA[$V{GRP_YEAR_COUNT}]]></textFieldExpression> </textField> <staticText> <reportElement x="14" y="16" width="94" height="20"/> <textElement/> <text><![CDATA[Measurements in]]></text> </staticText> <textField> <reportElement x="114" y="15" width="37" height="20"/> <textElement textAlignment="Left"/> <textFieldExpression class="java.lang.Long"><![CDATA[$F{YEAR}]]></textFieldExpression> </textField> </band> </groupFooter> </group> <group name="GRP_AFFILIATION_1"> <groupExpression><![CDATA[$F{AFFILITATION_1}]]></groupExpression> <groupHeader> <band height="36"> <rectangle> <reportElement x="60" y="2" width="494" height="34" backcolor="#E5E5E5"/> <graphicElement pen="None"/> </rectangle> <textField> <reportElement x="63" y="13" width="330" height="22"/> <textElement/> <textFieldExpression class="java.lang.String"><![CDATA[$F{AFFILITATION_1}]]></textFieldExpression> </textField> </band> </groupHeader> <groupFooter> <band height="41"> <textField> <reportElement x="66" y="28" width="80" height="13"/> <textElement/> <textFieldExpression class="java.lang.Integer"><![CDATA[$V{GRP_AFFILIATION_1_COUNT}]]></textFieldExpression> </textField> <staticText> <reportElement x="66" y="8" width="90" height="15"/> <textElement/> <text><![CDATA[Measurements of]]></text> </staticText> <textField> <reportElement x="161" y="8" width="330" height="14"/> <textElement/> <textFieldExpression class="java.lang.String"><![CDATA[$F{AFFILITATION_1}]]></textFieldExpression> </textField> </band> </groupFooter> </group> <group name="GRP_AFFILIATION_2"> <groupExpression><![CDATA[$F{AFFILIATION_2}]]></groupExpression> <groupHeader> <band height="32"> <textField> <reportElement x="63" y="11" width="330" height="20"/> <textElement/> <textFieldExpression class="java.lang.String"><![CDATA[$F{AFFILIATION_2}]]></textFieldExpression> </textField> </band> </groupHeader> <groupFooter> <band height="45"> <textField> <reportElement x="65" y="31" width="80" height="14"/> <textElement/> <textFieldExpression class="java.lang.Integer"><![CDATA[$V{GRP_AFFILIATION_2_COUNT}]]></textFieldExpression> </textField> <textField> <reportElement x="159" y="8" width="330" height="14"/> <textElement/> <textFieldExpression class="java.lang.String"><![CDATA[$F{AFFILIATION_2}]]></textFieldExpression> </textField> <staticText> <reportElement x="64" y="8" width="90" height="15"/> <textElement/> <text><![CDATA[Measurements of]]></text> </staticText> </band> </groupFooter> </group> <group name="GRP_EXp"> <groupExpression><![CDATA[$F{1_D}.toString()+$F{2_D}.toString()+$F{SPECIAL}.toString()+$F{HETERO}.toString()]]></groupExpression> <groupHeader> <band height="37"> <textField> <reportElement x="127" y="16" width="30" height="18"/> <textElement/> <textFieldExpression class="java.lang.Long"><![CDATA[$F{1_D}]]></textFieldExpression> </textField> <textField> <reportElement x="202" y="15" width="32" height="20"/> <textElement/> <textFieldExpression class="java.lang.Long"><![CDATA[$F{2_D}]]></textFieldExpression> </textField> <textField> <reportElement x="298" y="12" width="37" height="20"/> <textElement/> <textFieldExpression class="java.lang.Long"><![CDATA[$F{SPECIAL}]]></textFieldExpression> </textField> <textField> <reportElement x="396" y="13" width="42" height="20"/> <textElement/> <textFieldExpression class="java.lang.Long"><![CDATA[$F{HETERO}]]></textFieldExpression> </textField> <staticText> <reportElement x="88" y="17" width="30" height="20"/> <textElement/> <text><![CDATA[1D ?]]></text> </staticText> <staticText> <reportElement x="164" y="16" width="29" height="20"/> <textElement/> <text><![CDATA[2D ?]]></text> </staticText> <staticText> <reportElement x="242" y="14" width="47" height="20"/> <textElement/> <text><![CDATA[Special ?]]></text> </staticText> <staticText> <reportElement x="342" y="13" width="48" height="20"/> <textElement/> <text><![CDATA[Hetero ?]]></text> </staticText> <line> <reportElement x="88" y="1" width="466" height="1"/> <graphicElement/> </line> </band> </groupHeader> <groupFooter> <band height="41"> <textField> <reportElement x="88" y="29" width="80" height="12"/> <textElement/> <textFieldExpression class="java.lang.Integer"><![CDATA[$V{GRP_EXp_COUNT}]]></textFieldExpression> </textField> <staticText> <reportElement x="90" y="9" width="295" height="14"/> <textElement/> <text><![CDATA[Measurements with these types and all frequencies:]]></text> </staticText> </band> </groupFooter> </group> <group name="GROUP_FREQ"> <groupExpression><![CDATA[$F{VALUE}]]></groupExpression> <groupHeader> <band height="33"> <textField> <reportElement x="179" y="12" width="27" height="20"/> <textElement/> <textFieldExpression class="java.lang.String"><![CDATA[$F{VALUE}]]></textFieldExpression> </textField> <staticText> <reportElement x="116" y="13" width="52" height="20"/> <textElement/> <text><![CDATA[Frequency:]]></text> </staticText> <staticText> <reportElement x="212" y="12" width="102" height="20"/> <textElement/> <text><![CDATA[Mhz]]></text> </staticText> </band> </groupHeader> <groupFooter> <band height="43"> <textField> <reportElement x="116" y="30" width="80" height="13"/> <textElement/> <textFieldExpression class="java.lang.Integer"><![CDATA[$V{GROUP_FREQ_COUNT}]]></textFieldExpression> </textField> <staticText> <reportElement x="117" y="10" width="320" height="14"/> <textElement/> <text><![CDATA[Measurements with this frequency and these types:]]></text> </staticText> </band> </groupFooter> </group> </jasperReport> |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:18:57
|
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java OrderFullfillAction.java Log Message: this is the first part of the reports system for the lab system Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.40 retrieving revision 1.41 diff -C2 -r1.40 -r1.41 *** OrderAction.java 15 Nov 2006 13:38:24 -0000 1.40 --- OrderAction.java 17 Nov 2006 20:18:09 -0000 1.41 *************** *** 16,21 **** import org.apache.jetspeed.portal.portlets.VelocityPortlet; import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.security.User; ! import org.apache.turbine.services.security.TurbineSecurity; import org.apache.turbine.util.RunData; import org.apache.turbine.util.ServletUtils; --- 16,20 ---- import org.apache.jetspeed.portal.portlets.VelocityPortlet; import org.apache.turbine.om.NumberKey; ! import org.apache.turbine.om.peer.BasePeer; import org.apache.turbine.util.RunData; import org.apache.turbine.util.ServletUtils; *************** *** 579,582 **** --- 578,598 ---- + public void doMonthlystatistcs(RunData data, Context context) throws Exception { + try{ + int frommonth=data.getParameters().getInt("frommonth"); + int tomonth=data.getParameters().getInt("tomonth"); + int fromyear=data.getParameters().getInt("fromyear"); + int toyear=data.getParameters().getInt("toyear"); + Vector v=BasePeer.executeQuery("select count(*) from SAMPLE where DATE>='"+fromyear+"-"+frommonth+"-1' and DATE<='"+toyear+"-"+tomonth+"-1'"); + context.put("allinst", ((Record)v.get(0)).getValue(1).asInt()); + context.put("aff1",BasePeer.executeQuery("select count(*), AFFILITATION_1 from SAMPLE join TURBINE_USER using (USER_ID) where DATE>='"+fromyear+"-"+frommonth+"-1' and DATE<='"+toyear+"-"+tomonth+"-1' group by AFFILITATION_1")); + + + }catch(Exception ex){ + ex.printStackTrace(); + GeneralUtils.logError(ex,"guestbook/doentry",data,true); + } + } + public void doDeleteorder(RunData data, Context context) throws Exception { try{ Index: OrderFullfillAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderFullfillAction.java,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -r1.26 -r1.27 *** OrderFullfillAction.java 30 Oct 2006 15:45:32 -0000 1.26 --- OrderFullfillAction.java 17 Nov 2006 20:18:09 -0000 1.27 *************** *** 29,32 **** --- 29,34 ---- import org.openscience.nmrshiftdb.util.GeneralUtils; + import com.workingdogs.village.Record; + /** *Handles actions for the GuestbookPortlet *************** *** 70,73 **** --- 72,89 ---- context.put("data", data); context.put("submitorshow","submit"); + Vector v=BasePeer.executeQuery("select min(year(DATE)) from SAMPLE"); + int yearmin=((Record)v.get(0)).getValue(1).asInt(); + v=BasePeer.executeQuery("select max(year(DATE)) from SAMPLE"); + int yearmax=((Record)v.get(0)).getValue(1).asInt(); + Vector years=new Vector(); + for (int i=yearmin;i<=yearmax;i++){ + years.add(new Integer(i)); + } + context.put("years", years); + Vector months=new Vector(); + for (int i=1;i<=12;i++){ + months.add(new Integer(i)); + } + context.put("months", months); if(data.getParameters().get("submitorshow")!=null && data.getParameters().get("submitorshow").equals("show")){ DBSample toshow=DBSamplePeer.retrieveByPK(new NumberKey(data.getParameters().get("id"))); *************** *** 91,95 **** data.getSession().setAttribute("choosenfiles", new Vector()); } ! Vector v=(Vector)data.getSession().getAttribute("choosenfiles"); if(data.getParameters().get("nmrshiftdbaction")!=null && data.getParameters().get("nmrshiftdbaction").equals("addtochoosenfiles")){ if(!data.getParameters().get("filename").equals("..")){ --- 107,111 ---- data.getSession().setAttribute("choosenfiles", new Vector()); } ! v=(Vector)data.getSession().getAttribute("choosenfiles"); if(data.getParameters().get("nmrshiftdbaction")!=null && data.getParameters().get("nmrshiftdbaction").equals("addtochoosenfiles")){ if(!data.getParameters().get("filename").equals("..")){ |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:18:57
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/sql In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/sql Modified Files: nmrshiftdb-schema.sql turbine-schema.sql Log Message: this is the first part of the reports system for the lab system Index: nmrshiftdb-schema.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/nmrshiftdb-schema.sql,v retrieving revision 1.82 retrieving revision 1.83 diff -C2 -r1.82 -r1.83 *** nmrshiftdb-schema.sql 30 Oct 2006 15:45:32 -0000 1.82 --- nmrshiftdb-schema.sql 17 Nov 2006 20:18:09 -0000 1.83 *************** *** 843,846 **** --- 843,847 ---- SPECIAL_CARE VARCHAR (50) NOT NULL, WISHED_SPECTRUM VARCHAR (50) NOT NULL, + OTHER_WISHED_SPECTRUM VARCHAR (50) NOT NULL, FINISHED VARCHAR (8) NOT NULL, PROCESS VARCHAR (8) NOT NULL, Index: turbine-schema.sql =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/sql/turbine-schema.sql,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -r1.16 -r1.17 *** turbine-schema.sql 17 Jan 2006 08:42:18 -0000 1.16 --- turbine-schema.sql 17 Nov 2006 20:18:10 -0000 1.17 *************** *** 76,80 **** COUNTRY VARCHAR (99) NOT NULL, WEB_PAGE VARCHAR (99), ! AFFILIATION VARCHAR (99), EMAIL VARCHAR (99) NOT NULL, CONFIRM_VALUE VARCHAR (99), --- 76,81 ---- COUNTRY VARCHAR (99) NOT NULL, WEB_PAGE VARCHAR (99), ! AFFILIATION_1 VARCHAR (99), ! AFFILIATION_2 VARCHAR (99), EMAIL VARCHAR (99) NOT NULL, CONFIRM_VALUE VARCHAR (99), |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:18:57
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/db/map In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/java/org/openscience/nmrshiftdb/util/db/map Modified Files: TurbineMapBuilderAdapter.java Log Message: this is the first part of the reports system for the lab system Index: TurbineMapBuilderAdapter.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/util/db/map/TurbineMapBuilderAdapter.java,v retrieving revision 1.8 retrieving revision 1.9 diff -C2 -r1.8 -r1.9 *** TurbineMapBuilderAdapter.java 11 Jan 2006 15:30:49 -0000 1.8 --- TurbineMapBuilderAdapter.java 17 Nov 2006 20:18:09 -0000 1.9 *************** *** 33,37 **** tMap.addColumn(getCountry(), string); tMap.addColumn(getWebPage(), string); ! tMap.addColumn(getAffiliation(), string); tMap.addColumn(getBrokenSubmit(), string); tMap.addColumn(getHallOfFame(), string); --- 33,38 ---- tMap.addColumn(getCountry(), string); tMap.addColumn(getWebPage(), string); ! tMap.addColumn(getAffiliation1(), string); ! tMap.addColumn(getAffiliation2(), string); tMap.addColumn(getBrokenSubmit(), string); tMap.addColumn(getHallOfFame(), string); *************** *** 102,115 **** } ! public String getAffiliation() { ! return "AFFILIATION"; } ! public String getUser_Affiliation() { ! return getTableUser() + '.' +getAffiliation(); } public String getBrokenSubmit() { --- 103,127 ---- } ! public String getAffiliation1() { ! return "AFFILIATION_2"; } ! public String getAffiliation2() { ! return "AFFILIATION_2"; } + public String getUser_Affiliation1() + { + return getTableUser() + '.' +getAffiliation1(); + } + + public String getUser_Affiliation2() + { + return getTableUser() + '.' +getAffiliation2(); + } + + public String getBrokenSubmit() { |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:18:57
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/vmtemplates/portlets/html Modified Files: worker-order.vm Log Message: this is the first part of the reports system for the lab system Index: worker-order.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/portlets/html/worker-order.vm,v retrieving revision 1.23 retrieving revision 1.24 diff -C2 -r1.23 -r1.24 *** worker-order.vm 30 Oct 2006 15:45:35 -0000 1.23 --- worker-order.vm 17 Nov 2006 20:18:10 -0000 1.24 *************** *** 83,86 **** --- 83,121 ---- </td></tr> #end + </table> + <br><br> + Statistics: + <table> + <tr><th>Yearly:</th><th>Monthly:</th></tr> + <tr><td><form name="yearlyform" method="post" action="download/NmrshiftdbServlet/yearlyreport.pdf?nmrshiftdbaction=createreport&style=yearly">From:<select name="yearstart" size="1"> + #foreach($day in $years) + <option value="$day">$day</option> + #end + </select> + to: <select name="yearend" size="1"> + #foreach($day in $years) + <option value="$day">$day</option> + #end + </select> + <br><input type="submit" name="submityearly" value="Do statistics"/></form></td><td><form name="monthlyform" method="post" action="portal/pane0/NMR+lab+administration">From:<select name="frommonth" size="1"> + #foreach($day in $months) + <option value="$day">$day</option> + #end + </select>/<select name="fromyear" size="1"> + #foreach($day in $years) + <option value="$day">$day</option> + #end + </select> + to: <select name="tomonth" size="1"> + #foreach($day in $months) + <option value="$day">$day</option> + #end + </select>/<select name="toyear" size="1"> + #foreach($day in $years) + <option value="$day">$day</option> + #end + </select> + <br><input type="submit" name="eventSubmit_doMonthlystatistcs" value="Do statistics"/></form></td></tr> + </table> #end #else |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:18:57
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28040/src/java/org/openscience/nmrshiftdb Modified Files: AdminPanel.java NmrshiftdbServlet.java Log Message: this is the first part of the reports system for the lab system Index: AdminPanel.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/AdminPanel.java,v retrieving revision 1.235 retrieving revision 1.236 diff -C2 -r1.235 -r1.236 *** AdminPanel.java 10 Oct 2006 15:20:30 -0000 1.235 --- AdminPanel.java 17 Nov 2006 20:18:08 -0000 1.236 *************** *** 564,568 **** user.setCountry("dkfz"); user.setWebPage("dkfz"); ! user.setAffiliation("dkfz"); user.setEmail("dkfz"); user.setHallOfFame("false"); --- 564,569 ---- user.setCountry("dkfz"); user.setWebPage("dkfz"); ! user.setAffiliation1("dkfz"); ! user.setAffiliation2("dkfz"); user.setEmail("dkfz"); user.setHallOfFame("false"); *************** *** 812,816 **** user.setCountry("mainz"); user.setWebPage("mainz"); ! user.setAffiliation("mainz"); user.setEmail("mainz"); user.setHallOfFame("false"); --- 813,818 ---- user.setCountry("mainz"); user.setWebPage("mainz"); ! user.setAffiliation1("mainz"); ! user.setAffiliation2("mainz"); user.setEmail("mainz"); user.setHallOfFame("false"); *************** *** 1541,1545 **** user.setCountry("dkfz"); user.setWebPage("dkfz"); ! user.setAffiliation("dkfz"); user.setEmail("dkfz"); user.setHallOfFame("false"); --- 1543,1548 ---- user.setCountry("dkfz"); user.setWebPage("dkfz"); ! user.setAffiliation1("dkfz"); ! user.setAffiliation2("dkfz"); user.setEmail("dkfz"); user.setHallOfFame("false"); *************** *** 2576,2580 **** user.setCountry("bulkload"); user.setWebPage("bulkload"); ! user.setAffiliation("bulkload"); user.setEmail("bulkload"); user.setHallOfFame("false"); --- 2579,2584 ---- user.setCountry("bulkload"); user.setWebPage("bulkload"); ! user.setAffiliation1("bulkload"); ! user.setAffiliation2("bulkload"); user.setEmail("bulkload"); user.setHallOfFame("false"); *************** *** 2930,2934 **** user.setCountry("mikhova"); user.setWebPage("mikhova"); ! user.setAffiliation("mikhova"); user.setEmail("mikhova"); user.setHallOfFame("false"); --- 2934,2939 ---- user.setCountry("mikhova"); user.setWebPage("mikhova"); ! user.setAffiliation1("mikhova"); ! user.setAffiliation2("mikhova"); user.setEmail("mikhova"); user.setHallOfFame("false"); Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.98 retrieving revision 1.99 diff -C2 -r1.98 -r1.99 *** NmrshiftdbServlet.java 11 Nov 2006 15:42:22 -0000 1.98 --- NmrshiftdbServlet.java 17 Nov 2006 20:18:09 -0000 1.99 *************** *** 13,16 **** --- 13,17 ---- import java.io.StringReader; import java.io.StringWriter; + import java.sql.Connection; import java.sql.ResultSet; import java.sql.Statement; *************** *** 21,24 **** --- 22,26 ---- import java.util.Iterator; import java.util.List; + import java.util.Map; import java.util.Set; import java.util.StringTokenizer; *************** *** 43,51 **** import javax.xml.transform.stream.StreamSource; import nu.xom.Attribute; import nu.xom.Element; import nu.xom.Node; - import org.apache.ecs.StringElement; import org.apache.fop.apps.FOUserAgent; import org.apache.fop.apps.Fop; --- 45,58 ---- import javax.xml.transform.stream.StreamSource; + import net.sf.jasperreports.engine.JRResultSetDataSource; + import net.sf.jasperreports.engine.JasperExportManager; + import net.sf.jasperreports.engine.JasperFillManager; + import net.sf.jasperreports.engine.JasperPrint; + import net.sf.jasperreports.engine.JasperReport; + import net.sf.jasperreports.engine.util.JRLoader; import nu.xom.Attribute; import nu.xom.Element; import nu.xom.Node; import org.apache.fop.apps.FOUserAgent; import org.apache.fop.apps.Fop; *************** *** 57,60 **** --- 64,68 ---- import org.apache.turbine.util.TurbineConfig; import org.apache.turbine.util.db.Criteria; + import org.apache.turbine.util.db.pool.DBConnection; import org.apache.velocity.VelocityContext; import org.apache.velocity.app.Velocity; *************** *** 188,191 **** --- 196,227 ---- DBSample sample=DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); outstream.write(sample.getAttachment()); + }else if(action.equals("createreport")){ + res.setContentType("application/pdf"); + outstream=res.getOutputStream();//out = res.getWriter(); + //First, load JasperDesign from XML and compile it into JasperReport + boolean yearly=req.getParameter("style").equals("yearly"); + int yearstart=Integer.parseInt(req.getParameter("yearstart")); + int yearend=Integer.parseInt(req.getParameter("yearend")); + int monthstart=0; + int monthend=0; + if(!yearly){ + monthstart=Integer.parseInt(req.getParameter("monthstart")); + monthend=Integer.parseInt(req.getParameter("monthend")); + } + JasperReport jasperReport = (JasperReport)JRLoader.loadObject(relativepath+"/reports/"+(yearly ? "yearly" : "monthly")+"_report_1.jasper"); + //Second, create a map of parameters to pass to the report. + Map parameters = new HashMap(); + parameters.put("ReportTitle", "Basic JasperReport"); + parameters.put("MaxSalary", new Double(25000.00)); + //Third, get a database connection + DBConnection dbconn = TurbineDB.getConnection(); + Connection conn=dbconn.getConnection(); + Statement stmt=conn.createStatement(); + ResultSet rs=stmt.executeQuery("select YEAR(DATE) as YEAR, "+(yearly? "": " MONTH(DATE) as MONTH, ")+"AFFILITATION_1, AFFILIATION_2, (WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, (WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, OTHER_WISHED_SPECTRUM!='' as SPECIAL, OTHER_NUCLEI!='' as HETERO, VALUE from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE join CONDITION on MACHINE.FIELD_STRENGTH=CONDITION.CONDITION_ID where YEAR(DATE)>="+yearstart+" and YEAR(DATE)<="+yearend+" order by YEAR, "+(yearly ? "" : "MONTH, ")+"AFFILITATION_1, AFFILIATION_2, 1_D, 2_D, SPECIAL, HETERO, VALUE"); + //Fourth, create JasperPrint using fillReport() method + JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters,new JRResultSetDataSource(rs)); + //You can use JasperPrint to create PDF + JasperExportManager.exportReportToPdfStream(jasperPrint, outstream); + dbconn.close(); }else if(action.equals("exportcmlbyinchi")){ res.setContentType("text/xml"); |
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From: Stefan K. <sh...@us...> - 2006-11-17 20:14:41
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/reports In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv26692/src/reports Log Message: Directory /cvsroot/nmrshiftdb/nmrshiftdb/src/reports added to the repository |
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From: Stefan K. <sh...@us...> - 2006-11-16 10:49:41
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv12755/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: the multiplicities should now be included with web services submits Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.35 retrieving revision 1.36 diff -C2 -r1.35 -r1.36 *** NMRShiftDBServiceBindingImpl.java 9 Nov 2006 14:43:42 -0000 1.35 --- NMRShiftDBServiceBindingImpl.java 16 Nov 2006 10:49:38 -0000 1.36 *************** *** 257,260 **** --- 257,261 ---- vt.value2=(float)peak.getYValue(); } + vt.multiplicityString=peak.getPeakMultiplicity(); String[] atomrefs=peak.getAtomRefs(); if(atomrefs!=null){ |
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From: Stefan K. <sh...@us...> - 2006-11-15 15:39:09
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16143/src/java/org/openscience/nmrshiftdb/portlets Modified Files: SubmitPortlet.java Log Message: solves a bug discovered at gcc Index: SubmitPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/SubmitPortlet.java,v retrieving revision 1.425 retrieving revision 1.426 diff -C2 -r1.425 -r1.426 *** SubmitPortlet.java 30 Oct 2006 15:45:32 -0000 1.425 --- SubmitPortlet.java 15 Nov 2006 15:39:03 -0000 1.426 *************** *** 67,71 **** import org.openscience.nmrshiftdb.om.DBBookPeer; import org.openscience.nmrshiftdb.om.DBCanonicalName; - import org.openscience.nmrshiftdb.om.DBCondition; import org.openscience.nmrshiftdb.om.DBConditionPeer; import org.openscience.nmrshiftdb.om.DBConditionType; --- 67,70 ---- *************** *** 1595,1598 **** --- 1594,1600 ---- context.put("random", new java.util.Random()); context.put("spectrum",DBSpectrumPeer.retrieveByPK(subData.spectrumid)); + //handle the export templates + File templatedir = new File(ServletUtils.expandRelative(runData.getServletConfig(), "/WEB-INF/templates/vm/exporttemplates")); + context.put("templates",templatedir.listFiles()); // lets render the template StringWriter w = new StringWriter(); |
Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/html In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv16367/src/html Modified Files: jchempaint-applet-Jama.jar jchempaint-applet-com_ozten.jar jchempaint-applet-core.jar jchempaint-applet-editor-opts.jar jchempaint-applet-editor.jar jchempaint-applet-jas.jar jchempaint-applet-javax_media.jar jchempaint-applet-javax_vecmath.jar jchempaint-applet-nu.jar jchempaint-applet-org.jar jchempaint-applet-org_3pq.jar jchempaint-applet-org_apache.jar jchempaint-applet-org_omegahat.jar jchempaint-applet-org_openscience.jar jchempaint-applet-org_openscience_cdk.jar jchempaint-applet-org_openscience_cdk_applications.jar jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar jchempaint-applet-org_openscience_cdk_config.jar jchempaint-applet-org_openscience_cdk_dict.jar jchempaint-applet-org_openscience_cdk_io.jar jchempaint-applet-org_openscience_cdk_iupac.jar jchempaint-applet-org_openscience_cdk_math.jar jchempaint-applet-org_openscience_cdk_nonotify.jar jchempaint-applet-org_openscience_cdk_qsar.jar jchempaint-applet-org_openscience_cdk_structgen.jar jchempaint-applet-org_openscience_cdk_tools.jar jchempaint-applet-org_w3c.jar jchempaint-applet-org_xmlcml.jar jchempaint-applet-others.jar jchempaint-applet-resources.jar jchempaint-applet-viewer-opts.jar Log Message: new applet - there was a major bug Index: jchempaint-applet-Jama.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-Jama.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvs7u9E6h and /tmp/cvsdjbGkC differ Index: jchempaint-applet-com_ozten.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-com_ozten.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files 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jchempaint-applet-jas.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-jas.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvswQnc4D and /tmp/cvs3Myx4Y differ Index: jchempaint-applet-javax_media.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_media.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsRpEHlJ and /tmp/cvsGl59w4 differ Index: jchempaint-applet-javax_vecmath.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-javax_vecmath.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsg6fDpP and /tmp/cvsvwWjJa differ Index: jchempaint-applet-nu.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-nu.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsHle4cR and /tmp/cvsrXzoEc differ Index: jchempaint-applet-org.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsBtElXZ and /tmp/cvsAzlRyl differ Index: jchempaint-applet-org_3pq.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_3pq.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsg5kgQ4 and /tmp/cvsDdn6yq differ Index: jchempaint-applet-org_apache.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_apache.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsFgDrW8 and /tmp/cvsFztIVu differ Index: jchempaint-applet-org_omegahat.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_omegahat.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsDifTEh and /tmp/cvs3bHsQD differ Index: jchempaint-applet-org_openscience.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvs9DRX3o and /tmp/cvss2FhoL differ Index: jchempaint-applet-org_openscience_cdk.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvs3neXBr and /tmp/cvsOlwO2N differ Index: jchempaint-applet-org_openscience_cdk_applications.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvsCKCAzy and /tmp/cvsYWXT9U differ Index: jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_applications_jchempaint.jar,v retrieving revision 1.51 retrieving revision 1.52 diff -C2 -r1.51 -r1.52 Binary files /tmp/cvssxB86C and /tmp/cvs6HjdPZ differ Index: jchempaint-applet-org_openscience_cdk_config.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_config.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsMP2cdE and /tmp/cvsSAlGc1 differ Index: jchempaint-applet-org_openscience_cdk_dict.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_dict.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsGPVWjK and /tmp/cvswXuXp7 differ Index: jchempaint-applet-org_openscience_cdk_io.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_io.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files 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retrieving revision 1.9 diff -C2 -r1.8 -r1.9 Binary files /tmp/cvsrbPtwX and /tmp/cvszIn31k differ Index: jchempaint-applet-org_openscience_cdk_qsar.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_qsar.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsbdoRq0 and /tmp/cvsIegX2n differ Index: jchempaint-applet-org_openscience_cdk_structgen.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_structgen.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsREiQe9 and /tmp/cvsaO88Zw differ Index: jchempaint-applet-org_openscience_cdk_tools.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_openscience_cdk_tools.jar,v retrieving revision 1.20 retrieving revision 1.21 diff -C2 -r1.20 -r1.21 Binary files /tmp/cvsIraBV9 and /tmp/cvs8aQSLx differ Index: jchempaint-applet-org_w3c.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_w3c.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvsgva5Bf and /tmp/cvsELwHxD differ Index: jchempaint-applet-org_xmlcml.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-org_xmlcml.jar,v retrieving revision 1.21 retrieving revision 1.22 diff -C2 -r1.21 -r1.22 Binary files /tmp/cvstUFUmi and /tmp/cvsYffduG differ Index: jchempaint-applet-others.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-others.jar,v retrieving revision 1.51 retrieving revision 1.52 diff -C2 -r1.51 -r1.52 Binary files /tmp/cvsJTNA1r and /tmp/cvsHPllrQ differ Index: jchempaint-applet-resources.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-resources.jar,v retrieving revision 1.48 retrieving revision 1.49 diff -C2 -r1.48 -r1.49 Binary files /tmp/cvsxclM1C and /tmp/cvsAVmLE1 differ Index: jchempaint-applet-viewer-opts.jar =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/html/jchempaint-applet-viewer-opts.jar,v retrieving revision 1.47 retrieving revision 1.48 diff -C2 -r1.47 -r1.48 Binary files /tmp/cvse6jkPH and /tmp/cvs5Zx1L6 differ |
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From: Stefan K. <sh...@us...> - 2006-11-15 13:38:37
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv28932/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: looks like I forgot an else at a crucial point Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -r1.39 -r1.40 *** OrderAction.java 10 Nov 2006 14:14:05 -0000 1.39 --- OrderAction.java 15 Nov 2006 13:38:24 -0000 1.40 *************** *** 400,404 **** }else if(data.getParameters().get("applet") !=null && !data.getParameters().get("applet").equals("")){ message+=" "; ! } if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ //this means the link from the lab journal system is used, so we do not want immediate submit message+=" "; --- 400,404 ---- }else if(data.getParameters().get("applet") !=null && !data.getParameters().get("applet").equals("")){ message+=" "; ! }else if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ //this means the link from the lab journal system is used, so we do not want immediate submit message+=" "; |
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From: Stefan K. <sh...@us...> - 2006-11-11 15:42:24
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29620/src/vmtemplates/exporttemplates Modified Files: berkessel.vm griesbeck.vm schmalz.vm Log Message: worked on the exp section stuff Index: berkessel.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates/berkessel.vm,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** berkessel.vm 11 Nov 2006 12:17:31 -0000 1.1 --- berkessel.vm 11 Nov 2006 15:42:22 -0000 1.2 *************** *** 1,6 **** ! $spectrum.getDBMolecule().getMolecularFormula(false); $spectrum.getDBMolecule().get.getMolecularWeight() #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue()): delta = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.getMultiplicity()=="")#else$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum)J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file --- 1,6 ---- ! $molecule.getMolecularFormula(false); $molecule.getMolecularWeight() #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue()): delta = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.hasMultiplicity())$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum))J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file Index: griesbeck.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates/griesbeck.vm,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** griesbeck.vm 11 Nov 2006 12:17:31 -0000 1.1 --- griesbeck.vm 11 Nov 2006 15:42:22 -0000 1.2 *************** *** 1,5 **** #foreach($spectrum in $spectra) $spectrum.getDBSpectrumType().getName()-NMR: ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue()) ! delta (ppm) = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.getMultiplicity()=="")#else$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum)J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms()) #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file --- 1,5 ---- #foreach($spectrum in $spectra) $spectrum.getDBSpectrumType().getName()-NMR: ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue()) ! delta (ppm) = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.hasMultiplicity())$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum))J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms()) #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file Index: schmalz.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates/schmalz.vm,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** schmalz.vm 11 Nov 2006 12:17:31 -0000 1.3 --- schmalz.vm 11 Nov 2006 15:42:22 -0000 1.4 *************** *** 1,4 **** #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue(), #if($spectrum.getMeasurementConditionWithName("Temperature [K]").getValue()=="298")RT#else$spectrum.getMeasurementConditionWithName("Temperature [K]").getValue()#end): delta [ppm] = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.getMultiplicity()=="")#else$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum)J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file --- 1,4 ---- #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue(), #if($spectrum.getMeasurementConditionWithName("Temperature [K]").getValue()=="298")RT#else$spectrum.getMeasurementConditionWithName("Temperature [K]").getValue()#end): delta [ppm] = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.hasMultiplicity())$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum))J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file |
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From: Stefan K. <sh...@us...> - 2006-11-11 15:42:24
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29620/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSignal.java Log Message: worked on the exp section stuff Index: DBSignal.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSignal.java,v retrieving revision 1.18 retrieving revision 1.19 diff -C2 -r1.18 -r1.19 *** DBSignal.java 4 Aug 2005 21:55:20 -0000 1.18 --- DBSignal.java 11 Nov 2006 15:42:22 -0000 1.19 *************** *** 103,106 **** --- 103,115 ---- return (format.format(getIntensity())); } + + + /** + * Tells if a signal has a multiplictiy (i. e. if !getMulitplicity.equals("")) + * + * @return Does this has a multiplicity? + */ public boolean hasMultiplicity(){ + return !this.getMultiplicity().equals(""); + } } |
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From: Stefan K. <sh...@us...> - 2006-11-11 15:42:24
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29620/src/java/org/openscience/nmrshiftdb Modified Files: NmrshiftdbServlet.java Log Message: worked on the exp section stuff Index: NmrshiftdbServlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/NmrshiftdbServlet.java,v retrieving revision 1.97 retrieving revision 1.98 diff -C2 -r1.97 -r1.98 *** NmrshiftdbServlet.java 7 Nov 2006 14:44:42 -0000 1.97 --- NmrshiftdbServlet.java 11 Nov 2006 15:42:22 -0000 1.98 *************** *** 598,601 **** --- 598,602 ---- VelocityContext context = new VelocityContext(); context.put("spectra",v); + context.put("molecule",spectrum.getDBMolecule()); // lets render the template StringWriter w = new StringWriter(); |
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From: Stefan K. <sh...@us...> - 2006-11-11 15:42:24
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv29620/src/conf/jetspeed/WEB-INF/conf Modified Files: JetspeedResources.properties Log Message: worked on the exp section stuff Index: JetspeedResources.properties =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/conf/jetspeed/WEB-INF/conf/JetspeedResources.properties,v retrieving revision 1.24 retrieving revision 1.25 diff -C2 -r1.24 -r1.25 *** JetspeedResources.properties 22 Sep 2006 10:56:33 -0000 1.24 --- JetspeedResources.properties 11 Nov 2006 15:42:22 -0000 1.25 *************** *** 215,219 **** daemon.entry=buildhosecodetable #daemon.entry=buildsdf ! daemon.entry=buildsvm daemon.entry=robotdaemon --- 215,219 ---- daemon.entry=buildhosecodetable #daemon.entry=buildsdf ! #daemon.entry=buildsvm daemon.entry=robotdaemon |
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From: Stefan K. <sh...@us...> - 2006-11-11 12:17:42
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7559/src/vmtemplates/exporttemplates Modified Files: schmalz.vm Added Files: berkessel.vm griesbeck.vm Log Message: added more export templates --- NEW FILE: berkessel.vm --- $spectrum.getDBMolecule().getMolecularFormula(false); $spectrum.getDBMolecule().get.getMolecularWeight() #foreach($spectrum in $spectra) $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue()): delta = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.getMultiplicity()=="")#else$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum)J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end --- NEW FILE: griesbeck.vm --- #foreach($spectrum in $spectra) $spectrum.getDBSpectrumType().getName()-NMR: ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue()) delta (ppm) = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.getMultiplicity()=="")#else$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum)J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms()) #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end Index: schmalz.vm =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/vmtemplates/exporttemplates/schmalz.vm,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** schmalz.vm 9 Nov 2006 14:43:42 -0000 1.2 --- schmalz.vm 11 Nov 2006 12:17:31 -0000 1.3 *************** *** 1,4 **** #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue(), $spectrum.getMeasurementConditionWithName("Solvent").getValue(), RT): delta [ppm] = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() ($signal.getMultiplicity(),#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file --- 1,4 ---- #foreach($spectrum in $spectra) ! $spectrum.getDBSpectrumType().getName()-NMR ($spectrum.getMeasurementConditionWithName("Field Strength [MHz]").getValue() MHz, $spectrum.getMeasurementConditionWithName("Solvent").getValue(), #if($spectrum.getMeasurementConditionWithName("Temperature [K]").getValue()=="298")RT#else$spectrum.getMeasurementConditionWithName("Temperature [K]").getValue()#end): delta [ppm] = #foreach($signal in $spectrum.getDBSignals())$signal.getFirstShift().getValue() (#if($signal.getMultiplicity()=="")#else$signal.getMultiplicity(),#end#if($atom.hasCouplings($spectrum)J=$atom.getCouplingsString($spectrum) Hz, #end#foreach($atom in $signal.getAtoms())#if($spectrum.getDBSpectrumType().getName()=="1H")an#end #if($atom.getIdentifier($spectrum.getSpectrumId())=="")C-$atom.getMdlNumberPlus1Heavy()#else$atom.getIdentifier($spectrum.getSpectrumId())#end#end), #end #end \ No newline at end of file |
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From: Stefan K. <sh...@us...> - 2006-11-11 12:17:33
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv7559/src/java/org/openscience/nmrshiftdb/om Modified Files: DBAtom.java Log Message: added more export templates Index: DBAtom.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBAtom.java,v retrieving revision 1.56 retrieving revision 1.57 diff -C2 -r1.56 -r1.57 *** DBAtom.java 7 Nov 2006 14:44:42 -0000 1.56 --- DBAtom.java 11 Nov 2006 12:17:29 -0000 1.57 *************** *** 36,39 **** --- 36,40 ---- DBCoordinateSet2d coords2 = null; public boolean force3d=false; + private Vector couplings=null; *************** *** 363,366 **** --- 364,397 ---- /** + * Gets the couplings of this atom in a certain spectrum.as a string + * + * @param spectrum The spectrum. + * @return The couplings. + * @exception Exception Database problems. + */ + public boolean hasCouplings(DBSpectrum spectrum) throws Exception { + getCouplings(spectrum); + return couplings.size()>0; + } + + + /** + * Gets the couplings of this atom in a certain spectrum.as a string + * + * @param spectrum The spectrum. + * @return The couplings. + * @exception Exception Database problems. + */ + public String getCouplingsString(DBSpectrum spectrum) throws Exception { + getCouplings(spectrum); + StringBuffer couplingsstring=new StringBuffer(); + for(int i=0;i<couplings.size();i++){ + couplingsstring.append(((DBCoupling)couplings.get(i)).getConstant()+","); + } + return (GeneralUtils.removeLastComma(couplingsstring).toString()); + } + + + /** * Gets the couplings of this atom in a certain spectrum. * *************** *** 370,383 **** */ public Vector getCouplings(DBSpectrum spectrum) throws Exception { ! Criteria crit = new Criteria(); ! crit.add(DBCouplingPeer.ATOM_ID_1, getAtomId()); ! crit.add(DBCouplingPeer.SPECTRUM_ID, spectrum.getSpectrumId()); ! Vector v1 = DBCouplingPeer.doSelect(crit); ! crit = new Criteria(); ! crit.add(DBCouplingPeer.ATOM_ID_2, getAtomId()); ! crit.add(DBCouplingPeer.SPECTRUM_ID, spectrum.getSpectrumId()); ! Vector v2 = DBCouplingPeer.doSelect(crit); ! v2.addAll(v1); ! return (v2); } --- 401,417 ---- */ public Vector getCouplings(DBSpectrum spectrum) throws Exception { ! if(couplings==null){ ! Criteria crit = new Criteria(); ! crit.add(DBCouplingPeer.ATOM_ID_1, getAtomId()); ! crit.add(DBCouplingPeer.SPECTRUM_ID, spectrum.getSpectrumId()); ! Vector v1 = DBCouplingPeer.doSelect(crit); ! crit = new Criteria(); ! crit.add(DBCouplingPeer.ATOM_ID_2, getAtomId()); ! crit.add(DBCouplingPeer.SPECTRUM_ID, spectrum.getSpectrumId()); ! Vector v2 = DBCouplingPeer.doSelect(crit); ! couplings=new Vector(); ! couplings.addAll(v1); ! } ! return (couplings); } |
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From: Stefan K. <sh...@us...> - 2006-11-10 14:14:15
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv18623/src/java/org/openscience/nmrshiftdb/portlets Modified Files: ResultPortlet.java Log Message: this should include the possibility of external link for submitting to lab system, but this is not working and I do not know why Index: ResultPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ResultPortlet.java,v retrieving revision 1.286 retrieving revision 1.287 diff -C2 -r1.286 -r1.287 *** ResultPortlet.java 9 Nov 2006 14:43:42 -0000 1.286 --- ResultPortlet.java 10 Nov 2006 14:14:06 -0000 1.287 *************** *** 20,23 **** --- 20,24 ---- import org.apache.ecs.StringElement; import org.apache.jetspeed.portal.portlets.AbstractPortlet; + import org.apache.turbine.modules.ActionLoader; import org.apache.turbine.om.NumberKey; import org.apache.turbine.om.security.User; *************** *** 118,150 **** if(action.equals("submitfromlabjournal")){ try{ ! String username = runData.getParameters().get("username"); ! String password = runData.getParameters().get("password"); ! User user = null; ! // Authenticate the user and get the object. ! user = TurbineSecurity.getAuthenticatedUser(username, password); ! ! ! // Store the user object. ! runData.setUser(user); ! ! // Mark the user as being logged in. ! user.setHasLoggedIn(new Boolean(true)); ! ! // Set the last_login date in the database. ! user.updateLastLogin(); ! ! // This only happens if the user is valid; otherwise, we ! // will get a valueBound in the User object when we don't ! // want to because the username is not set yet. Save the ! // User object into the session. ! runData.save(); ! //this.doSubmitorder(data, context); ! ! runData.getResponse().sendError(302,"www.web.de"); }catch(Exception ex){ ex.printStackTrace(); } ! ! return(new StringElement("<head><meta HTTP-EQUIV=\"REFRESH\" content=\"0; url=http://www.yourdomain.com/index.html/"+runData.getSession().getId()+"\"></head><a href=\"\">If you are not redirected, please click here</a>")); } //The molecule displaying starts with 0 if new search --- 119,127 ---- if(action.equals("submitfromlabjournal")){ try{ ! ActionLoader.getInstance().exec(runData, "LoginUser"); }catch(Exception ex){ ex.printStackTrace(); } ! return(new StringElement("<head><meta HTTP-EQUIV=\"REFRESH\" content=\"0; url=http://127.0.0.1:8080/portal/pane0/Results;jsessionid="+runData.getSession().getId()+"\"></head><a href=\"\">If you are not redirected, please click here</a>")); } //The molecule displaying starts with 0 if new search |
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From: Stefan K. <sh...@us...> - 2006-11-10 14:14:13
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv18623/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: this should include the possibility of external link for submitting to lab system, but this is not working and I do not know why Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.38 retrieving revision 1.39 diff -C2 -r1.38 -r1.39 *** OrderAction.java 9 Nov 2006 14:43:42 -0000 1.38 --- OrderAction.java 10 Nov 2006 14:14:05 -0000 1.39 *************** *** 84,116 **** try{ context.put("ordertype",OrderAction.WORKER); ! if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ ! String username = data.getParameters().get("username"); ! String password = data.getParameters().get("password"); ! User user = null; ! // Authenticate the user and get the object. ! user = TurbineSecurity.getAuthenticatedUser(username, password); ! ! ! // Store the user object. ! data.setUser(user); ! ! // Mark the user as being logged in. ! user.setHasLoggedIn(new Boolean(true)); ! ! // Set the last_login date in the database. ! user.updateLastLogin(); ! ! // This only happens if the user is valid; otherwise, we ! // will get a valueBound in the User object when we don't ! // want to because the username is not set yet. Save the ! // User object into the session. ! data.save(); ! //this.doSubmitorder(data, context); ! ! data.getResponse().sendError(302,"www.web.de"); ! ! }else{ ! buildOrderContext(context,data); ! } } catch(Exception ex){ --- 84,88 ---- try{ context.put("ordertype",OrderAction.WORKER); ! buildOrderContext(context,data); } catch(Exception ex){ *************** *** 429,433 **** message+=" "; } if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ ! //this means the link from the lab journal system is used message+=" "; }else{ --- 401,405 ---- message+=" "; } if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ ! //this means the link from the lab journal system is used, so we do not want immediate submit message+=" "; }else{ |
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From: Stefan K. <sh...@us...> - 2006-11-10 14:14:12
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv18623/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: this should include the possibility of external link for submitting to lab system, but this is not working and I do not know why Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.193 retrieving revision 1.194 diff -C2 -r1.193 -r1.194 *** DBSpectrum.java 9 Nov 2006 14:43:42 -0000 1.193 --- DBSpectrum.java 10 Nov 2006 14:14:06 -0000 1.194 *************** *** 884,888 **** substance.setDictRef(condtype.getDictRef()); substance.setRole(condtype.getUnits()); ! substance.appendChild(condition.getValue()); sl.addSubstance(substance); } --- 884,888 ---- substance.setDictRef(condtype.getDictRef()); substance.setRole(condtype.getUnits()); ! substance.setTitle(condition.getValue()); sl.addSubstance(substance); } |
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From: Stefan K. <sh...@us...> - 2006-11-09 14:43:55
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19751/src/java/org/openscience/nmrshiftdb/om Modified Files: DBSpectrum.java Log Message: submits of h spectra also possible with h shifts assigned to heavy atoms Index: DBSpectrum.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/om/DBSpectrum.java,v retrieving revision 1.192 retrieving revision 1.193 diff -C2 -r1.192 -r1.193 *** DBSpectrum.java 25 Oct 2006 10:51:09 -0000 1.192 --- DBSpectrum.java 9 Nov 2006 14:43:42 -0000 1.193 *************** *** 206,214 **** * @exception Exception Database problems. */ ! /** ! * @return ! * @throws Exception ! */ ! public Vector getOptions() throws Exception { if (options == null) { if(runData!=null && runData.getSession().getAttribute("trueonly")==null) --- 206,210 ---- * @exception Exception Database problems. */ ! public Vector getOptions() throws Exception { if (options == null) { if(runData!=null && runData.getSession().getAttribute("trueonly")==null) |
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From: Stefan K. <sh...@us...> - 2006-11-09 14:43:54
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19751/src/java/org/openscience/nmrshiftdb/portlets Modified Files: ResultPortlet.java Log Message: submits of h spectra also possible with h shifts assigned to heavy atoms Index: ResultPortlet.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/portlets/ResultPortlet.java,v retrieving revision 1.285 retrieving revision 1.286 diff -C2 -r1.285 -r1.286 *** ResultPortlet.java 18 Oct 2006 13:07:27 -0000 1.285 --- ResultPortlet.java 9 Nov 2006 14:43:42 -0000 1.286 *************** *** 21,24 **** --- 21,26 ---- import org.apache.jetspeed.portal.portlets.AbstractPortlet; import org.apache.turbine.om.NumberKey; + import org.apache.turbine.om.security.User; + import org.apache.turbine.services.security.TurbineSecurity; import org.apache.turbine.util.Log; import org.apache.turbine.util.RunData; *************** *** 114,117 **** --- 116,151 ---- } } + if(action.equals("submitfromlabjournal")){ + try{ + String username = runData.getParameters().get("username"); + String password = runData.getParameters().get("password"); + User user = null; + // Authenticate the user and get the object. + user = TurbineSecurity.getAuthenticatedUser(username, password); + + + // Store the user object. + runData.setUser(user); + + // Mark the user as being logged in. + user.setHasLoggedIn(new Boolean(true)); + + // Set the last_login date in the database. + user.updateLastLogin(); + + // This only happens if the user is valid; otherwise, we + // will get a valueBound in the User object when we don't + // want to because the username is not set yet. Save the + // User object into the session. + runData.save(); + //this.doSubmitorder(data, context); + + runData.getResponse().sendError(302,"www.web.de"); + }catch(Exception ex){ + ex.printStackTrace(); + } + + return(new StringElement("<head><meta HTTP-EQUIV=\"REFRESH\" content=\"0; url=http://www.yourdomain.com/index.html/"+runData.getSession().getId()+"\"></head><a href=\"\">If you are not redirected, please click here</a>")); + } //The molecule displaying starts with 0 if new search int startMolecule = 0; |
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From: Stefan K. <sh...@us...> - 2006-11-09 14:43:52
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19751/src/java/org/openscience/nmrshiftdb/webservices Modified Files: NMRShiftDBServiceBindingImpl.java Log Message: submits of h spectra also possible with h shifts assigned to heavy atoms Index: NMRShiftDBServiceBindingImpl.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/webservices/NMRShiftDBServiceBindingImpl.java,v retrieving revision 1.34 retrieving revision 1.35 diff -C2 -r1.34 -r1.35 *** NMRShiftDBServiceBindingImpl.java 26 Oct 2006 17:18:48 -0000 1.34 --- NMRShiftDBServiceBindingImpl.java 9 Nov 2006 14:43:42 -0000 1.35 *************** *** 10,13 **** --- 10,14 ---- import java.util.Date; import java.util.HashMap; + import java.util.Iterator; import java.util.List; import java.util.Properties; *************** *** 260,264 **** for(int l=0;l<atomrefs.length;l++){ IAtom atom=AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l]); ! vt.atoms.add(atom); } subData.getSignalstable().add(vt); --- 261,275 ---- for(int l=0;l<atomrefs.length;l++){ IAtom atom=AtomContainerManipulator.getAtomById(subData.getMolWithH(),atomrefs[l]); ! if(subData.getChoosenSpectrumType().getName().equals("1H") && !atom.getSymbol().equals("H")){ ! Iterator it=subData.getMolWithH().getConnectedAtomsList(atom).iterator(); ! while(it.hasNext()){ ! IAtom connatom=(IAtom)it.next(); ! if(connatom.getSymbol().equals("H")){ ! vt.atoms.add(connatom); ! } ! } ! }else{ ! vt.atoms.add(atom); ! } } subData.getSignalstable().add(vt); |
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From: Stefan K. <sh...@us...> - 2006-11-09 14:43:50
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Update of /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets In directory sc8-pr-cvs7.sourceforge.net:/tmp/cvs-serv19751/src/java/org/openscience/nmrshiftdb/modules/actions/portlets Modified Files: OrderAction.java Log Message: submits of h spectra also possible with h shifts assigned to heavy atoms Index: OrderAction.java =================================================================== RCS file: /cvsroot/nmrshiftdb/nmrshiftdb/src/java/org/openscience/nmrshiftdb/modules/actions/portlets/OrderAction.java,v retrieving revision 1.37 retrieving revision 1.38 diff -C2 -r1.37 -r1.38 *** OrderAction.java 6 Nov 2006 13:40:07 -0000 1.37 --- OrderAction.java 9 Nov 2006 14:43:42 -0000 1.38 *************** *** 16,19 **** --- 16,21 ---- import org.apache.jetspeed.portal.portlets.VelocityPortlet; import org.apache.turbine.om.NumberKey; + import org.apache.turbine.om.security.User; + import org.apache.turbine.services.security.TurbineSecurity; import org.apache.turbine.util.RunData; import org.apache.turbine.util.ServletUtils; *************** *** 80,90 **** */ protected void buildNormalContext(VelocityPortlet portlet, Context context, RunData data) { ! try{ ! context.put("ordertype",OrderAction.WORKER); ! buildOrderContext(context,data); ! } ! catch(Exception ex){ ! GeneralUtils.logError(ex,"order action",data,true); ! } } --- 82,120 ---- */ protected void buildNormalContext(VelocityPortlet portlet, Context context, RunData data) { ! try{ ! context.put("ordertype",OrderAction.WORKER); ! if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ ! String username = data.getParameters().get("username"); ! String password = data.getParameters().get("password"); ! User user = null; ! // Authenticate the user and get the object. ! user = TurbineSecurity.getAuthenticatedUser(username, password); ! ! ! // Store the user object. ! data.setUser(user); ! ! // Mark the user as being logged in. ! user.setHasLoggedIn(new Boolean(true)); ! ! // Set the last_login date in the database. ! user.updateLastLogin(); ! ! // This only happens if the user is valid; otherwise, we ! // will get a valueBound in the User object when we don't ! // want to because the username is not set yet. Save the ! // User object into the session. ! data.save(); ! //this.doSubmitorder(data, context); ! ! data.getResponse().sendError(302,"www.web.de"); ! ! }else{ ! buildOrderContext(context,data); ! } ! } ! catch(Exception ex){ ! GeneralUtils.logError(ex,"order action",data,true); ! } } *************** *** 343,347 **** } }else{ ! if(data.getRequest().getContentType().indexOf("multipart/form-data")>-1){ FileItem[] fi = data.getParameters().getFileItems("datei"); if(fi!=null){ --- 373,377 ---- } }else{ ! if(data.getRequest().getContentType()!=null && data.getRequest().getContentType().indexOf("multipart/form-data")>-1){ FileItem[] fi = data.getParameters().getFileItems("datei"); if(fi!=null){ *************** *** 398,403 **** }else if(data.getParameters().get("applet") !=null && !data.getParameters().get("applet").equals("")){ message+=" "; }else{ ! sample.save(); } if(!message.equals("")){ --- 428,436 ---- }else if(data.getParameters().get("applet") !=null && !data.getParameters().get("applet").equals("")){ message+=" "; + } if(data.getParameters().getString("nmrshiftdbaction","none").equals("submitfromlabjournal")){ + //this means the link from the lab journal system is used + message+=" "; }else{ ! sample.save(); } if(!message.equals("")){ |
