Changeset 3873


Ignore:
Timestamp:
Sep 29, 2010, 11:24:15 AM (13 years ago)
Author:
Gregory Vincic
Message:

Refs #698. Removed method getPIKEParameterSetForm from FormFactory and placed it within the one action that uses it.

Location:
trunk/client/servlet/src/org/proteios
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • trunk/client/servlet/src/org/proteios/action/file/UseProteinListFileForPIKESearchExtension.java

    r3461 r3873  
    3030import org.proteios.action.ProteiosAction;
    3131import org.proteios.action.pike.SearchPIKE;
    32 //import org.proteios.action.pike.ViewActivePIKEParameterSetStorage;
    3332import org.proteios.core.DbControl;
    3433import org.proteios.core.Include;
    3534import org.proteios.core.ItemQuery;
    36 //import org.proteios.core.PIKEParameterSetStorage;
    3735import org.proteios.core.User;
    3836import org.proteios.gui.Title;
    3937import org.proteios.gui.Toolbar;
    40 import org.proteios.gui.form.Form;
    41 import org.proteios.gui.form.FormFactory;
     38import org.proteios.gui.form.*;
    4239import org.proteios.gui.form.Option;
    4340import org.proteios.gui.layout.RowLayout;
    … …  
    4845import se.lu.thep.waf.ActionException;
    4946import se.lu.thep.waf.constraints.InvalidParameterValue;
     47import se.lu.thep.waf.constraints.VString;
    5048
    5149import java.util.ArrayList;
    … …  
    103101     */
    104102    DbControl dc = newDbControl();
    105     // Get PIKE parameter set option alternatives
    106     /*
    107     // Get PIKEParameterSetOptionsUtil instance
    108     PIKEParameterSetOptionsUtil pikeParameterSetOptionUtil = new PIKEParameterSetOptionsUtil();
    109     //pikeParameterSetOptionUtil.setWebInterfaceUsed(useWebInterfaceFlag);
    110     // Get source database option data
    111     List<String> sourceDatabaseStringList = pikeParameterSetOptionUtil.fetchSourceDatabaseStringList();
    112     List<Option> sourceDatabaseOptionList = stringListToOptionList(sourceDatabaseStringList);
    113     // Get field select option data
    114     List<String> fieldSelectStringList = pikeParameterSetOptionUtil.fetchFieldSelectStringList();
    115     List<Option> fieldSelectOptionList = stringListToOptionList(fieldSelectStringList);
    116     // Get input file type option data
    117     List<String> inputFileTypeStringList = pikeParameterSetOptionUtil.fetchInputFileTypeStringList();
    118     List<Option> inputFileTypeOptionList = stringListToOptionList(inputFileTypeStringList);
    119     */
    120103    List<Option> sourceDatabaseOptionList = null;
    121104    List<Option> fieldSelectOptionList = null;
    … …  
    134117    pikeOutputFileTypeList.add(new String("csv"));
    135118    // PIKE parameter set form
    136     Form pikeParameterSetForm = getFormFactory().getPIKEParameterSetForm(
     119    Form pikeParameterSetForm = getPIKEParameterSetForm(
    137120      pikeUserName,
    138121      pikeUserMail,
    … …  
    148131      outputFileTypeOptionList);
    149132    /***********************************************************************
    150      * Table of PIKE Inputs
    151      */
    152     /*
    153     TableFactory tableFactory = getTableFactory();
    154     tableFactory.setItemClass(PIKEParameterSetStorage.class);
    155     ItemQuery<PIKEParameterSetStorage> query = PIKEParameterSetStorage.getQuery();
    156     // Only include PIKEParameterSetStorage belonging to the active project.
    157     query.include(Include.IN_PROJECT);
    158     query.setCacheResult(false);
    159     tableFactory.setQuery(query);
    160     tableFactory.setSelectCheckBoxColumnHidden(false);
    161     // Build table
    162     Table table = tableFactory.build();
    163     table.setTitle("PIKEParameterSetsInDatabase");
    164     // Add the tool bar with 'Next' button(s) to the form.
    165     Toolbar toolbar = new Toolbar();
    166     // Add 'Next' button to create search jobs
    167     ActionLink nextSearch = getActionFactory().getActionLink(
    168       SearchPIKE.class, "NextPIKECreateSearchJobs");
    169     for (Integer proteinListFileId : proteinListFileIds)
    170     {
    171       nextSearch.addParameter(SearchPIKE.VPROTEINLISTFILEID, proteinListFileId);
    172     }
    173     nextSearch.addParameter(SearchPIKE.VPIKEUSEWEBINTERFACEFLAG, true);
    174     toolbar.add(nextSearch);
    175     // Add 'Next' button to edit parameters before creating search jobs
    176     ActionLink nextEdit = getActionFactory().getActionLink(
    177       ViewActivePIKEParameterSetStorage.class, "NextPIKEEditParametersBeforeCreatingSearchJobs");
    178     for (Integer proteinListFileId : proteinListFileIds)
    179     {
    180       nextEdit.addParameter(SearchPIKE.VPROTEINLISTFILEID, proteinListFileId);
    181     }
    182     nextEdit.addParameter(SearchPIKE.VPIKEUSEWEBINTERFACEFLAG, true);
    183     toolbar.add(nextEdit);
    184     //
    185     table.setToolbar(toolbar);
    186     // Build and set the layout used to display our form
    187     RowLayout layout = getLayoutFactory().getRowLayout();
    188     layout.add(new Title("SelectPIKEParameterSetStorage"));
    189     //layout.add(selectForm);
    190     layout.add(table);
    191     setLayout(layout);
    192     */
    193     /***********************************************************************
    194133     * Toolbar
    195134     */
    … …  
    245184
    246185
     186  public Form getPIKEParameterSetForm(String pikeUserName,
     187      String pikeUserMail, String pikeSourceDatabase,
     188      List<String> pikeFieldSelectList, String pikeGeneOntologyCheck,
     189      String pikeMaxDeep, String pikeInputFileType,
     190      List<String> pikeOutputFileTypeList,
     191      List<Option> sourceDatabaseOptionList,
     192      List<Option> fieldSelectOptionList,
     193      List<Option> inputFileTypeOptionList,
     194      List<Option> outputFileTypeOptionList)
     195  {
     196    Form form = new Form("PIKEParameterSetForm");
     197    /*
     198     * String select box variables
     199     */
     200    VString validStringParam = null;
     201    List<String> stringList = null;
     202    List<Option> optionList = null;
     203    String selected = null;
     204    List<String> selectedList = null;
     205    /*
     206     * Input field set
     207     */
     208    Fieldset inputFS = new Fieldset();
     209    inputFS.setTitle("PIKEParameterSetInput");
     210    form.addFieldset(inputFS);
     211    //
     212    // Input, user name
     213    TextField<String> userName = new TextField<String>(SearchPIKE.VPIKEUSERNAME);
     214    userName.setLabel("PIKEUserNameInput");
     215    userName.setValue(pikeUserName);
     216    inputFS.add(userName);
     217    //
     218    // Input, user e-mail
     219    TextField<String> userMail = new TextField<String>(SearchPIKE.VPIKEUSERMAIL);
     220    userMail.setLabel("PIKEUserMailInput");
     221    userMail.setValue(pikeUserMail);
     222    inputFS.add(userMail);
     223    //
     224    // Input, source database
     225    validStringParam = SearchPIKE.VPIKESOURCEDATABASE;
     226    optionList = new ArrayList<Option>();
     227    optionList.add(new Option("NCBI", "NCBI nr"));
     228    optionList.add(new Option("SP", "SwissProt / UniProt"));
     229    optionList.add(new Option("IPI", "IPI"));
     230    // Use input source database option list if present
     231    if (sourceDatabaseOptionList != null && sourceDatabaseOptionList.size() > 0)
     232    {
     233      optionList = sourceDatabaseOptionList;
     234    }
     235    selected = pikeSourceDatabase;
     236    Select<VString> sourceDatabaseSelectBox = new Select<VString>(validStringParam, optionList);
     237  sourceDatabaseSelectBox.selectOption( selected);
     238    sourceDatabaseSelectBox.setLabel("PIKESourceDatabaseSelect");
     239    inputFS.add(sourceDatabaseSelectBox);
     240    //
     241    // input, field select list (multiple selection)
     242    validStringParam = SearchPIKE.VPIKEFIELDSELECT;
     243    optionList = new ArrayList<Option>();
     244    optionList.add(new Option("0_Protein name", "Protein name"));
     245    optionList.add(new Option("0_Gene name", "Gene name"));
     246    optionList.add(new Option("1_FUNCTION", "Function"));
     247    optionList.add(new Option("1_SUBCELLULAR LOCATION",
     248      "Subcellular location"));
     249    optionList
     250      .add(new Option("1_TISSUE SPECIFICITY", "Tissue specificity"));
     251    optionList.add(new Option("1_DISEASE", "Disease"));
     252    optionList.add(new Option("2_dbxref?GO", "Gene Ontology Terms"));
     253    optionList.add(new Option("2_dbxref?MIM", "MIM References"));
     254    optionList.add(new Option("4_dbxref?KEGG", "KEGG Pathways"));
     255    optionList.add(new Option("3_Keywords", "Keywords"));
     256    optionList.add(new Option("5_Intact", "IntAct Interactions"));
     257    // Use input field select option list if present
     258    if (fieldSelectOptionList != null && fieldSelectOptionList.size() > 0)
     259    {
     260      optionList = fieldSelectOptionList;
     261    }
     262    selectedList = pikeFieldSelectList;
     263    Select<VString> fieldSelect = new Select<VString>(
     264      validStringParam, optionList, selectedList);
     265    fieldSelect.setLabel("PIKEFieldSelect");
     266    fieldSelect.setMultiple(true);
     267    fieldSelect.setSize(8);
     268    inputFS.add(fieldSelect);
     269    //
     270    // Input, gene ontology check
     271    validStringParam = SearchPIKE.VPIKEGENEONTOLOGYCHECK;
     272    optionList = new ArrayList<Option>();
     273    optionList.add(new Option("1", "yes"));
     274    optionList.add(new Option("0", "no"));
     275    selected = pikeGeneOntologyCheck;
     276    Select<VString> geneOntologyCheckSelectBox = new Select<VString>(
     277      validStringParam, optionList);
     278  geneOntologyCheckSelectBox.selectOption( selected);
     279    geneOntologyCheckSelectBox.setLabel("PIKEGeneOntologyCheckSelect");
     280    inputFS.add(geneOntologyCheckSelectBox);
     281    //
     282    // Input, max deep
     283    TextField<String> maxDeep = new TextField<String>(SearchPIKE.VPIKEMAXDEEP);
     284    maxDeep.setLabel("PIKEMaxDeepInput");
     285    maxDeep.setValue(pikeMaxDeep);
     286    inputFS.add(maxDeep);
     287    //
     288    // Input, input file type
     289    validStringParam = SearchPIKE.VPIKEINPUTFILETYPE;
     290    optionList = new ArrayList<Option>();
     291    optionList.add(new Option("xml", ".XML (PRIDE XML)"));
     292    optionList.add(new Option("txt",
     293      ".TXT (<b>Format:</b> accession_code(tab)protein_name(new line))"));
     294    // Use input input file type option list if present
     295    if (inputFileTypeOptionList != null && inputFileTypeOptionList.size() > 0)
     296    {
     297      optionList = inputFileTypeOptionList;
     298    }
     299    selected = pikeInputFileType;
     300    Select<VString> inputFileTypeSelectBox = new Select<VString>(
     301      validStringParam, optionList);
     302  inputFileTypeSelectBox.selectOption( selected);
     303    inputFileTypeSelectBox.setLabel("PIKEInputFileTypeSelect");
     304    inputFS.add(inputFileTypeSelectBox);
     305    /*
     306     * Output field set
     307     */
     308    Fieldset outputFS = new Fieldset();
     309    outputFS.setTitle("PIKEParameterSetOutput");
     310    form.addFieldset(outputFS);
     311    //
     312    // Output, output file type list (multiple selection)
     313    validStringParam = SearchPIKE.VPIKEOUTPUTFILETYPE;
     314    optionList = new ArrayList<Option>();
     315    optionList.add(new Option("xml", "PRIDE XML"));
     316    optionList.add(new Option("csv", "CSV"));
     317    // Use input output file type option list if present
     318    if (outputFileTypeOptionList != null && outputFileTypeOptionList.size() > 0)
     319    {
     320      optionList = outputFileTypeOptionList;
     321    }
     322    selectedList = pikeOutputFileTypeList;
     323    Select<VString> outputFileTypeSelect = new Select<VString>(
     324      validStringParam, optionList, selectedList);
     325    outputFileTypeSelect.setLabel("PIKEOutputFileTypeSelect");
     326    outputFileTypeSelect.setMultiple(true);
     327    outputFileTypeSelect.setSize(optionList.size());
     328    // Disable output file type select box for now
     329    // outputFileTypeSelect.setDisabled(true);
     330    outputFS.add(outputFileTypeSelect);
     331    //
     332    return form;
     333  }
     334
     335
    247336  /**
    248337   * Tell the application in which context this action should be available

  • trunk/client/servlet/src/org/proteios/gui/form/FormFactory.java

    r3872 r3873  
    22132213
    22142214
    2215   public Form getPIKEParameterSetForm(String pikeUserName,
    2216       String pikeUserMail, String pikeSourceDatabase,
    2217       List<String> pikeFieldSelectList, String pikeGeneOntologyCheck,
    2218       String pikeMaxDeep, String pikeInputFileType,
    2219       List<String> pikeOutputFileTypeList,
    2220       List<Option> sourceDatabaseOptionList,
    2221       List<Option> fieldSelectOptionList,
    2222       List<Option> inputFileTypeOptionList,
    2223       List<Option> outputFileTypeOptionList)
    2224   {
    2225     Form form = new Form("PIKEParameterSetForm");
    2226     /*
    2227      * String select box variables
    2228      */
    2229     VString validStringParam = null;
    2230     List<String> stringList = null;
    2231     List<Option> optionList = null;
    2232     String selected = null;
    2233     List<String> selectedList = null;
    2234     /*
    2235      * Input field set
    2236      */
    2237     Fieldset inputFS = new Fieldset();
    2238     inputFS.setTitle("PIKEParameterSetInput");
    2239     form.addFieldset(inputFS);
    2240     //
    2241     // Input, user name
    2242     TextField<String> userName = new TextField<String>(SearchPIKE.VPIKEUSERNAME);
    2243     userName.setLabel("PIKEUserNameInput");
    2244     userName.setValue(pikeUserName);
    2245     inputFS.add(userName);
    2246     //
    2247     // Input, user e-mail
    2248     TextField<String> userMail = new TextField<String>(SearchPIKE.VPIKEUSERMAIL);
    2249     userMail.setLabel("PIKEUserMailInput");
    2250     userMail.setValue(pikeUserMail);
    2251     inputFS.add(userMail);
    2252     //
    2253     // Input, source database
    2254     validStringParam = SearchPIKE.VPIKESOURCEDATABASE;
    2255     optionList = new ArrayList<Option>();
    2256     optionList.add(new Option("NCBI", "NCBI nr"));
    2257     optionList.add(new Option("SP", "SwissProt / UniProt"));
    2258     optionList.add(new Option("IPI", "IPI"));
    2259     // Use input source database option list if present
    2260     if (sourceDatabaseOptionList != null && sourceDatabaseOptionList.size() > 0)
    2261     {
    2262       optionList = sourceDatabaseOptionList;
    2263     }
    2264     selected = pikeSourceDatabase;
    2265     Select<VString> sourceDatabaseSelectBox = new Select<VString>(validStringParam, optionList);
    2266   sourceDatabaseSelectBox.selectOption( selected);
    2267     sourceDatabaseSelectBox.setLabel("PIKESourceDatabaseSelect");
    2268     inputFS.add(sourceDatabaseSelectBox);
    2269     //
    2270     // input, field select list (multiple selection)
    2271     validStringParam = SearchPIKE.VPIKEFIELDSELECT;
    2272     optionList = new ArrayList<Option>();
    2273     optionList.add(new Option("0_Protein name", "Protein name"));
    2274     optionList.add(new Option("0_Gene name", "Gene name"));
    2275     optionList.add(new Option("1_FUNCTION", "Function"));
    2276     optionList.add(new Option("1_SUBCELLULAR LOCATION",
    2277       "Subcellular location"));
    2278     optionList
    2279       .add(new Option("1_TISSUE SPECIFICITY", "Tissue specificity"));
    2280     optionList.add(new Option("1_DISEASE", "Disease"));
    2281     optionList.add(new Option("2_dbxref?GO", "Gene Ontology Terms"));
    2282     optionList.add(new Option("2_dbxref?MIM", "MIM References"));
    2283     optionList.add(new Option("4_dbxref?KEGG", "KEGG Pathways"));
    2284     optionList.add(new Option("3_Keywords", "Keywords"));
    2285     optionList.add(new Option("5_Intact", "IntAct Interactions"));
    2286     // Use input field select option list if present
    2287     if (fieldSelectOptionList != null && fieldSelectOptionList.size() > 0)
    2288     {
    2289       optionList = fieldSelectOptionList;
    2290     }
    2291     selectedList = pikeFieldSelectList;
    2292     Select<VString> fieldSelect = new Select<VString>(
    2293       validStringParam, optionList, selectedList);
    2294     fieldSelect.setLabel("PIKEFieldSelect");
    2295     fieldSelect.setMultiple(true);
    2296     fieldSelect.setSize(8);
    2297     inputFS.add(fieldSelect);
    2298     //
    2299     // Input, gene ontology check
    2300     validStringParam = SearchPIKE.VPIKEGENEONTOLOGYCHECK;
    2301     optionList = new ArrayList<Option>();
    2302     optionList.add(new Option("1", "yes"));
    2303     optionList.add(new Option("0", "no"));
    2304     selected = pikeGeneOntologyCheck;
    2305     Select<VString> geneOntologyCheckSelectBox = new Select<VString>(
    2306       validStringParam, optionList);
    2307   geneOntologyCheckSelectBox.selectOption( selected);
    2308     geneOntologyCheckSelectBox.setLabel("PIKEGeneOntologyCheckSelect");
    2309     inputFS.add(geneOntologyCheckSelectBox);
    2310     //
    2311     // Input, max deep
    2312     TextField<String> maxDeep = new TextField<String>(SearchPIKE.VPIKEMAXDEEP);
    2313     maxDeep.setLabel("PIKEMaxDeepInput");
    2314     maxDeep.setValue(pikeMaxDeep);
    2315     inputFS.add(maxDeep);
    2316     //
    2317     // Input, input file type
    2318     validStringParam = SearchPIKE.VPIKEINPUTFILETYPE;
    2319     optionList = new ArrayList<Option>();
    2320     optionList.add(new Option("xml", ".XML (PRIDE XML)"));
    2321     optionList.add(new Option("txt",
    2322       ".TXT (<b>Format:</b> accession_code(tab)protein_name(new line))"));
    2323     // Use input input file type option list if present
    2324     if (inputFileTypeOptionList != null && inputFileTypeOptionList.size() > 0)
    2325     {
    2326       optionList = inputFileTypeOptionList;
    2327     }
    2328     selected = pikeInputFileType;
    2329     Select<VString> inputFileTypeSelectBox = new Select<VString>(
    2330       validStringParam, optionList);
    2331   inputFileTypeSelectBox.selectOption( selected);
    2332     inputFileTypeSelectBox.setLabel("PIKEInputFileTypeSelect");
    2333     inputFS.add(inputFileTypeSelectBox);
    2334     /*
    2335      * Output field set
    2336      */
    2337     Fieldset outputFS = new Fieldset();
    2338     outputFS.setTitle("PIKEParameterSetOutput");
    2339     form.addFieldset(outputFS);
    2340     //
    2341     // Output, output file type list (multiple selection)
    2342     validStringParam = SearchPIKE.VPIKEOUTPUTFILETYPE;
    2343     optionList = new ArrayList<Option>();
    2344     optionList.add(new Option("xml", "PRIDE XML"));
    2345     optionList.add(new Option("csv", "CSV"));
    2346     // Use input output file type option list if present
    2347     if (outputFileTypeOptionList != null && outputFileTypeOptionList.size() > 0)
    2348     {
    2349       optionList = outputFileTypeOptionList;
    2350     }
    2351     selectedList = pikeOutputFileTypeList;
    2352     Select<VString> outputFileTypeSelect = new Select<VString>(
    2353       validStringParam, optionList, selectedList);
    2354     outputFileTypeSelect.setLabel("PIKEOutputFileTypeSelect");
    2355     outputFileTypeSelect.setMultiple(true);
    2356     outputFileTypeSelect.setSize(optionList.size());
    2357     // Disable output file type select box for now
    2358     // outputFileTypeSelect.setDisabled(true);
    2359     outputFS.add(outputFileTypeSelect);
    2360     //
    2361     return form;
    2362   }
    2363 
    23642215
    23652216  /**
    … …  
    30222873      methodArr = itemClass.getMethods();
    30232874    }
    3024     log
    3025       .debug("FormFactory::getFormImpl(): methodArr.length = " + methodArr.length);
    3026     for (int i = 0; i < methodArr.length; i++)
    3027     {
    3028       log
    3029         .debug("FormFactory::getFormImpl(): methodArr[" + i + "].getName() = \"" + methodArr[i]
    3030           .getName() + "\"");
    3031     }
     2875
    30322876    /*
    30332877     * Methods declared in object class (not inherited)
    … …  
    30382882      declaredMethodArr = itemClass.getDeclaredMethods();
    30392883    }
    3040     log
    3041       .debug("FormFactory::getFormImpl(): declaredMethodArr.length = " + declaredMethodArr.length);
    30422884    for (int i = 0; i < declaredMethodArr.length; i++)
    30432885    {
    … …  
    30512893      if (!getExcludedDeclMethods().contains(methodName))
    30522894      {
    3053         log
    3054           .debug("FormFactory::getFormImpl(): " + modStr + " " + methodReturnType + " declaredMethodArr[" + i + "].getName() = \"" + methodName + "\"");
    30552895        String attrName = new String("");
    30562896        String attrValueStr = new String("");
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