MeLuDi v.1.0 bug fixes and improvements

[olle]

This ticket covers bug fixes and improvements to MeLuDi v.1.0.

[olle]

Ticket accepted.

[olle]

Traceability note:

• MeLuDi v.1.0 was introduced in Ticket #690 (MeLuDi - Registration wizard for melanoma-lung cancer projects).

[olle]

(In [3035]) Refs #718. Outermost Ant build file build.xml in / updated by setting version number to "1.1-dev" in preparation for new development.

[olle]

(In [3041]) Refs #718. Case summary input field hint and notification message updated to "Please enter a case id ("ML" + 5 digits)", where double quotes have been escaped:

1. JSP file index.jsp in resources/ updated in case summary input field hint.
2. Javascript file index.js in resources/ updated in function index.caseSummary() to set new case summary input field notification message (displayed if field is empty when submitted).
3. JSP file case_summary.jsp in resources/reports/ updated in case summary input field hint.
4. Javascript file case_summary.js in resources/reports/ updated in function index.caseSummary() to set new case summary input field notification message (displayed if field is empty when submitted).

[olle]

Functional specification update:

• When searching for a free well (position) in a bioplate (storage box), the first empty well starting from the first column in the first row should be used, even if non-empty wells are found after it, e.g. gaps should be filled. Previously, it was required that all wells after the first free well was empty.

[olle]

Design update to allow gaps in the pattern of used wells in a bioplate to be filled:

1. Java class/file SpecimenTubeServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Private method BioWell getFirstFreeWell(BioPlate plate, Integer numberOfWells) updated to only use argument BioPlate plate, and to return the first empty well starting from the first column in the first row, even if non-empty wells are found after it, e.g. gaps should be filled.
   b. Private method BioWell getNextFreeWell(BioWell well) updated to return the next empty well after the input one, even if non-empty wells are found after it, e.g. gaps should be filled.
   c. Private method JSONArray findFreeWells(DbControl dc, Integer nofTubes, String storageBoxSuffix) updated in call of private method BioWell getFirstFreeWell(...) to only use a single argument BioPlate plate.

[olle]

(In [3042]) Refs #718. MeLuDi updated to allow gaps in the pattern of used wells in a bioplate to be filled:

1. Java class/file SpecimenTubeServlet.java in src/net/sf/basedb/meludi/servlet/ updated:
   a. Private method BioWell getFirstFreeWell(BioPlate plate, Integer numberOfWells) updated to only use argument BioPlate plate, and to return the first empty well starting from the first column in the first row, even if non-empty wells are found after it, e.g. gaps should be filled.
   b. Private method BioWell getNextFreeWell(BioWell well) updated to return the next empty well after the input one, even if non-empty wells are found after it, e.g. gaps should be filled.
   c. Private method JSONArray findFreeWells(DbControl dc, Integer nofTubes, String storageBoxSuffix) updated in call of private method BioWell getFirstFreeWell(...) to only use a single argument BioPlate plate.

[olle]

(In [3043]) Refs #718. Java class/file SpecimenTubeServlet.java in src/net/sf/basedb/meludi/servlet/ updated by code cleanup, and removal of debug output, that couldn't be configured through configuration files.

[olle]

(In [3044]) Refs #718. Currently unused subtype items have been removed or commented out:

1. Java data access object classes/files BioplateType.java, Datafiletype.java, Rna.java, and Subtype.java in src/net/sf/basedb/meludi/dao/ updated by removal or commenting out of unused items.
2. Java servlet class/file InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) to exclude unused items in subtype checks for Subtype.DNA and Subtype.RNA.

[olle]

(In [3046]) Refs #718. Java class/file ReportTableUtil.java and Java servlet class/file SampleReportServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private convenience method Site fetchSite(DbControl dc, SnapshotManager manager, ItemSubtype subtypeCase, ItemSubtype subtypeSpecimen, Sample s) to check for null values for sample and case items before using them. If either item is null, Site.UNKNOWN is returned.

[olle]

(In [3047]) Refs #718. Java servlet classes/files CaseSummaryServlet.java, PersonalRegistrationServlet.java, and SampleReportServlet.java in src/net/sf/basedb/meludi/servlet/ updated by removal of debug output, that couldn't be configured through configuration files. Also some removal of unused items.

[olle]

Design update:

• Annotation type AnnotationType.FLAG should be removed, since it is currently not used. RNA items are not prepared for the annotation at installation, and the program therefore crashes when loading RNA annotations.
• Annotation type AnnotationType.BIOPSY_TYPE should be removed, since it is currently not used.

[olle]

(In [3050]) Refs #718. MeLuDi updated by removal of annotation types AnnotationType.BIOPSY_TYPE and AnnotationType.FLAG:

1. Java data access object class/file Annotationtype.java in src/net/sf/basedb/meludi/dao/ updated by commenting out definitions of annotation types BIOPSY_TYPE and FLAG.
2. Java servlet CaseSummaryServlet.java in src/net/sf/basedb/meludi/servlet/ updated in private method void loadRnaInfo(DbControl dc, Rna rna) by commenting out command loading value for AnnotationType.FLAG.
3. Java servlet InstallServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) to not including AnnotationType.BIOPSY_TYPE in list of used annotation types for specimen items.

[olle]

(In [3053]) Refs #718. Updates due to version number change to "1.1".

1. Version number change to "1.1":
   a. Outermost Ant XML build file build.xml in / updated.
   b. Extensions XML configuration file extensions.xml in META-INF/ updated.
   c. Javascript file meludi-2.js in resources/ updated.
   d. Javascript file samplereportgenerator.js in resources/reports/ updated.
   e. Java class/file Meludi.java in src/net/sf/basedb/meludi/ updated.

[olle]

Ticket closed as MeLuDi version 1.1 has been created. Its released was prompted by bug fix needed for cases containing RNA extracts.