Changes between Version 11 and Version 12 of Ticket #725, comment 37


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Timestamp:
Mar 17, 2015, 11:49:06 AM (9 years ago)
Author:
olle

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  • Ticket #725, comment 37

    v11 v12  
    55 2. JSP file `index.jsp` i `resources/` updated:[[BR]]a. Entry for "Lab Tracking protocol for Allprep isolation" updated by exchanging the counter "`specimens-without-extract`" for "`unprocessed-extract-source-items`" and counter title "`Number of unprocessed selections`" for "`Number of unprocessed specimens and unquantified RNA/DNA`".[[BR]]b. Entry for "DNA/RNA registration/quantification" updated by exchanging the counter "`specimens-without-extract`" for "`dna-plates-without-eventdate`" and counter title "`Number of unprocessed specimens and unquantified RNA/DNA`" for "`Number of unprocessed start DNA plates`".
    66
    7  3. Data access object (DAO) class/file `Annotationtype.java` in `src/net/sf/basedb/meludi/dao/` updated with new annotation types:[[BR]]
     7 3. JSP file `extraction_preparation.jsp` and Javascript file `extraction_preparation.js` in `resources/sampleproc/` updated to support extra QIAcube items outside the !MeLuDi project, and get a "Register" functionality to create a start DNA reaction plate with all values for annotations necessary to recreate the selections made in step 1 and 2 of the wizard. Step 2 also updated by removal of the input fields for default DNA/RNA volumes. The table shown in step 3 has been simplified by removal of unused columns.
     8
     9 4. JSP file `extraction_protocol2.jsp` and Javascript file `extraction_protocol.js` in `resources/sampleproc/` updated to show start plate name in header of created form. Also updated to use exchange "`Tracking Sheet`" in header for "`Tracking Report`", when the created form contains measurement values, i.e. it is being requested from the "DNA/RNA registration/quantification" wizard.
     10
     11 5. JSP file `extraction_registration.jsp` and Javascript file `extraction_registration.js` in `resources/sampleproc/` updated to support extra QIAcube items outside the !MeLuDi project, and to get input date from a selected start DNA reaction plate in step 1, instead of having to make exactly the same extract source item selections, as for the "Lab tracking protocol for Allprep isolation" wizard. When registering extracts, chosen default DNA/RNA volumes are transmitted to the `Extraction` servlet, to be stored as annotations for the used start DNA reaction plate.
     12
     13 6. Data access object (DAO) class/file `Annotationtype.java` in `src/net/sf/basedb/meludi/dao/` updated with new annotation types:[[BR]]
    814|| '''Name''' || '''Type''' || '''Item type''' || '''Multi-valued''' ||
    915|| `IsolationDate` || `Type.DATE` || `Item.EXTRACT` || `No` ||
    … …  
    2329|| `BatchQiacubeOperator` || `Type.STRING` || `Item.BIOPLATE` || `No` ||
    2430
    25  4. Data access object (DAO) class/file `BioplateType.java` in `src/net/sf/basedb/meludi/dao/` updated with new bioplate type `DNA`.
     31 7. Data access object (DAO) class/file `BioplateType.java` in `src/net/sf/basedb/meludi/dao/` updated with new bioplate type `DNA`.
    2632
    27  5. Data access object (DAO) class/file `Dna.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static method `Dna findByName(DbControl dc, String name)`.
     33 8. Data access object (DAO) class/file `Dna.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static method `Dna findByName(DbControl dc, String name)`.
    2834
    29  6. Data access object (DAO) class/file `ReactionPlate.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static method `List<ReactionPlate> findActiveByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation)`. It returns a list of active reaction plates which can hold biomaterial items of the given subtype and have names starting with an optional prefix.
     35 9. Data access object (DAO) class/file `ReactionPlate.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static method `List<ReactionPlate> findActiveByBioPlateType(DbControl dc, BioplateType bioPlateType, Subtype subtype, String prefix, int numFreeWells, Annotationtype runDateAnnotation)`. It returns a list of active reaction plates which can hold biomaterial items of the given subtype and have names starting with an optional prefix.
    3036
    31  7. Data access object (DAO) class/file `Rna.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static methods `Rna findByName(DbControl dc, String name)` and `List<Rna> findUnquantifiedRna(DbControl dc)`.
     37 10. Data access object (DAO) class/file `Rna.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static methods `Rna findByName(DbControl dc, String name)` and `List<Rna> findUnquantifiedRna(DbControl dc)`.
    3238
    33  8. Data access object (DAO) class/file `Subtype.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static final subtype `EXTRACTION_PROTOCOL` for protocol items.
     39 11. Data access object (DAO) class/file `Subtype.java` in `src/net/sf/basedb/meludi/dao/` updated with new public static final subtype `EXTRACTION_PROTOCOL` for protocol items.
    3440
    35  9. Java servlet class/file `InstallServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated with new bioplate type `BioplateType.DNA`, annotation type category `Subtype.DNA`, and new annotation types.
     41 12. Java servlet class/file `InstallServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated with new bioplate type `BioplateType.DNA`, annotation type category `Subtype.DNA`, and new annotation types.
    3642
    37  10. Java servlet class/file `ExtractionServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated:[[BR]]a. Protected method `void doGet(HttpServletRequest req, HttpServletResponse resp)` updated with support for new commands "`GetUnprocessedStartPlates`" and "`GetSourceItemListFromStartPlate`", as wells as exchanging command "`GetNextLibraryPlateName`" for "`GetNextStartPlateName`". The latter method is also updated to get the next plate name from the stored plate with highest number, and not assume that the number of this plate equals the number of plates, i.e. that there is no gaps in the number sequence.[[BR]]b. Protected method `void doPost(HttpServletRequest req, HttpServletResponse resp)` updated with support for new commands "`RegisterStartPlate`". Command "`RegisterDnaRna`" updated to store isolation date as annotation for created DNA/RNA extracts, and store default DNA/RNA volumes as annotations for the start plate.[[BR]]c. Names of package private methods `long findNumberOfLibraryPlates(DbControl dc, String libraryPlatePrefix)` and `List<BioPlate> findLibraryPlates(DbControl dc, String libraryPlatePrefix)` exchanged for `long findNumberOfPlates(DbControl dc, String platePrefix)` and `List<BioPlate> findPlates(DbControl dc, String platePrefix)`, respectively.[[BR]]d. New package private method `BioPlate findPlateWithHighestNumber(DbControl dc, String platePrefix)` added.
     43 13. Java servlet class/file `ExtractionServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated:[[BR]]a. Protected method `void doGet(HttpServletRequest req, HttpServletResponse resp)` updated with support for new commands "`GetUnprocessedStartPlates`" and "`GetSourceItemListFromStartPlate`", as wells as exchanging command "`GetNextLibraryPlateName`" for "`GetNextStartPlateName`". The latter method is also updated to get the next plate name from the stored plate with highest number, and not assume that the number of this plate equals the number of plates, i.e. that there is no gaps in the number sequence.[[BR]]b. Protected method `void doPost(HttpServletRequest req, HttpServletResponse resp)` updated with support for new commands "`RegisterStartPlate`". Command "`RegisterDnaRna`" updated to store isolation date as annotation for created DNA/RNA extracts, and store default DNA/RNA volumes as annotations for the start plate.[[BR]]c. Names of package private methods `long findNumberOfLibraryPlates(DbControl dc, String libraryPlatePrefix)` and `List<BioPlate> findLibraryPlates(DbControl dc, String libraryPlatePrefix)` exchanged for `long findNumberOfPlates(DbControl dc, String platePrefix)` and `List<BioPlate> findPlates(DbControl dc, String platePrefix)`, respectively.[[BR]]d. New package private method `BioPlate findPlateWithHighestNumber(DbControl dc, String platePrefix)` added.