| 20 | | 1. Java servlet class/file `SpecimenTubeServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated:[[BR]]a. Protected method `doGet(HttpServletRequest req, HttpServletResponse resp)` updated for command "`FindStoragePositions`" to find three storage locations in separate boxes for each specimen tube, for the specimen itself (except the first tube), the DNA extract, and the RNA extract.[[BR]]b. Protected method `doPost(HttpServletRequest req, HttpServletResponse resp)` updated for command "`CreateSpecimenTubes`" to create a DNA and RNA extract for each specimen, and set storage position to the ones allocated earlier on.[[BR]]c. Private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec)` updated to call new private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec, String boxType)` with value for argument `boxType` set to `null`.[[BR]]d. New private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec, String boxType)` added. It fetches the `BioWell` specified in JSONObject `jsonSpec` for the storage box specified by argument `boxType`, with values `null` (default, specimen), "`DNA`", or "`RNA`". |
| | 20 | 1. Java servlet class/file `SpecimenTubeServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated:[[BR]]a. Protected method `void doGet(HttpServletRequest req, HttpServletResponse resp)` updated for command "`FindStoragePositions`" to find three storage locations in separate boxes for each specimen tube, for the specimen itself (except the first tube), the DNA extract, and the RNA extract.[[BR]]b. Protected method `void doPost(HttpServletRequest req, HttpServletResponse resp)` updated for command "`CreateSpecimenTubes`" to create a DNA and RNA extract for each specimen, and set storage position to the ones allocated earlier on.[[BR]]c. Private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec)` updated to call new private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec, String boxType)` with value for argument `boxType` set to `null`.[[BR]]d. New private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec, String boxType)` added. It fetches the `BioWell` specified in JSONObject `jsonSpec` for the storage box specified by argument `boxType`, with values `null` (default, specimen), "`DNA`", or "`RNA`". |
| | 21 | 2. Java servlet class/file `PersonalRegistrationServlet.java` in `src/net/sf/basedb/meludi/servlet/` updated:[[BR]]a. Protected method `void doPost(HttpServletRequest req, HttpServletResponse resp)` updated for command "`CreateCase`" to create a DNA and RNA extract for each specimen, and set storage position to the ones allocated earlier on.[[BR]]b. Private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec)` updated to call new private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec, String boxType)` with value for argument `boxType` set to `null`.[[BR]]c. New private method `BioWell fetchBioWell(DbControl dc, JSONObject jsonSpec, String boxType)` added. It fetches the `BioWell` specified in JSONObject `jsonSpec` for the storage box specified by argument `boxType`, with values `null` (default, specimen), "`DNA`", or "`RNA`". |
| | 22 | 3. 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 for command "`GetUnprocessedItems`" to load info for DNA and RNA extracts to specimens, including storage locations for the former. Storage location info will also be included for input DNA and RNA. Only DNA and RNA extracts passing new filter method `boolean itemIsExtractSourceItem(String itemName)` will now be included in the returned list.[[BR]]b. Protected method `void doPost(HttpServletRequest req, HttpServletResponse resp)` updated for command "`RegisterDnaRna`" to not create new DNA or RNA extract items, but update the items related to the specimen.[[BR]]c. New `boolean itemIsExtractSourceItem(String itemName)` added. It calls new private method `int numberOfSpecificCharacters(String str, char c)` to check if the number of dots in the item name is 1, in which case the item is classified as an extract source item, else not.[[BR]]d. New private method `int numberOfSpecificCharacters(String str, char c)` added. It returns the number of times the specified character occurs in the input string. |
