Changes between Version 3 and Version 4 of Ticket #690, comment 30


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Timestamp:
Dec 4, 2014, 8:47:26 AM (9 years ago)
Author:
olle

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  • Ticket #690, comment 30

    v3 v4  
    1 Functional specification/design update:
    2 
    3 Functional specification update:
     1Background information update:
    42
    53 1. If input tube content is DNA/RNA:[[BR]]a. Either a single tube with DNA or RNA is delivered, or one tube with DNA and one tube with RNA.[[BR]]b. If RNA is delivered, the full amount is put in a freezer storage box.[[BR]]c. If DNA is delivered, the full amount is used to create a DNA extract for further analysis.
    … …  
    75 3. Storage box name suffices should all be in lower-case, forcing the storage box suffix "`_Sp`" to be exchanged for "`_sp`".
    86
    9 Design specification update related to the functional specification update:
     7!Functional/Design specification update related to the background information update:
    108
    11  1. If input tube content is DNA or RNA:[[BR]]a. Instead of a specimen item, a DNA extract or RNA extract item should be created.[[BR]]b. A DNA extract item from an input tube should have a name consisting of the case name followed by "`.d`", e.g. for case "`ML00001`" the DNA extract name will be "`ML00001.d`".[[BR]]c. An RNA extract item from an input tube should have a name consisting of the case name followed by "`.r`", e.g. for case "`ML00001`" the RNA extract name will be "`ML00001.r`".
     9 1. If input tube content is DNA or RNA:[[BR]]a. Instead of a specimen item, a DNA extract or RNA extract item should be created.[[BR]]b. A DNA extract item from an input tube should have a name consisting of the case name followed by "`.d`", e.g. for case "`ML00001`" the DNA extract name will be "`ML00001.d`".[[BR]]c. An RNA extract item from an input tube should have a name consisting of the case name followed by "`.r`", e.g. for case "`ML00001`" the RNA extract name will be "`ML00001.r`".[[BR]]d. Currently annotation `SAMPLE_TYPE` ("`SampleType`") with possible value [`unknown`, `Primary tumour`, `Metastasis`, `DNA`, `RNA`] is used to indicate the input content of a specimen tube, and is stored both for the created case and child items. There are several problems with this; one is that the two options `Primary tumour` and `Metastasis` are intended for FFPE specimen items, another is that the name "`SampleType`" is inappropriate for DNA and RNA items, that are of type `Extract`, instead of `Sample`, like cases and specimens. Options [`unknown`, `Primary tumour`, `Metastasis`] should be stored in annotation of type `SPECIMEN_TYPE` ("`SpecimenType`") for specimen items, while a new annotation type `INPUT_TUBE_CONTENT_TYPE` ("`InputTubeContentType`") with options [`FFPE specimen`, `DNA`, `RNA`, `DNA + RNA`] should be created and stored with the created case item.
     10 2. For FFPE input tube content:[[BR]]a.Annotationtype `NOF_PIECES` ("`NofPieces`"), used for tissue specimens, should be exchanged for new annotation type `NOF_SECTIONS` ("`NofSections`"), which is more appropriate for FFPE specimens.[[BR]]b. When registering an FFPE sample, an input field for the number of sections should be added (default should be "`1`"). The value should be stored in the new `NOF_SECTIONS` ("`NofSections`") annotation type for the created specimen item.
     11 3. Java servlet class/file `SpecimenTubeServlet.java` in `src/net/sf/basedb/meludi/servlet/` should be updated in storage box queries to search for names ending with "`_sp`", instead of "`_Sp`".
     12
     13Other design specification updates:
     14
     15 1. Several annotations that are currently stored both for a case and its children specimen items, should be set for either case or specimens:[[BR]]a. Annotations of types `MUTATION_ANALYSIS` ("`MutationAnalysis`"), `PROJECT_FOCUS` ("`ProjectFocus`"), and `SITE` ("`Site`") should be stored with the case item.[[BR]]b. Annotations of types `MUTATION_ANALYSIS` ("`MutationAnalysis`"), `PROJECT_FOCUS` ("`ProjectFocus`"), should be stored with the specimen items.