| 7 | | == Part 1: provide a Molgenis Research Portal for each study == |
| | 9 | Stories: |
| | 10 | * StoryCreateBiobankCatalog - |
| | 11 | * StoryBrowseCatalogAndSelectFeatures - User can browse and select features in a treeview; Selected features are put in shopping cart. |
| | 12 | * StoryRequestData - User can request access to data set; Includes summary of research, power calculation, etc. |
| | 13 | * StoryApproveRequest - LifeLines approves request; selected features and targets is passed to scenario 2. |
| | 14 | |
| | 15 | {{{ |
| | 16 | #!YumlUseCase |
| | 17 | [Admin]-(CreateBiobankCatalo) |
| | 18 | [Researcher]-(BrowseCatalogAndSelectFeatures) |
| | 19 | [Researcher]-(RequestData) |
| | 20 | [LifeLines]-(RequestData) |
| | 21 | [LifeLines]-(ApproveRequest) |
| | 22 | (note: shopping cart of features is passed to scenario 2 {bg:beige}) |
| | 23 | }}} |
| | 44 | }}} |
| | 45 | |
| | 46 | == Scenario 3: user can access data via research portal == |
| | 47 | Module/ResearchPortal |
| | 48 | |
| | 49 | * StoryBrowseAndSelectFeatures - User can browse and select features in a treeview; Selected features are put in shopping cart. |
| | 50 | * StoryViewAndFilterInMatrix - user can browse and filter data in matrix view; repeated values can be made cols/rows |
| | 51 | * StoryDownloadAsPlink - user can select one feature and download with associated genotypes |
| | 52 | * StoryDownloadAsSpss - use can select multiple features and download as spss |
| | 53 | * StoryRunGwasAnalysis |
| | 54 | |
| | 55 | {{{#!YumlUseCase |
| | 56 | |
| | 57 | [Researcher]-BrowseAndSelectFeatures |
| | 58 | [Researcher]-ViewAndFilterInMatrix |
| | 59 | [Researcher]-DownloadAsPlink |
| | 60 | [Researcher]-DownloadAsSpss |
| | 61 | [Researcher]-RunGwasAnalysis |
| | 62 | |
| 39 | | Original Requirements on [[Modules/Matrix]] |
| 40 | | |
| 41 | | Acceptance criteria: |
| 42 | | * One viewer! |
| 43 | | * Has options to export to Excel and SPSS. |
| 44 | | * Has column filters that can be stacked. |
| 45 | | * Has row and column header filters. |
| 46 | | |
| 47 | | Status: |
| 48 | | * Unclear. We have one !MatrixViewer but seem to have at least two back-ends now: the original !SliceableMatrix and the one from Joris that supports multiple values in separate rows. |
| 49 | | * Suggestion: coming Monday, discuss what applications and modules there are, what added value they provide with regard to xQTL, and if they do, find a way to integrate them. |
| 50 | | == As a user, I want to select a phenotype and a list of individuals in the Molgenis Research Portal and then run a GWAS on the LL geno data == |
| 51 | | Scrum: ticket:1052 |
| 52 | | |
| 53 | | Acceptance criteria: |
| 54 | | |
| 55 | | Status per sub-story: |
| 115 | | Acceptance criteria: |
| 116 | | |
| 117 | | Status: |
| 118 | | |
| 119 | | * Functional design / mock-up of Catalog on [[Catalogue]] |
| 120 | | * We still need a technical design of the Catalog. |
| 121 | | * Despoina and Chao need LL metadata to fill their first version of the catalog with. Joris will provide them these data, however, they are still incomplete and will probably change. |
| 122 | | |
| 123 | | == As a LL data manager, I want to load data from publish layer into EAV (pheno model) == |
| 124 | | Scrum: ticket:1067 |
| 125 | | |
| 126 | | Acceptance criteria: |
| 127 | | |
| 128 | | Status: |
| 129 | | |
| 130 | | To-do's: |
| 131 | | |
| 132 | | * Add logging (so we can see what going on when it crashes in production environment, if it ever occurs) |
| 133 | | * Add Thread Monitor |
| 134 | | * How to handle/load/implement descriptive tables like LAB_BEPALING, this table is actually big list of Measurements with a lot of extra fields. |
| 135 | | * options: |
| 136 | | * Create a new type that extends Measurement and hold the additional fields |
| 137 | | * Merge data into the label of Category |
| 138 | | * How to handle/load/implement the table that describes which foreign keys are used between the tables. |
| 139 | | * The matrix viewer should know this info as well to build correct queries |
| 140 | | * Re-factor lifelines packages (it a little bit messy), remove old not used code anymore and place in descriptive packages |
| 141 | | * Remove JPA dependencies |
| 142 | | * Many-to-many in JPA are not working properly with Labels, for example ov.setTarget_Name("x"). In JDBCMapper this is solved, but know not where and how we could best do this for JPA. This set by label should also be put into generated test |
| 143 | | * Remove change org.molgenis.[wiki:JpaDatabase] interface to prevent this |
| 144 | | * //trick to prevent compilation problem in Hudson, should be changed! |
| 145 | | * this.em = ((JpaDatabase)db).getEntityManager().getEntityManagerFactory().createEntityManager(); |
| 146 | | * Jpa reverse relation cause hudson to give compile error. Should be added to molgenis for non-jpa entities. And implement as @deprecated of throw unsupportedOperationException. |
| 147 | | * Update CSV readers to be multi threaded? |
| 148 | | * In (production) environment it's not a bad idea to put the java executable in the Oracle VM that part of the database. |
| 149 | | * Last but not least, Test if data is loaded correctly (Test from Anco). |
| 150 | | * We should make sure that the data is always loaded into the right format (this means that it always end up the right way in database). |
