par12005/TPPS: 7.x-1.2
| Main Authors: | par12005, claytonSMichael, Michael Wynne, NicHerndon |
|---|---|
| Format: | info software eJournal |
| Terbitan: |
, 2020
|
| Online Access: |
https://zenodo.org/record/3715364 |
Daftar Isi:
- This release requires a restart of the Tripal Job Daemon. Switch user to your HTTP server user (usually apache, nginx, or www-data), then do: drush trpjob-daemon stop drush trpjob-daemon start This release also requires a database update: drush updatedb Features TPPS Details page: Provides a search function which allows users to filter TPPS submissions by title, author, data type, study type, phenotype ontologies, etc. The search function also accepts HTTP GET parameters to support linking to a specific search query. Displays extensive information about an approved submission and links to all of the appropriate Tripal Entities associated with the submission. Thumbnail map with all of the trees from the study. Information on the publication itself. Link to download a compressed folder of all uploaded files. Tabs with additional details about the species, study details, trees, phenotypes, and genotypes. Maintains compatibility with old TGDR submissions. Additional information and features in TPPS admin panel: Name of submitting user. Relevant submission timestamps. Incomplete submissions and incomplete submission stages. Admins can now view the full file on TPPS pages if they so choose. Admins can now change the release date of an un-released submission. Admins can now upload revised versions of user-provided files and those files will be used instead of the user-provided files during the submission process. cvterm overhaul: TPPS version 7.x-1.1 and earlier uses a lot of locally defined cvterms, which defeats the purpose of using ontologies cvterms from older TPPS versions will be migrated to new cvterms defined in TPPS versions 7.x-1.2 and up. Support for old cvterms is maintained through the cvtermsynonym table. New cvterm information comes directly from the OLS API. Additional documentation: a Doxygen reference build is periodically updated and pushed to tpps.rtfd.io. File parsing overhaul: Files are now parsed using a generator. This greatly improves the performance of parsing files, both in memory and time complexity. File column comparison time complexity went from O(n^2) to O(nlogn) TPPSc dependency: Admin panel, submit functions, and form build functions are now almost all compatible with TPPSc. This means that TPPSc now uses each of those functions and displays, so changes made to these in the future will be reflected in TPPSc. Additional information in TPPS Submission arrays: Statistics such as tree count, study duration, unique phenotype count, etc. Important timestamps, including submission creation, latest update, completion, approval, and load completion. Any and all files that were uploaded are kept track of in one place. Added species photo field: uploaded photos should be visible in the admin panel and TPPS sidebar. Use Tripal EUtils for all NCBI queries. Retrieve taxon information from NCBI, including subkingdom and family. Add the Dryad db record to chado on install. TPPSc studies now receive a Dryad dbxref record. User friendliness upates. Added test files and some basic file utility unit tests. Install php-zip extension if it cannot be found on install. No longer removing tpps_submission table from database schema on uninstall. Bug Fixes Entity count/id issue. .csv file parsing and validation issue. Check for conflicting primary keys during record insertion. Clear database of old TGDR records before re-submitting. Properly center landing page figure. Condensed a lot of repetitive code down with utilities in includes/form_utils.inc. Missing submission status bug. Missing tpps_type bug. Front-end display bugs. .xlsx file dates bug. User access bug. File no-header bugs. Bugs with TravisCI configuration and testing. Phenotype definitions bug. Genotype spreadsheet support bug. Analysis file description bug.