Issues

#	Tracker	Status	Priority	Subject	Author	Assignee	Updated
8732	Amélioration	Closed	Normal	Pipeline rev 471 ; improve the accessibility of the VM by simplifying the pipeline into 1 master script (keeping error handling proper)	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:09 PM
8731	Bug	Closed	Normal	Pipeline rev 471 ; check_for_element_types_and_reorganize_elements_into_organisms.pl want to update already updated element type from previous run	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:08 PM
8730	Bug	Closed	Normal	Pipeline rev 471 ; ObjectElement.pm -> setaccession -> deal with multiple digit in accnum name, do not file prefix and postfix	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:07 PM
8729	Amélioration	Closed	Normal	Pipeline rev 471 ; check_db_consistency.pl : test that element lenght = sequence lenght	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:07 PM
8728	Amélioration	Closed	Normal	Pipeline rev 471 ; check_db_consistency.pl : test that genes.residues = micado.prot.feat.residues	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:06 PM
8727	Amélioration	Closed	Normal	Pipeline rev 471 ; script download_from_ncbi.pl : add the option -restrict_to_list_taxon_id_and_subnodes	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:05 PM
8726	Feature	Closed	Normal	Pipeline rev 471 ; organize molecules into living organisms using assembly info	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:01 PM
8725	Feature	Closed	Normal	adapt to database schema rev 2: additional links and info from ncbi, add columns for convenience when querying the database (avoid cross tables querying)	Thomas Lacroix	Thomas Lacroix	08/25/2017 12:00 PM
8724	Amélioration	Closed	Normal	Pipeline rev 471 ; Task_add_entry (insert of primary data) : Make the script more resilient to errors and re-run, faster (generator and integrator)	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:47 AM
8723	Amélioration	Closed	Normal	Pipeline rev 471 ; fill_gene_entry.pl : generate data for table gene directly instead of after schema micado is filled w/ data	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:46 AM
8722	Amélioration	Closed	Normal	Pipeline rev 471 ; fill_gene_entry.pl : infer correct type directly here instead of subsequent script	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:45 AM
8721	Feature	Closed	Normal	Pipeline rev 471 ; add bdlink info on ncbi assembly id and accession, etc... for the table organisms (trough element accnum)	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:44 AM
8720	Feature	In Progress	Normal	Pipeline rev 471 ; avoid non essential redondant data, decrease total database size by around 2 fold	Thomas Lacroix	Thomas Lacroix	08/28/2017 10:33 AM
8719	Amélioration	Closed	Normal	Pipeline rev 471 ; improved analyse_stats_db.pl	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:34 AM
8718	Feature	Closed	Normal	Pipeline rev 471 ; created script download_genome_files_from_ncbi.pl	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:33 AM
8717	Amélioration	Closed	Normal	Pipeline rev 471 ; fill_gene_entry.pl : add Locus_tag directly in table genes	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:30 AM
8716	Amélioration	Closed	Normal	Pipeline rev 471 ; Task_add_entry : cleaner option -GENOME_FILES_FORMAT	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:25 AM
8715	Amélioration	Closed	Normal	Pipeline rev 471 ; Task_add_entry : added option -SKIP_NEIGHBOR_INFO as this info is not useful	Thomas Lacroix	Thomas Lacroix	08/25/2017 11:23 AM
8714	Bug	Closed	Normal	Navigation jumps when moving with >> or << in ortholog table or genomic organisation	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:58 AM
8713	Bug	Closed	Normal	Compared organisms not sorted correctly for scope Whole organism	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:58 AM
8712	Bug	Closed	Normal	Synteny symbol not displaying correct number of pairs, it was missing gene mismatch and insertion	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:57 AM
8711	Bug	Closed	Normal	When transfering q genes from synteny to ortholog table view, s_insertion genes were transeferd as well	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:57 AM
8710	Bug	Closed	Normal	Error when the database was empty. Redirect user to use the guide to add data or check out http://genome.jouy.inra.fr/Insyght/ to test functionalities	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:57 AM
8709	Amélioration	Closed	Normal	Modified user interface to deal with database changes in schema: removal of elements.description (-> sequences.definition), elements.date_seq (-> sequences.date_seq), elements.version (-> sequences.version), genes.residue (-> prot_feat.proteine)	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:56 AM
8708	Bug	Closed	Normal	Fixed functionality to send email via smtp inra to report uncaught exception	Thomas Lacroix	Thomas Lacroix	08/25/2017 10:55 AM