soybase / curatortools Goto Github PK

All branding needs to reflect the term CuratorTools

The architecture documentation needs to updated to reflect the architectural changes (browse, similarity, upcoming security)

Instead of calling the study_structures_script.php multiple times (once for each structure), it would be likely be faster for a single PHP process to create all structure tables in a transaction; e.g., consider the following (shell script) benchmark that creates 1000 structure tables within a transaction:

$ cat create.sh
#!/bin/bash
id=1
(
  echo 'START TRANSACTION;'
  id=1
  for structure_id in {1..1000}
  do
    echo "
    CREATE TABLE tblStudy${id}Structure${structure_id}SNPs (
        id int(11) unsigned NOT NULL AUTO_INCREMENT,
        position int(11) DEFAULT NULL,
        names json DEFAULT NULL,
        reference char(1) DEFAULT NULL,
        alternate json DEFAULT NULL,
        results json DEFAULT NULL,
        PRIMARY KEY (id),
        KEY k_position (position)
    ) ENGINE=InnoDB;"
  done
  echo 'COMMIT;'
) | mysql dbCuratorTools

$ docker-compose up -d mysql
Creating network "curatortools_default" with the default driver
Creating curatortools_mysql_1 ... done
$ docker cp create.sh curatortools_mysql_1:/tmp
$ docker-compose exec mysql bash -c 'time bash /tmp/create.sh'
real	0m7.827s
user	0m0.071s
sys	0m0.075s

New assembly upload needs to be updated for the code transition. It is currently experiencing errors.

The draw.io needs to be updated to include login and logout functionality.

The database schema documentation needs to be updated to reflect the similarity and similarity job results tables.

User management needs to be added to the application.

Certain files need to be removed from version tracking.

Header links need to be updated to reflect the removal of the download section.

In addition to file upload from client, allow user to enter URLs of VCF and FASTA files to fetch; e.g., https://foo.bar/dir/vcf
or file:///path/to/vcf

The database documentation needs to be updated to reflect recent changes.

The initial code from the previously developed project needs to be moved into the new repository.

This analysis is time consuming and causes a bottleneck. If possible, it needs to be redesigned for efficiency, but for now it should be removed.