Lioscro
commented
5 years ago For "Make sample description & factor choices easier to fill out at a larger scale.", the simplest solution is to add a "Copy" button next to certain repetitive fields (especially the sample description, sample factor, and sample specific characteristics fields), when pressed brings up a popover for the user to select which samples to copy the values to.
This can be implemented as follows
- Add a "Copy" button to each of the fields (with HTML) that we want to have this functionality on. These buttons have a common class (for instance "copy_btn") and are dummy buttons in HTML, but their functionality is added by javascript.
- In the javascript, when the sample meta forms are being set up, find all the elements of the "copy_btn" class and implement its popover & copying functionality.
- Reminder that the popover itself is not located at the location of the button that triggers it, so it is not possible to do clever javascript magic to find the parent of the button, which is required to find which field must be copied. Need to find out a way to figure out, from within the popover (more specifically, within the
onfunction forshown.bs.popover), which field's "Copy" button was pressed. - On the other hand, finding out which particular sample id from which to copy from is easy to find, using the global
current_sample_formvariable.
User must see directory structure modal (shown when "See Examples" button is clicked) before uploading their reads. Make the modal show up when "See FTP details" is clicked. At the bottom, have a button that reads "I have prepared my reads," when clicked shows the FTP details.Fixed on 1/12/2019 commit d5acc2b68299960ca86e029aaa76ad64f19ca6f5Fix FTP server not accepting passive connections.Fixed on 1/11/2019 by reusing old ftpd_server.Testing buttons show even though "testing=true" is not present in the url.Fixed on 1/12/2019 commit d5acc2b68299960ca86e029aaa76ad64f19ca6f5Fix issue where sometimes the "Start a new project!" button isn't disabled even though a project id was given through the url.Fixed on 1/12/2019 commit d5acc2b68299960ca86e029aaa76ad64f19ca6f5Make user-expandable list inputs more intuitive to use. When the "Add" button is clicked, add new row for the specified input and reset the textbox.Implemented on 1/13/2019 commit 2ba411baf0f656f161e9acfbfebed8cc4ef0e30dFor custom dropdowns (dropdowns where there is a choice for "other"), make it obvious for the user that they must fill in the textbox when "other" is selected. This may be achieved by either 1) hide the textbox until "other" is selected or 2) put a placeholder value in the textbox that reads "If "other" selected".Implemented on 1/13/2019 commit 2ba411baf0f656f161e9acfbfebed8cc4ef0e30dWhen inputting all factor values, values that have been removed with the "Remove" button still show up in the factor dropdown of individual samples.Fixed on 1/13/2019 commit 2ba411baf0f656f161e9acfbfebed8cc4ef0e30dMake sample description & factor choices easier to fill out at a larger scale.Implemented on 2/22/2019 commit 3b1f109fb054f57280b8ff4d2aadfd71df37de6dImplement new isoform annotations into sleuth analysis. Currently, annotations are pulled directly from Ensembl through BioMart. However, BioMart only supports C. elegans genome version 235, which is very outdated compared to the more recent 266. Gene isoform annotations can be found here: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/geneIDs/.Implemented on 1/16/2019 commit 4d04a0f4528a5c8402cf0065e93f84df02843509. Alaska no longer fetches annotation data from Ensembl BioMart, but instead uses an annotation flatfile.