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Use framecode type from dictionary rather than just removing spaces and unicode. Also ensure to limit length.

Should we make the middle name tag visible?

The chemical shift reference data section tags become required whenever the user specifies "no" to whether or not they have data for certain types of shifts.

When you do either of the pre-fill options it changes the Sf_framecode of the assembly to whatever the name of the assembly is. In the three entries I tested two of them had it where the entity and assembly both had the same Sf_framecode's so it kept bringing up an error. To fix it I changed the assembly name, but noticed that you cannot change the entity name. Every time I tried to change it it would restore itself to whatever was in the reference entry. I think this has something to do with the fix implemented in issue #49 .

Consider some sort of alternative layout for loops with many values?

This tag would allow you to select which image file you uploaded, but no image file type is defined in the standard file upload types dictionary. Therefore the tag has an empty enumeration list. I imagine ADIT had custom code for handling uploaded images. Need to discuss with Eldon best way to address this.

On a page with multiple radio buttons for the yes/no selection, if you select one of the options it sets all other options on that page to the same value. For example on the Ligands, Cofactors, etc. page if you select yes for paramagnetic the aromatic option is put to yes. If you change the value for aromatic it also changes the paramagnetic selection. This seems to be happening on all pages with the radio buttons.

For both Molecular assembly and Ligands, cofactors, etc. the very first field, for name, always resets to chem_comp_1 or assembly_1 (the 1 is replaced by 2 if you duplicate or add a new section) regardless of what you type in. The help says that both of these fields point to the name section, but the fact that it keeps resetting to the above values makes me feel like it's pointing to Sf_framecode. It currently sets both the name and Sf_framecode values when you submit it. I am not sure if there is a reason for this or if perhaps these should be two different fields.

Software name field has an enumeration in the dictionary that should be available to the depositor to select from. They should also be able to enter something that is not in the enumerated list.

http://dev-bmrbdep.bmrb.wisc.edu/entry/cdb49f48-349e-4776-867f-996b975c9552/saveframe/software/category

Remove 'NMR spectral processing protocols' from left hand view default (dictionary issue)

The "data files" saveframe can get a valid status after uploading files but prior to selecting a data type for the files. This should not be allowed. It may be better to update the dictionary than build in a custom validation rule.

Remove 'NMR probe description' from view (dictionary issue)

1. Ensure font casing consistency throughout application (title casing versus sentence casing)
2. Change font - check Google fonts
3. Add hover tips on tree menu
4. Error red too red
5. Explain you can either go section by section or use tree to navigate
6. Black text with red asterisk for mandatory fields rather than red text
7. Legend to explain mandatory fields toggle - no longer relevant, this option is hidden
8. Make plus button to add row in loop tab-able (no way to click it if using only keyboard with no mouse)
9. Do a better job than just an indentation to visually indicate that loops are children of their parents. Perhaps put them in a grey box?

Need a discussion on how some kinds of information will be displayed to the user. STAR requirements like $ for frame code values and no white space in values that will become frame codes.

Currently the file adit_cat_grp_o.csv describes the super groups to use for the deposition interface, but it doesn't provide the readable names for them. I imagine ADIT has this hardcoded, because I can't track down the values that ADIT actually displays.

I added my own hardcodings in 20a9f57 but I would like to remove them if we can add these values to adit_cat_grp_o.csv. @elulrich - is this a change we can make?

Polymer one letter code is a good example of such a tag.

Needs to be changed in adit_interface_dict.txt.

InstantDep originally displayed the saveframes using the order tags from xlschem_ann.csv. adit_cat_grp_o.csv has a different ordering of the saveframes. This means that the "next category" and "previous category" buttons don't work as intended with the new supergroups, as they are still navigating using the native order of the NMR-STAR file rather than the order from adit_cat_grp_o.csv. @elulrich - should I use the ordering from the super groups file or the one from the main schema?

'General tensors' appears in left hand box when user first enters deposition system (dictionary issue). However, the prompt disappears after a data file is selected and uploaded.

As for all of the 'Remove' issues that were just submitted, these prompts/selections appear in the left hand box before any data files are uploaded.

The tag _Chem_shift_perturbation_list.Type has a value of 'n' for 'Sf pointer' when it should be 'N'.

With temperature, ph, pressure and ionic strength?

Remove 'Sample content purity' from left hand box (dictionary issue)

For all saveframes that have a "Name" tag, that tag should be visible and the "sf_framecode" should be hidden - it will be set automatically from the sanitized "Name" value.

An example of a saveframe that needs to be fixed is the Software saveframe.

Remove 'Methods' from left hand box view (dictionary issue)

Must implement #53 first in order to fully implement this.

In left had box change 'NMR experiments and samples' to 'NMR experiments' or 'NMR experiment descriptions'. Including 'samples' in this prompt can be confusing as users might be confused and think they have to enter sample information in two different places.

The prompt is 'Software name' in Software descriptions but in other sections the prompt is 'Sample label'. Should the software prompt be changed for consistency?

If you go to the sample page, which is a required field, you have the option to hit delete. Upon doing so it removes the page from the sidebar menu and you cannot access it from the next/previous category buttons either. Immediately after deleting the selection the following appears "No matching saveframes found in this entry. Click here to return to a category that exists." This can be done for any page that has the delete option at the top and I have yet to find a way to recover the deleted sections. I think these pages should be like the Citations and Molecular entity page where the first block does not have a delete option, but subsequent ones do.

1. The display non-mandatory tags button is only visible in the side bar menu. Should that be visible on every page at the top by the next category buttons?

2. When you click it and it hides the non-mandatory tags it changes the sizing of nearly everything. This is from when a non-mandatory tag is bigger than a mandatory tag. When the larger non-mandatory tag disappears it resizes whatever screen your on to the smaller tags that are mandatory. For example this happens on the side bar menu itself and moves the location of the non-mandatory/mandatory button to the line below.

3. If you are on a non-mandatory page and then click the on-mandatory/mandatory button to hide the non-mandatory fields, the page goes blank (as expected), but both of the next/previous category buttons become review deposition buttons. A next mandatory or previous mandatory category button could be useful here. The next category that is mandatory could just appear also rather than having the page become blank, but I am not sure how easy that would be to do.

Received an 'invalid email address' message after entering email and then clicking on the start deposition button. Email was correct and when hit the start deposition button again deposition did start.

Try to tab though the fields on the ligand or molecular entity saveframes for examples.

I imagine this will be a doozy to track down, and perhaps an issue with the browser rather than the deposition code.

Due to a bug in Angular, we can either have:

*) Scrolling to the top of the page on a navigation event
*) Full height pages regardless of content

Creating this issue to track the status of the Angular issue and to try to find a work-around.

angular/angular#24547

Stop actually deleting them, and instead mark them as deleted. Then don't emit them during submission if deleted.

The file type "constraints" is missing in file type choices.

In the left hand box, suggest changing 'Sample' to 'Sample descriptions' for consistency.

For example, when going next from "NMR Spectrometer".

Got network error notification every time after each entries.

Easy solution, trigger a saveframe editor view refresh on saveframe delete.

It also does not have the option to input any information about what the natural sources common name or scientific name or even NCBI code. It shows in ADIT. Need to determine if this is a dictionary or code issue.

The isotope number field in this table has 'n/a' as the prompt.

Change NMR spectrometer to NMR spectrometers in left hand box.

To reproduce:

1. Upload a file, select type as "Other kinds of data".
2. Go to chem_shift_perturbation saveframe and try to select the file

Nothing appears because the file selection is based on the saveframe category defined in the data upload types schema.

The tag _Chem_shift_reference.Carbon_shifts_flag has a typo in it's interface text. The current text is "13C chemcial shifts deposited" but it should be "13C chemical shifts deposited".

These values should be floats and the depositor needs to explicitly type them into the deposition.

https:// needs to be added to the link sent by email after finishing an entry at BMRBDep.

Place it where the "next category" button would be.