search

TreeBASE / treebase

Source code for TreeBASE web application and database
http://www.treebase.org
BSD 3-Clause "New" or "Revised" License
9 stars 3 forks source link

Select errors should prevent Changing to Ready State #213

Closed ghost closed 8 years ago

ghost commented 13 years ago

When a submitter tries to toggle the submission to "Ready" state, s/he is taken to this page: http://www.treebase.org/treebase-web/user/readyState.html?submissionid=xxxxx. At that point the submitter is warned if some taxon labels have not been matched. The warning says "We notice that some of your taxon labels have failed to be validated against an external taxonomy. Unless it is impossible to validate these labels, TreeBASE may refuse or delay the acceptance of your data." This test and warning is excessively stringent and should be disabled. However, there are other warnings that should be inserted, as follows. The Tool Box has a system where if an item has not be visited or has an error, the item is highlighted in yellow. One of those items is "Notes", which appears in yellow if the user has not entered information in the "Notes for study" filed. This is an excessive warning, especially seeing as these Notes are not shown to the public. Instead, yellow highlighting warning should be removed from the Notes. What remains are highlight warnings for Citation, Authors, Files, Taxa, Matrices, Trees, and Analyses -- which is fine. So, having removed the Notes highlighting and the taxon labels warning, what we need is a new quality check that hides the "Submit" button from the user unless there are no more remaining yellow highlighted items. If the Submit button is hidden because of a yellow highlighted item, the message to show is the following:

The items in the Tool Box on the right that are highlighted in yellow indicate that the item either has not been visited or there is an error. Hovering your mouse over the item will indicate the nature of the problem. Your submission cannot be changed to "Ready" state until all highlighted items are addressed. Please return to your submission to complete it. If you think this request is in error, please contact <a href='mailto:help@treebase.org?subject=TreeBASE Submission Sxxxxx'>help</a>.

The most common problems include:

(1) The submitter has not entered a citation that at a minimum must include the authors, year, title, and journal name. (2) The submitter has "orphaned" matrices or trees: i.e., there are matrices that are not listed as inputs to at least one analysis; or trees that are not listed as outputs from at least one analysis. If your paper does not include a tree, please submit a generic neighbor joining tree to satisfy this requirement. (3) The output tree of an analysis has taxon labels that do not match with the input matrix (i.e. there are taxon labels in the tree that are missing from the matrix or matrices that produced the tree). Preparing your submission using <a href='http://mesquiteproject.org/'&gt;Mesquite&lt;/a&gt;, in which both matrices and trees are part of the same Mesquite project and share a common taxon block, will avoid the problem of mismatched taxon labels. (4) The submitter has not attempted to validate the taxon labels by clicking the "Validate Taxon Labels" button in the Taxa section.

Reported by: piel

ghost commented 13 years ago

This is fixed, except that the session may not be set properly -- that is recorded in a separate bug.

Original comment by: piel

ghost commented 13 years ago

Original comment by: piel