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From Mark:

Instead of the initial page with just the search box, just
enter the results page with the full list of BAMs sorted
newest to oldest

What to do:

On main page show results for a query

last_modified=[NOW-3MONTH TO NOW]

(no search_xml parameter). Sorted by latest to oldest. Paginated.

From Mark:
in filters, "select all" and "deselect all" could be replaced with a global checkbox on the same line as the filter section label, as is done in the list of files. Or, at least putting them at the top of each section would make them easier to find before you start checking/unchecking boxes.

Artem's note:
Experiment and see where the checkboxes would look better.

From Mark:

how about moving this up a level and calling it devtools? since it's
tools for development and not really part of the final code
we will distribute.

Scripts from utils are mentioned in docs. Fix this.

Do only after every ticket before #82 is closed!

A link at the bottom of each header in the form ">>>" or "Expand>", which makes table width fit the data. It becomes "<<<" or "Compress<" when expanded and allows to make the column narrow.

This is an alternative to dragging a line between columns.

From Mark:
Leading zeros in the sample type is being trimmed, this is a code, not a number, we need the leading zero

Artem's note:
Investigate why this happens.

From Mark:

Cart:
drop "You can manage contents of your cart"
"Download XML" button should be "Download metadata"

Change everywhere cghub_api to wsapi. Check that tests pass.

submitting https://stage.cghub.ucsc.edu/gui/ to http://validator.w3.org/..

Result: 31 Errors, 10 warning(s)

There should be no warnings or errors.

From Makr:

SRA XSD problems are caused by what is suppose to be
the same schema as part of an international agreement between
the US, UK, and Japan, not being the same.
Please used the attached script to get the NCBI version.

#!/bin/bash

#ver=1-3
ver=1-4
fetchXsd() {
   local w=$1
   wget -nv http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_$ver/SRA.$w.xsd?view=co -O SRA.$w.xsd
}

fetchXsd analysis
fetchXsd common
fetchXsd experiment
fetchXsd run

Plan:

• Update schemas at
  https://github.com/dudarev/cghub/tree/master/devtools/data/schemas
• Make analysis in try_pyxb work
  https://github.com/dudarev/cghub/tree/master/devtools/try_pyxb

From Mark:

The filters should be multi-select.  With the filters in on
category being 'or-ed' and then between categories 'and-ed'.
For example:    (Baylor or Havard) and (DNA or WGA).

What to do:

Create checkboxes in sidebar. If several items are selected in one category
use them in query with OR. In WSI API documentation links to Solr syntax is given

http://wiki.apache.org/solr/SolrQuerySyntax

Try composing OR queries with it.

From Mark:
may be better for the filter sections to stay as is after pressing apply,
rather than collapsing. Could be irritating for a user to have to keep opening
these if they are refining a search.

Artem's note:
Open filter categories where selections were made.

Mark gets an error occasionally:

XMLSyntaxError at /search/
None
Request Method: GET
Request URL:    https://stage.cghub.ucsc.edu/gui/search/?q=gbm
Django Version: 1.4
Exception Type: XMLSyntaxError
Exception Value:
None
...
 Local vars
/usr/local/lib/python2.7/site-packages/django/views/generic/base.py in view
            return self.dispatch(request, *args, **kwargs) ...
 Local vars
/usr/local/lib/python2.7/site-packages/django/views/generic/base.py in dispatch
        return handler(request, *args, **kwargs) ...
 Local vars
/usr/local/lib/python2.7/site-packages/django/views/generic/base.py in get
        context = self.get_context_data(**kwargs) ...
 Local vars
/cghub/home/cwilks/42cups/cghub/cghub/apps/core/views.py in get_context_data
            results = api_request(query=query, sort_by=sort_by, offset=offset, limit=limit) ...
 Local vars
/cghub/home/cwilks/42cups/cghub/cghub/cghub_api/api.py in request
        results = objectify.fromstring(open(cache_file_name, 'r').read()) ...
 Local vars
Request information

The problem seems to be in cghub_api/api.py. Introduce handling exception before:

results = objectify.fromstring(open(cache_file_name, 'r').read()) ...

The exception is XMLSyntaxError probably from lxml.

If this exception is raised download query from server, not use it from cache.

From Mark:

Use of a cache should be optional and be implementable
independent of specific caching technology (abstract API).  For instance,
we might want to do memcached in the future.

Introduce a variable in request function to use or not to use cache. Describe it in documentation. Update documentation.

Do only after every ticket before #82 is closed!

A page with options, where one may select which columns are shown in data table. This information is saved in session.