0.1.6 beta release
0.1.6 beta release
Layout changed.
0.1.6 beta release
changed from marker_tye_str to marker_type
multiple continuous data graphs but not restricted by gene at the moment and on continuousData.jsp
continuous data continuous stats page working with 1 graph. needs to be moved to stats.jsp and have multiple graphs in model and page
0.1.6 beta release
dataTable modification code
0.1.6 beta release
use respond.js instead of css3-mediaqueries
baseUrl is now defined by the DeploymentInterceptor class for all requests
- added preliminary custom 403/404/500 pages
- updated web.xml for custom 403/404/500 pages
- added MpController to check for solr query result on the server side and direct users to the custom 404 page if 0 doc is found
  Ie, this is no longer controlled from the client side
0.1.6 beta release
dalliance hidden but loading at page load - on click it won't display, also currently the popups don't work if the div is hidden initially... can look at this again ....
with link not button for synonym toggle, which is better?
Genes page updated to new layout with dalliance hidden and extra synonyms hidden if more than 2
clean up and fix missing div tag close
add rawZygosity for EuroPhenome
Add xref to get the external IDs for the gene.  Remove reliance on sanger service and JS for those IDs
points to current Ensembl release
genes page info tag removed from dalliance label as per Terry request
Rearranged gene status and register interest buttons
disbabled button for gene status on gene page
correct class added to interest button that should work with ajax call
Gene status and register interest added
small change in button to test register interest cchanges made
added gene status and procedure name for sanger images
use the mgi id from the page variable (not the URL)
add missing tr to thead of phenotypes table
don't display type if the gene doesn't have a type
introduce global mediaBaseUrl variable
New page breadcrumb tag;
genes page updated to use the new breadcrumb
clean up; formatting; remove extra style information
update the image URLs to correct for the URL scheme changes (genes/phenotypes)
Update URL structure from mp?mp_id=xxx to phenotypes/xxx;
don't print a br tag at the end of the synonyms list / remove blank line at the bottom of the list
Update URL structure from geneDetails?gene_id=xxx to genes/xxx;
Update URL structure from /searchAndFacet to /search
default logging to not log debug messages for springframework.web
added code for datatable export: on current pagination and all data in a table
changed organisation to institute to match new solr images index
put back synonyms
catch IE 7 and earlier users
dalliance info and all by default visible gene info in gene panel is now generated on the back end so google will pick it up
fixed bug with info span still showing in IE but with no content
info on dalliance and IE alternative i.e. no interaction info
info added to encourage people to click
added numbers to image titles so obvious there are images in dropdown???
added context to title of genedetails, mp and images pages
change text to Europhenome
Add EuroPhenome link
testing mode so chrome will use gbrowse
commas added
debugging removed js gbrowse image getter
Add condition to run allele javascript code
all images link from pheno images panel does not now show expression images!
Gene name removed from the phenotype association panel
add some space between Sanger and PhenoDCC logos and text to please the product owner.
change wording for Phenotype Association
Add a message to explain what are the phenotype association
production asfand panel
alert info added to images info/disclaimer
new images disclaimer
Added PreQC and Sanger Legacy data information in the phenotype Association panel
small disclaimer on pheno images added
add real menu links; add button for show/hide (instead of bold text)
fix female icon and superscript showthrough bugs
Gene details updated with PhenoDCC panel
cks extra data table columns added
Link removed on Allele if not a MGI allele
Link to EuroPhenome data added for every phenotype call extracted from Europhenome biomart
added links in images dataTable on searchAndFacet page
asfand bottom panel working locally all.js file
gene location in jsp from our db then dalliance picks up location from the jsp page span contents
fixed data export bug and included gene part of images index
put grid.js back into gene details page for bottom allele panel for vvis stuff
update http to https
attribution on the bottom of the image labels
Fixed solr gene details page images not limited to expression and gene id!
baseUrl is now defined by the DeploymentInterceptor class for all requests
capitalized dropdowns and attribution to images WTSI
sample group commented out, but may need this later on for filtering control, experimental etc
add gene details page table for file download
toggle moved from imageutils.js to js/general/toggle.js
image dropdowns working for both pheno images and expression images on genedetails pages
with div toggle style from bootstrap for first images set no extra javascript needed - but all toggles open on page load where we want only the first.
use baseUrl for css file paths
code changes to fit new solr images index so that higherLevelAnnotationTermName was changed to higherLevelMaTermName to reflect we have ma and mp annotation terms not just ma
dataTable coding stuff with bootstrap
add the dalliance JS back in on other than IE browsers (doh)
Update title
Add datatable to genedetails and supporting HTML to page template and tools.js
apply dataTable code to geneDetails page
added code to render normal table to jquery dataTable
Add phenotype table to phenotype association section on gene detail page
add age to gene details page images
Add phenotype association section; fix typo
changed images files to be /media/images and image web uri /komp2/images
define baseUrl in the gene details page
genedetails with image expand collapse logic and icons
images links working on gene details and new server side icon on mp page
with links to all results page
new backend images jsps for geneDetails and mp pages
images paginated
add in responsive table for alleles
include dalliance JS for all non-IE browsers and IE browsers above IE9
added a topic class for a page which displays something like 'Phenotype: xxx' or 'Gene: xxx' on top region of a page
- implemented generic css for table (td, th, caption)
- change svgholder with for dalliance on gene_details page
- change layout for gene details page (span4/8)
geneDetails and Mp pages working with images well - before any moving to new widgets!
GeneDetails and mp page updated to have better images and legends - but will probably be replaced by new widgets anyway!
Remove the jutting out of the images and gene details boxes on the gene details page; add in the custom styles from drupal; resize the logo and position it more accurately; fix the navbar responsive layout
gene details has local dalliance js and no jquery of own
geneDetailsB moved to geneDetails
dynamic accession request to vvis code added
genedetails images positioned correctly
gene details page with css from drupal site added - before bootstrap added
added images/properties.js to jsps which is where the images url and solr url are now specified in one place
moved images html files to jsps in view directory so urls consistent with others and removed unecessary spring configs for images now
0.1.6 beta release
convert to use page template
genomic feature details page
0.1.6 beta release
Change home page view
Move PhenotypeArchive to trunk
Phenotype Archive Project (Java/Maven/Spring/Hibernate/MySQL)
0.1.6 beta release
works for phenotype pages too
provide an example for users
add tag library
for identifier errors
0.1.6 beta release
added gene status and procedure name for sanger images
update so the breadcrumb always says "Result";
Use the new breadcrumb stringification in the header instead of the breadcrumb
images breadcrumb;
include "box" around breadcrumb pieces to test out separating the query fields;
move the ikmcbreadcrumbs into the cutsom.css file
introduce global mediaBaseUrl variable
New page breadcrumb tag;
genes page updated to use the new breadcrumb
image results page fails gracefully if image index is down
organisation working on imageresults
changed organisation to institute to match new solr images index
added context to title of genedetails, mp and images pages
attribution at the bottom of imageResults text table now
baseUrl is now defined by the DeploymentInterceptor class for all requests
capitalized dropdowns and attribution to images WTSI
sample group commented out, but may need this later on for filtering control, experimental etc
Use the name of th gene and accession ids on the view  (rather than the IDs)
use gene symbol when a gene ID is used as the search parameter
add label for age in weeks
Remove page, increase bottom margin on thimbail to match left margin
image results works from mp, genedetails and search???
added ma term names to imageResults as some images only seem to have this info
changed images files to be /media/images and image web uri /komp2/images
preserve filterparam and filterfield when paginating
update all images to use SOLR only (no hibernate); reformat page to be the same as detail page layout; add MGI term search
Update style of TH; push pagination to the bottom; include page numbers (like google does); include page header
add autopager to view all images page; refactor code to do query on the server, then display the results
image helper changed to accommodate nulls for mouse view - odd that these didn't occur before??? "imaMouseImageVw":null,"foreignTableName":"MTS_MOUSE","fullResolutionFilePath":"527/M00077951_00003183_download_full.jpg"
Images jsps use tags for templating also a template.jsp for starting new pages- these also use bootstrap.js for layouts though largeImage.jsp is not working well with this at present because of absolute positioning necessary for scroller - but may be able to change this in future
added images/properties.js to jsps which is where the images url and solr url are now specified in one place
moved images html files to jsps in view directory so urls consistent with others and removed unecessary spring configs for images now
0.1.6 beta release
image helper changed to accommodate nulls for mouse view - odd that these didn't occur before??? "imaMouseImageVw":null,"foreignTableName":"MTS_MOUSE","fullResolutionFilePath":"527/M00077951_00003183_download_full.jpg"
added image data back into large image - needs better layout now
added caption for large image to even out layout and allow for a title or extra info from javascript
changed large image and gene details so images display in correct positions within the bootstrap grid and move under other elements as should for smaller screens
Images jsps use tags for templating also a template.jsp for starting new pages- these also use bootstrap.js for layouts though largeImage.jsp is not working well with this at present because of absolute positioning necessary for scroller - but may be able to change this in future
added images/properties.js to jsps which is where the images url and solr url are now specified in one place
moved images html files to jsps in view directory so urls consistent with others and removed unecessary spring configs for images now
0.1.6 beta release
use solrUrl config
use global variable for solrUrl
new examples to work with the new hash urls;
phenotype breadcrumbs
update to use new mediaBaseUrl
formatting
update the image URLs to correct for the URL scheme changes (genes/phenotypes)
Update URL structure from mp?mp_id=xxx to phenotypes/xxx;
changed organisation to institute to match new solr images index
added context to title of genedetails, mp and images pages
use global drupal base url for solr endpoint
attribution on the bottom of the image labels
baseUrl is now defined by the DeploymentInterceptor class for all requests
capitalized dropdowns and attribution to images WTSI
datatable code for filtering and mp table collapsing
export table as csv/excel stuff
fixed url to be relative for large image in MP page
toggle icon for images fixed - style issue in that other headers are now inside a table?
changed images files to be /media/images and image web uri /komp2/images
mp page image links working
images links working on gene details and new server side icon on mp page
Added code for image facet
merged
new backend images jsps for geneDetails and mp pages
- added preliminary custom 403/404/500 pages
- updated web.xml for custom 403/404/500 pages
- added MpController to check for solr query result on the server side and direct users to the custom 404 page if 0 doc is found
  Ie, this is no longer controlled from the client side
images paginated
mp page updated to include ovRight div in jsp
- changed coding style to jquey-widget factory way.
- resolved problem of MP text/image sections loading asynchronously
added a topic class for a page which displays something like 'Phenotype: xxx' or 'Gene: xxx' on top region of a page
Use consistent capitalization for page sections
geneDetails and Mp pages working with images well - before any moving to new widgets!
Merge format changes with new image container/pagination
GeneDetails and mp page updated to have better images and legends - but will probably be replaced by new widgets anyway!
geneDetailsB moved to geneDetails
added search/facet and mp pages
0.1.6 beta release
procedure stats page added
0.1.6 beta release
Stats procedure page working upside down though...
0.1.6 beta release
- changed coding style to jquey-widget factory way.
- resolved problem of MP text/image sections loading asynchronously
0.1.6 beta release
uncommented console
modified code to work with new gene/allele core created using httpdatasource
fixed bugs in search hash due to lack of encodeURI and added jumping straight to gene/mp page code when select from list
use globals to point to solr server
fixed search? bug not picking up some fq= in url
modified variable name to work for hash in url
Update URL structure from mp?mp_id=xxx to phenotypes/xxx;
Update URL structure from geneDetails?gene_id=xxx to genes/xxx;
Update URL structure from /searchAndFacet to /search
default logging to not log debug messages for springframework.web
fixed spinner bug
fixed bug in images index to capture case insensitive search and synonym, eg, xay -> x-ray
use drupalBaseUrl for solr url
changed wording in table column from legacy data to data.
added legacy data col to datatable for mp page
changed label from experiment to procedure for images sub facet and in datatable
Update (and revert) solr to (and from) local copy
baseUrl issues
code development for dataTable to replace sanger Grid
image datatable switcher code
added code for creating image grid from server-side using jquery dataTable
change look of facet panel
update gene_details link to geneDetails
fixed gene name result sorting bug: do not use qf=auto_suggest, as at sanger, the gene has diff. config
fixed displaying the correct facet in grid from redirected page
point grid js to EBI repository copy
Facet default behavior will not fired when searchAndFacet.jsp is loaded from redirection. Rather, it should fire as if a search has been performed: ie, calls left side bar widget directly and bypass autosuggest widget
updated code for redirected search
Added code for image facet
fixed problem of automatic fire of use search due to keyup events that are not 'enter'
- added preliminary custom 403/404/500 pages
- updated web.xml for custom 403/404/500 pages
- added MpController to check for solr query result on the server side and direct users to the custom 404 page if 0 doc is found
  Ie, this is no longer controlled from the client side
fixed MP/MA facet count not displayed issue when search was coming from redirected page
dont override ALL pagination -- only the stuff in the search page
Use global baseUrl variable to define relative paths for javascript link generation
correct path for JS gene detail page rewrites
increase time out for rewriting the urls
move the update links code outside of the redirect JS
add grid css/js here instead of generic page template
Use POSTed variables to display required JS when redirected
added search/facet and mp pages
0.1.6 beta release
introduce global mediaBaseUrl variable
New page breadcrumb tag;
genes page updated to use the new breadcrumb
baseUrl is now defined by the DeploymentInterceptor class for all requests
humanize query and has smallImagesFragment which may or may not be used?
0.1.6 beta release
Categorical Stats bar chart refactored to be like timeSeries in basic setup - some tweaks to look and titles.
timeseries on stats page shows correct time on xAxis not categorised! and Style changes such as larger numerics on axis
timeseries shows but needs error bars wired in and wrong table? time is in center of bars not at ends......eeeek!
time series graph related objects added
stable stats controller before addition of time series data/objects
continuousBarchart single working - minor visual changes needed!
categorical stats graphs with tables should handle any number of categories or sexes/graphs???
stats tables working - needs a couple more for loops to  be fully generic and cope with more categories or xAxisCategories (Zygocity)
stats tables under chart hard coded - needs appropriate model to mvc added...
stats graphs working and should work when generating multiple male and female sets per page...
stats working with JSONObjects mocked for male and female
with example fishers stacked graphs
Begginings of Stats pages with StatsController
0.1.6 beta release
Images jsps use tags for templating also a template.jsp for starting new pages- these also use bootstrap.js for layouts though largeImage.jsp is not working well with this at present because of absolute positioning necessary for scroller - but may be able to change this in future