AVH2 public release priority task plan

From HISCOM

Compiled in first instance on 22nd and 23rd May by Paul Coddington (incl. input at keyboard), Shunde Zhang, Gerson Galang, Bill Barker.

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Timelines from here

Propose:

HISCOM review 26-29 May. Use History to view amendments. Use Discussion to promote debate.
CHAH. Raise with Brett Summerell to ensure OK in concept; CHAH teleconference agenda item: 17 June, for info, clarification and for discussion of time for announcing public release and launch
Design, Help, Programming commence ASAP.
EWS: QA testers approached 26-29 May, testing in June as early as possible.

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Design of revised user interface

(Ben Richardson, Siobahn Duffy; Jim Croft coordinator)

Simple changes to header, footer, CSS of each page can be done easily. Can easily fix up hyperlinks from each input field to relevant section of a user guide
Any other major changes to the design and user interface will require significant JSP programming effort, will not be feasible within the initial 3 weeks effort, will need to be costed as future work.
Prompts for queries should specify which ones are not indexed so search on these fields may be slow.
Look at suggestions from Chris Brodie about modifying map interface, presentation and output, and decide which of these changes should be made, specify required interface.
Specify what should be done to add Google Maps output option.
Suggested top priority in development for public release: bring AVH WeedTracker to sufficient acceptable look and feel for Weeds industry testers to utilise with clarity; provide feedback and produce a design upgrade specification (Issue: ideally part of AVH2 public release implementation - if too many tasks then separate and follow hard on AVH2).

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Page content - licensing, help, business description

(Alison Vaughan help pages, prompts; Jim Croft business description; Laurence Paine licensing)

Consistency of field names in prompts and outputs. Don't use ABCD concept names like unitID, but clear descriptors. Alison to provide.
Information about which query fields are supported by which herbaria, and which fields are well populated. Alison to do.
Change: name of states and Canberra to Herbarium names; change prompt to State/Territory Herbarium. HISCOM to provide correct prompts.
HISCOM to consider how to address cultivated data and ensure all herbaria are proving information in agreement with HISPID5

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Programming

(Gerson Galang, Shunde Zhang, Paul Coddington; Rex Croft, Bill Barker vetting).

debugs -
high priority tasks -

AVH Programming Progress

Issues of data in AVH

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Prioritized programming tasks for SAPAC

Total time: 18 days (average of 16-20 days)

Provide hyperlinks from each input field to a help page.
- Estimated Time: 3 hours
Make changes to page content from HISCOM specifications, including
1. Consistency of field names in prompts and outputs. Don't use ABCD concept names like unitID, but clear descriptors. Alison to provide.
2. Name of states and Canberra to Herbarium names; change prompt to State/Territory Herbarium.
- Estimated Time: 1-2 days - will need to review and provide a complete list of changes to be done and a more accurate estimate of time required
Input field validation - and provide appropriate error message
1. Restrict to minimal, high-priority/high-usage fields in the first instance
2. type checking for all input fields that are not just general string - lat/long, dates, numbers, etc
3. queries must have genus as well as species
4. query on record ID needs instituion ID and accession number
- Estimated Time: 1-2 days - will need to review and provide a complete list of checks to be done and a more accurate estimate of time required
Add support for auto wildcarding of left parts of dates and geocodes not specified, including date range queries.
- Estimated Time: Bug fix
Fix HTML-output: There are no borders around some of the output boxes in the HTML table, eg. "Other collecters" boxes (Rex suggests add )
- Estimated Time: Bug fix
Geocodes outputs should be accurate in restricted area. But should limit to 5 decimal places (this allows for accuracies to 1 m)
- Estimated Time: < 0.5 hour
Clear button in Simple Query page
- Estimated Time: 0.5 hour
Create a pull down menu listing standard HISPID5 Infraspecific rank options for ease of use, for public and extended queries. Changing the interface is easy. However most herbaria are not providing standard HISPID values - e.g. ssp ssp. subsp subsp. - so need some work to edit and standardize them.
- Estimated Time: 3 hours
Allow query on NULL to find records with NULL value for that field ?
- Estimated Time: If we can just specify in the user guide that users can use isNull then no work is required, if we want to accept a string like NULL it will require more effort.
Add: toggle button to either select all Herbaria or clear.
- Estimated Time: 0.5 hour
Deliver records collected from one or more States (location of collection), drop down list of States (SA, NSW, WA etc.), and All. Like in extended query, but ability to choose more than one state (this should also be changed in extended query)
- Estimated Time: 3 hours
Data download just in CSV for public simple query? HISCOM to decide as part of user interface review.
- Estimated Time: 0.5 hour
Wider box size that can handle full genus or species name - 12 characters?
- Estimated Time: 0.2 hours
Make names of fields in outputs consistent with names of query fields, and for extended fields modify which fields to output and default order of output. Specification to be provided by HISCOM/Alison.
- Estimated Time: 3 hours
For CSV and HTML outputs of all queries, add separate fields for genus, species, infra rank, infra name and qualifier, before full scientific name.
- Estimated Time: 1 hour
For extended query, input a list of species names (genus species subspecies) for bulk searching
- Estimated Time: 1 day
How to deliver large outputs - provide option of a URL for a data file, which is removed after a couple of days. This requires modifying AVH code to directly generate CSV rather than XML, which will take some time.
- Estimated Time: 2-3 days
Data consistency - modify some fields to HISPID5 standards on data load and during database load and dynamic indexing from BioCASE providers.
1. countries
2. nearest named place - null values replaced with "not available"
3. Standardize collectors field number so that null values are replaced with "s.n."
4. null date fields replaced with "s.dat." if it is a text fields
5. remove family name from Darwin full sci name
6. states - there are currently 110 values in the AVH database, many of them are actually regions rather than states (need to investigate and work with herbaria to fix this problem), some are islands (Norfolk, Lord Howe). However consistency for most fields is easy - just consistency with South Australian vs SOUTH AUSTRALIA vs SA. Use HISCOM/HISPID5 standard.
- Estimated Time: 1.5 day for dealing with simple conversions to HISPID5 standard.
For public output, decimal lat/long changed to 0.00, 0.17, 0.33 etc rather than 0.2, 0.4, etc and for the public mapper, points on the map should be on a 10min grid and 10 mins in size
- Estimated Time: 3 hours
Problems with querying on different countries in login simple query.
- Estimated Time: Bug fix
No family column in extended query output
- Estimated Time: Bug fix
Addition to existing wildcard searches. For queries on strings (e.g. names, localities, etc), if user puts in a word but not a wildcard, e.g. Barker, Adelaide, etc then return all records that include this word in the string. To be done for:
1. full scientific name
2. determined by
3. determination/determiner
4. collector
5. other collectors
6. nearest named place
7. locality text
- Estimated Time: 1 day
Query for gecode precision less than X returns values with precsion greater than X.
- Estimated Time: Bug fix
Add drop-down menu to allow selection of <=, >= or =, with default being <=
- Estimated Time: 0.5 hour
Wrap text for long output strings in HTML to keep fixed box width, e.g. Notes
- Estimated Time: Bug fix
Drop down selection menu for a small number of countries in the Australasian region, as well as text input. HISCOM to specify countries required.
- Estimated Time: 2 hours
Split into two URLs for public and restricted. Restricted page should have specification for no web indexing from Google etc. HISCOM to provide HTML for each screen.
- Estimated Time: 1/2 day
New Proposed Task. Simple query for restricted login should return same outputs as extended query by default. HISCOM needs to specify what default fields should be returned in resticted login. Suggest MoU plus a few other useful fields. Extended query allows users the option to request more fields.
- Estimated Time: 1 day
New Task. Cron script to check that all AVH instances are working and email sysadmin if not. Requires modifying admin web interface to specify AVH URLs and emails for sysadmins This could be run at multiple sites (which would mean multiple emails to sysadmins).
- Estimated Time: 4 hours
New Task. Synchronize user accounts between multiple AVH instances.
- Estimated Time: 1-2 days
New Task. Provide data for how many queries are processed, how many records returned in total and from each herbarium. Information required should be specified by HISCOM.
- Estimated Time: will depend on what info is required, but at least 2 days
When state or states are selected in extended query, automatically provide drop down list of herbarium regions for those states. HISCOM would need to provide the lists. This is currently listed as Medium priority - to be done only if there is time in initial 3 weeks of work.
- Estimated Time: approx 1 day

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Mapping and priority contingencies

Time: up to 2 days

High-priority contingencies arising during the work
Changes to map output as specified by HISCOM

Proposed changes to mapper include:

Minor changes to map results page:
1. Overlay text on the map should say "Generated on day/month/year, copyright Australia's Virtual Herbarium"
2. Under list of records for each herbarium, don't need to say e.g. BRI 54 records , just BRI 54
3. Ibra should be IBRA
4. Better explanation about clicking on dots to query point
- Estimated time: 0.5 hour
Change default so that it uses different icons for different species, not different herbaria.
- Estimated time: 0.5 hour
Legend should be downloadable as well as the map. Move the location of the legend to be level with the top of the map. Currently you have to scroll up and down between the map and the legend.
- Estimated time: 3 hours
Clarify presentation and explanation of the actions of checkboxes and buttons.
- Estimated time: 0.5 hour
Add a "Redraw map" button on the right hand side after "Display options" and before "Click between dots" so you don't have to move the mouse from side to side. The text about "Click on dot ..." can go after "Click between dots" or even under the map, to save vertical realestate.
- Estimated time: 0.5 hour
Default icon (e.g. for query on 1 species) should be red circle with white border. Bill suggests the first icon be a red circle (or square) outlined in white. Solid red (no outline) makes it difficult to distinguish many overlapping points.
- Estimated time: 1 hour
Investigate performance of mapper for large numbers of specimens and modify specification of warning limits and hard limits. SHould be able to handle more than 10K specimen records.
- Estimated time: 1 hour
Change the icons used - no one seems to like the ones we inherited from AVH1. Could change to instead use circle, triangle, upside-down triangle, with different colours.
- Estimated time: 2-3 hours
Make it clear that only one of terrain, temperature and rainfall can be selected. Could use radio buttons but then you can't turn it off once if is clicked by mistake. Probably use Javascript plus text to explain
- Estimated time: 1 hour
Help needs to be writen to document the actions of the many checkboxes and buttons. Eg. what does "Show by precision" and "Do not separate" mean?
- Estimated time: 4 hours

LIKELY END OF FIRST TWO DAYS WORK - HIGHEST PRIORITY TASKS FOR PUBLICLY RELEASABLE SEP 2008

Change default layers to not include terrain. However if we were to do that, we would first need a new version of the default coastline layer - otherwise land and sea are all white. Has anyone got a shapefile like that from their AVH1? NSW?
- Estimated time: 3 hours if we get the shape file
If New Zealand or New Guinea are selected for country query, move the default map view to show them rather than Australia
- Estimated time: 2-3 hours
Layers for major roads, rivers and elevation contours. These are apparently available in some implementations of AVH1 - maybe NSW? If we can get the shape files we can easily add them to AVH2.
- Estimated time: 1/2 day if we have the shape files
Improve the performance of the mapper and increase the number of specimens that the mapper can handle with reasonable response time.
- Estimated time: 1-2 days
Make the size of the dot be related to the geocode precision
- Estimated time: this would require a fair amount of work, maybe a couple of days, since current code uses images for the dots.
The latitude and longitude needs to expand to a finer granularity as you zoom in. Labels of the latitude and longitude values need to be added.
Clicking on a point or specimen should not resize the whole browser window under Firefox (1.5).
Add a "Monochrome map" button for grey scale printing.
Do we need a "Collapse subspecies" button so that only one symbol is used for all infraspecific names, rather than the current situation of a different symbol for each infraspecific name. We could also have options to "Collapse species" to the genus level, and "Collapse all" for one symbol for all specimens.
Might need to set a limit on the extent to which you can zoom in or out, so that the map redraws properly.

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Tasks for HISCOM

Full scientfic name should include authorities (and not family). HISCOM to provide.
Date last edited needs to provided for all records by all herbaria.

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To be done later

Some user interface modifications in the output data specification section.
- Estimated Time: 0. Some of this has already been done, some is suggestions that will be considered as part of revised user interface spec.
Data consistency for Habit, Habitat, and Notes. Rex Croft to investigate extending his existing script that loads Melbourne data into Adelaide database so that it can do data loads from all different data providers into the AVH database in a consistent way.
Taxon group. This has been reduced to medium priority.

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Future wish list

A location to record future requests / improvements

Rather than have the user select 'sort order' on the query pages, can they re-sort the results in the output (by clicking on the column headers)? This is how these things usually work, so it will be a bit more sophisticated and intuitive for the user. (Alison)
- Most versions that I have investigated are commercial javascript packages. I haven't found a good free routine that will sort the rows of a table based on a column heading, locally within the browser. (Rex)

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AVH WeedTracker - an Early Warning System for Weeds

(Bill Barker, coordinate).

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Design of revised user interface

(AVH2 Design team plus a Weeds person)

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Page content, Licensing, Help

(TBA)

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Programming

(SAPAC, AD as above)

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QA

Confirm EWS working appropriately by addition of record to AD data
Roll out to Weeds testers - those agreeing two years ago: John Moore WA, John Virtue and David Cooke SA, Kate Blood Vic., Matt Baker and John Thorp Tas., John Hosking NSW, Jane Morton Qld (add Dane Panetta back from sick leave); add Paul Pheloung ACT.

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Hosting

Consider who hosts. Adelaide willing and IT infrastructure management considers feasible with little difficulty. SA DEH already run tomcat applications and have MySQL installed to support BioCase.

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