AVHProgrammingProgress08

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Prioritized programming tasks 2008

  1. DONEProvide hyperlinks from each input field to a help page.(HISCOM to provide help information on wiki.)
    • Estimated Time: 4 hours
  2. DONEMake changes to page content from HISCOM specifications, including (HISCOM to provide.)
    1. DONEConsistency of field names in prompts and outputs. Don't use ABCD concept names like unitID, but clear descriptors which are provided by the AVH help information.
    2. DONEName of states and Canberra to Herbarium names; change prompt to State/Territory Herbarium.
    3. DONEHeader and footer can be replaced with HTML provided by HISCOM
    4. DONEEnsure new query can remember input values of previous query
    • Estimated Time: 1 days
  3. DONEInput 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 institution ID and record number
    • Estimated Time: 1-2 days
  4. DONEAdd support for auto wildcarding of left parts of dates and geocodes not specified, including date range queries.
    • Estimated Time: Bug fix
  5. DONEFix HTML-output: There are no borders around some of the output boxes in the HTML table, eg. "Other collectors" boxes (Rex suggests add )
    • Estimated Time: Bug fix
  6. DONEGeocodes 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
  7. DONEClear button in Simple Query page
    • Estimated Time: 0.5 hour
  8. DONECreate 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
  9. DONEAllow query on NULL to find records with NULL value for infraspecific name. Ensure that help specifies how to do this, by entering the string NULL.
    • Estimated Time: 2 hours
  10. DONEAdd: toggle button to either select all Herbaria or clear.
    • Estimated Time: 0.5 hour
  11. DONEFor public query, enable delivery of records collected from one or more States (location of collection), drop down pick 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
  12. DONEData download just in CSV for public simple query? Do not provide email distribution of data to public interface since potential problems with malicious use.
    • Estimated Time: 0.5 hour
  13. DONEWider box size that can handle full genus or species name - 20 characters?
    • Estimated Time: 0.2 hours
  14. DONEMake 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 as above #2.
    • Estimated Time: 3 hours
  15. DONEFor 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
  16. DONEFor extended query, input a list of species names (genus species irank iname) for bulk searching. Support both space delimited and comma delimited inputs, with comma delimited used to handle phrase names with spaces in them.
    • Estimated Time: 1.5 days
  17. DONEEnable delivery of large outputs by providing an option of a URL for a data file, which is removed after a couple of days. Send email to specify URL. This requires modifying AVH code to directly generate CSV rather than XML, which will take some time.
    • Estimated Time: 3 days
  18. DONEData consistency - modify some fields to HISPID5 standards on data load and during database load and dynamic indexing from BioCASE providers.
    1. DONEcountries
    2. DONEnearest named place - null values replaced with "not available"
    3. DONEStandardize collectors field number so that null values are replaced with "s.n."
    4. DONEnull date fields replaced with "s.dat." if it is a text fields
    5. DONEremove family name from Darwin full sci name
    6. DONEstates - 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: 2 days for dealing with simple conversions to HISPID5 standard and providing feedback on problems to herbaria
  19. DONEFor 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: 2 hours
  20. DONEProblems with querying on different countries in login simple query.
    • Estimated Time: Bug fix
  21. DONENo family column in extended query output
    • Estimated Time: Bug fix
  22. NOT NEEDEDAddition to existing wildcard searches for string fields but ensure that the help provides clear instructions on how to do wildcard search 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 hour
  23. DONEQuery for geocode precision less than X returns values with precsion greater than X.
    • Estimated Time: Bug fix
  24. DONEAllow selection of a range of geocode precision, <= textbox >= textbox
    • Estimated Time: 0.5 hour
  25. DONEWrap text for long output strings in HTML to keep fixed box width, e.g. Notes
    • Estimated Time: Bug fix
  26. DONEAllow search for a small number of countries in the Australasian region, as with selection of multiple states. HISCOM to specify countries required by 31 August
    • Estimated Time: 3 hours
  27. DONESplit into two URLs for public and restricted. Restricted page should have specification for no web indexing from Google etc.
    • Estimated Time: 1/2 day
  28. DONESimple query for restricted login should return same outputs as extended query by default. Extended query should return MoU fields by default, with option to add or remove individual fields (as in current implementation) and checkboxes to request All fields or Default (MoU) fields.
    • Estimated Time: 1 day
  29. DONECron 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).</strike>
    • Estimated Time: 4 hours
  30. Synchronize user accounts between multiple AVH instances. Will be done using standard database synchronization approach
    • Estimated Time: 1-2 days
  31. DONEProvide data for how many queries are processed, how many records returned in total and from each herbarium. Initially just make available a monthly text log file containing date stamp, the query , userID if restricted query, and number of records returned for each herbarium. Nice web pages presenting and histogramming this data to be added as part of future work.
    • Estimated Time: will depend on what info is required, but at least 2 days
  32. Project meetings
    • Estimated Time: 2 days

Mapper

Proposed changes to mapper include:

  1. DONEMinor 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
  2. DONEChange default so that it uses different icons for different species, not different herbaria.
    • Estimated time: 0.5 hour
  3. Legend should be downloadable as well as the map.
    • Estimated time: 3 hours
  4. NOT NEEDEDDefault icon (e.g. for query on 1 species) should be red circle (or square?).
    • Estimated time: 1 hour
  5. Increase the number of specimens that the mapper can handle with reasonable response time.
    • Estimated time: 4-8 hours
  6. DONEMake 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
  7. 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?HISCOM to give shapefile
    • Estimated time: 3 hours if we get the shape file
  8. If New Zealand or New Guinea are selected for country query, move the default map view to show them rather than AustraliaHISCOM to give shapefile
    • Estimated time: 2-3 hours
  9. 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. HISCOM to give shapefile
    • Estimated time: 1/2 day if we have the shape files
  10. Change the icons used - no one seems to like the ones we inherited from AVH1. Could change to instead use circle, square, triangle, upside-down triangle, diamond, solid or outlined, different colours if more are needed.
    • Estimated time: 2-3 hours
  11. 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.
  12. DONEMove 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.
  13. 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?HISCOM to do
  14. DONEAdd 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.
  15. 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.
  16. Clicking on a point or specimen should not resize the whole browser window under Firefox (1.5).
  17. 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.
  18. Add a "Monochrome map" button for grey scale printing.
  19. 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.