bsed / ala Goto Github PK

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=953


Project Member Reported by [email protected], Apr 27, 2012 
We currently calculate the inter-layer dissimilarity using full extent. It woul 
dbe very nice to be able to do it for user-selected/generated area.

Set as Medium until we see difficulty and how CRITICAL issues are cleared.
 May 6, 2012 Project Member #1 [email protected] 
I think this is lower priority than other criticals before June 30. Set low.
 Labels: -Priority-Medium Priority-Low Jul 10, 2013 Project Member #2 [email protected] 
This is a significant ecological issue as local/regional environmental 
relationships could be very different to full geographic extent of layers.

The problem is current dynamic computational limits. E.g., if someone had an 
area a few percent smaller than full extent, calculating all environmental 
layer differences would be not be possible in minutes or maybe hours. 

Possible solution would be to check area extent and if < ~20% full extent, 
computation may be possible. The downside is the increasing number of layers 
and basic grid resolution. If we move over time to 250m, we are back in the too 
hard area, at least as an interactive option, even for 'smallish' areas.

Reassign and remain Low.
 Owner: [email protected] Cc: moyesyside Jul 11, 2013 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Summary: Dynamic layer correlation by Area? (was: Layer relation by area?)

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1078


Project Member Reported by [email protected], Aug 5 (2 days ago) 
What steps will reproduce the problem?

1. Add to Map | Layers | IBRA 7 

2. Zoom to Tasmanian extent

3. Add to Map | Areas | Select from polygonal layer | select "Furneaux" 
(northeastern most polygon in Tasmania)

4. Add to Map | Areas | Select from polygonal layer | select "Ben Lomand" 
(southwest of Furneaux

5. Export | Areas | All areas | shapefile

6. De-select areas

7. Import | Areas | 'all areas shapefile'

You see lines everywhere. So, either the export in shapefile format or the  
import isn't working correctly.

If the scenario is repeated with KML or WKT formats, the import appears to be 
ok BUT in all cases, AREA REPORTS of the shapefile, kml and wkt imported area 
definitions are all BUNG which raises another serious issue. 
 Aug 5 (2 days ago) Project Member #1 [email protected] 
Forgot image
 Shape.jpg 199 KB   View   Download Aug 5 (2 days ago) Project Member #2 [email protected] 
Exported files added.
 All_area_layers_Shapefile.zip 97.4 KB   Download All_area_layers_KML.kml 379 KB   Download All_area_layers_WKT.txt 286 KB   View   Download

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=914


Project Member Reported by [email protected], Mar 19, 2012 
What steps will reproduce the problem?

1. Click on any entry under the Action tab and then click on 'Application' 
(e.g., 
http://spatial.ala.org.au/actions/app/view/a6ed8f73232300467682b6a203699dbacaa32
a35) and you get an error 404

2. Sessions tab: Need date/time on session record

 Apr 4, 2012 #1 ajay.ranipeta 
Yea, haven't done that part yet as no other applications yet. Need to figure 
out a way for 3rd party apps to register, et al so we can monitor usage et al.
 Apr 12, 2012 #2 ajay.ranipeta 
(No comment was entered for this change.)
 Status: InTest Apr 12, 2012 Project Member #3 [email protected] 
Thanks Ajay. Not sure what I am testing.
 Apr 12, 2012 #4 ajay.ranipeta 
1. Click on any entry under the Action tab and then click on 'Application' and 
you don't get a 404 error.

 Apr 12, 2012 Project Member #5 [email protected] 
Thanks Ajay. Tried that and aok, but then tried to click on Application 

http://spatial.ala.org.au/actions/app/view/a6ed8f73232300467682b6a203699dbacaa32
a35

and got a 404
 Status: Started May 8, 2012 #6 ajay.ranipeta 
this is fine now. the link has now changed and doesn't have the "view" part in 
the url
 Status: InTest May 8, 2012 Project Member #7 [email protected] 
Thanks Ajay. 

Ideally, we need at least an email address associated with sessions/actions if 
user is logged in (otherwise IP ok). I have to get seriously into some stats on 
the logs in the next month and it would be good to see individuals popping up 
that I could put a context on.
 Status: Started May 9, 2012 #8 ajay.ranipeta 
code updated to display email and user ip. In SVN
 Status: ToDev May 9, 2012 #9 ajay.ranipeta 
(No comment was entered for this change.)
 Status: InTest May 10, 2012 Project Member #10 [email protected] 
Error when clicking View All Activity: HTTP Status 500

Also: Should also report name/ip on your own sessions
 Status: Started May 10, 2012 #11 ajay.ranipeta 
Why should it return your own email and ip? 

If they are already logged in and see their IP on top, isn't that a redundant 
information?

Does it make sense for them to view the ip, esp. if they are on DHCP? We need 
to see the IP to figure out which country/other reason, but they don't need to? 
 May 10, 2012 #12 ajay.ranipeta 
btw, the View All Activity works fine for me. Maybe Adam was restarting 
services.
 Status: InTest May 10, 2012 Project Member #13 [email protected] 
Still getting 500 error on Chrome and FF with cleared cache.
 Status: Started May 21, 2012 Project Member #14 [email protected] 
Just checked: Same as Comment 13.
 May 21, 2012 #15 ajay.ranipeta 
yes, the problem is that there is too much data there to look at between the db 
and the page, too much to handle and not enough memory. I'll just need to setup 
a paging system and grab a set of data at a time. 
 Jun 4, 2012 Project Member #16 [email protected] 
1. Urgently need ability to get a dump of all usage for EU meetings and ALA 
report.

2. Also need to SORT the entries so that last in is up top.

3. We do need some form of date/time against entries, however and wherever is 
possible. The Actions tables could be wider?
 Jun 5, 2012 #17 ajay.ranipeta 
issues fixed, enhancements added. code up on dev and prod. 

if good, please set to Fixed.
 Status: InTest Jun 5, 2012 Project Member #18 [email protected] 
Thanks Ajay - much improved. This will be very useful. Some hopefully minor 
suggestions

1. Can date/time to right-justified to align? Would make it heaps easier to 
scan.

2. Can Session table be sorted by date/time with latest at top? Ditto for 'All 
Activity'

3. Download of Session table for All Activity doesn't include all displayed 
table fields.

4. Download of Records table for All Activity doesn't include all displayed 
table fields.

5. Greatly prefer Records table uses email address rather than IP address 
(alignment between Session and Records table?).

6. Records table 'Filter within results' is neat Ajay: Can we add same function 
for Session table?

Thanks Ajay. This is terrific data.
 Status: Started Jun 5, 2012 Project Member #19 [email protected] 
Aay: Also noticed that about 45% of the sessions have a 'Duration' of '0' 
minutes while the rest are display with 1-2 decimal places. I'm assuming the 
'0' sessions are less than 1 minute?

 Summary: User Dashboard needs update Jun 5, 2012 #20 ajay.ranipeta 
1. the right-justified was looking a bit odd, hence the current string. might 
have to re-think this view?

2. done.

3. done.

4. done.

5. email can usually be [email protected] (default) and you requested IP 
initially. changed it back to email now.

6. done.

re: Duration of 0, it's probably because the user just loaded a single layer or 
maybe just loaded the app and left without adding anymore layers. and the 
session id changed as they might've come back and done something else with a 
new session id (automatically generated).
 Status: InTest Jun 5, 2012 Project Member #21 [email protected] 
Thanks Ajay. Good to talk. Here are the issues discused (I think that's them 
all)...

1. Add IP address next to email address in sessions download so I can 
differentiate guests

2. Substitute Duration of 0.01 for any session duration = 0

3. Remove App ID column from Records download
 Status: Started Jun 14, 2012 #22 ajay.ranipeta 
fixed. on svn. need to push to dev for testing.
 Status: ToDev Jun 14, 2012 #23 ajay.ranipeta 
now on dev.
 Status: InTest Jun 15, 2012 Project Member #24 [email protected] 
Sorry Ajay: Forgot to ask to add IP next to email for all Records table as well 
as Sessions table. My mistake. Otherwise, it looks great.
 Status: Started Jun 15, 2012 #25 ajay.ranipeta 
done.
 Status: InTest Jun 16, 2012 Project Member #26 [email protected] 
Great! ToProd please.
 Status: ToProd Jun 19, 2012 #27 ajay.ranipeta 
code now up on dev and prod.
 Status: InTest Jun 19, 2012 Project Member #28 [email protected] 
Prod (All activities)-

HTTP Status 500 -

type Exception report

message

description The server encountered an internal error () that prevented it from 
fulfilling this request.

exception

org.springframework.web.util.NestedServletException: Handler processing failed; 
nested exception is java.lang.OutOfMemoryError: Java heap space
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:839)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:719)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:669)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:574)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    au.org.ala.cas.client.AlaHttpServletRequestWrapperFilter.doFilter(AlaHttpServletRequestWrapperFilter.java:65)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.validation.AbstractTicketValidationFilter.doFilter(AbstractTicketValidationFilter.java:167)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.authentication.AuthenticationFilter.doFilter(AuthenticationFilter.java:93)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)

root cause

java.lang.OutOfMemoryError: Java heap space
    java.lang.StringCoding$StringDecoder.decode(StringCoding.java:133)
    java.lang.StringCoding.decode(StringCoding.java:173)
 Status: Started Jun 19, 2012 Project Member #29 [email protected] 
Suggest for 'All activities' display only first page (most recent) and then 
ability to download all of Action and Session table (separately or together - 
whatever) zipped.
 Jun 20, 2012 #30 ajay.ranipeta 
- added base code for paging
- currently set limit of 500 for both logs and sessions
- TODO: full paging

 Status: ToDev Jun 21, 2012 #31 ajay.ranipeta 
(No comment was entered for this change.)
 Status: InTest Jun 21, 2012 Project Member #32 [email protected] 
Thanks Ajay: 

View All activity-

1. Not sure if we need full paging: What you have is fine for preview of 
recents as would not be able to or want to page through all records anyway (but 
charts of all is vital)

2. Do the Charts reflect all records or only 500?

3. For download (all), I think it may be expedient to only export (for actions)

id, email, userip, time, type, sessionid, category1, category2, name, layers

as I don't see an easy way to analyse the rest at this point.

 Status: Started Jun 21, 2012 Project Member #33 [email protected] 
Looking at stats (all)

1. Under Species, you have search, n/a, facet, assemblage, occurrence. Search 
ok, but don't fully grasp the others. We may need better terms?

2. What the difference between Import | Species and Import | LSID?

3. Is Import | LSID the same as Import | assemblage?




 Jun 21, 2012 #34 ajay.ranipeta 
From comment#32:
1. this is just a pretend paging. does only the last 500 records

2. Nope, it's the whole dataset

3. done.

From comment#33
1. maybe

2. Import | Species = CSV update. Import | LSID = importing assemblage

3. There is no Import | Assemblage. There is Search | Assemblage which involves 
the user generating the assemblage. Import | LSID is importing it. 
 Status: InTest Jun 22, 2012 Project Member #35 [email protected] 
Please see if ambiguous terms can be clarified (agree - minimal changes).
 Status: Started Jun 22, 2012 #36 ajay.ranipeta 
more info plz?
 Jun 22, 2012 Project Member #37 [email protected] 
Via

Species sub-Chart: Occurrences -> In Area
Import sub-Chart: LSID -> Assemblage
Export sub-chart: Species list -> Checklist
Area sub-Chart: RadiusManual -> Radius
                AddressRadius -> Address
                Polygon -> Polygon (assume this is interactive?)
                Map polygon -> MapPolygon?
                RegionSelection -> GazPolygon ?
                RegionSelection -> GazPolygon ?

 Dec 3, 2012 Project Member #38 [email protected] 
(No comment was entered for this change.)
 Owner: moyesyside Cc: [email protected] Labels: -Priority-Critical Priority-Medium Jan 21, 2013 Project Member #39 [email protected] 
22 January 2013: I am getting problem No 1
1. Click on any entry under the Action tab and then click on 'Application' 
(e.g., 
http://spatial.ala.org.au/actions/app/1a9f378201b02bf120e2d5a6a8ba601a48049438) 
and 
and get an error 500

HTTP Status 500 -

type Exception report

message

description The server encountered an internal error () that prevented it from 
fulfilling this request.

exception

org.springframework.web.util.NestedServletException: Request processing failed; 
nested exception is java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:681)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:574)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    au.org.ala.cas.client.AlaHttpServletRequestWrapperFilter.doFilter(AlaHttpServletRequestWrapperFilter.java:65)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.validation.AbstractTicketValidationFilter.doFilter(AbstractTicketValidationFilter.java:167)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.authentication.AuthenticationFilter.doFilter(AuthenticationFilter.java:93)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)

root cause

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
    java.util.ArrayList.RangeCheck(ArrayList.java:547)
    java.util.ArrayList.get(ArrayList.java:322)
    org.ala.spatial.services.dao.ApplicationDAOImpl.findApplicationByAppId(ApplicationDAOImpl.java:85)
    org.ala.spatial.services.web.ApplicationController.appInfo(ApplicationController.java:62)
    sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    java.lang.reflect.Method.invoke(Method.java:597)
    org.springframework.web.bind.annotation.support.HandlerMethodInvoker.invokeHandlerMethod(HandlerMethodInvoker.java:176)
    org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.invokeHandlerMethod(AnnotationMethodHandlerAdapter.java:436)
    org.springframework.web.servlet.mvc.annotation.AnnotationMethodHandlerAdapter.handle(AnnotationMethodHandlerAdapter.java:424)
    org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:790)
    org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:719)
    org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:669)
    org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:574)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:617)
    javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
    au.org.ala.cas.client.AlaHttpServletRequestWrapperFilter.doFilter(AlaHttpServletRequestWrapperFilter.java:65)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.validation.AbstractTicketValidationFilter.doFilter(AbstractTicketValidationFilter.java:167)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.authentication.AuthenticationFilter.doFilter(AuthenticationFilter.java:93)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)


 Jul 8, 2013 Project Member #40 [email protected] 
The user dashboard appears totally busted so upping this to Critical. 
http://spatial.ala.org.au/actions/dashboard produces (in part)

HTTP Status 500 -

type Exception report

message

description The server encountered an internal error () that prevented it from 
fulfilling this request.

exception

java.lang.RuntimeException: javax.net.ssl.SSLHandshakeException: 
sun.security.validator.ValidatorException: PKIX path validation failed: 
java.security.cert.CertPathValidatorException: timestamp check failed
    org.jasig.cas.client.util.CommonUtils.getResponseFromServer(CommonUtils.java:295)
    org.jasig.cas.client.validation.AbstractCasProtocolUrlBasedTicketValidator.retrieveResponseFromServer(AbstractCasProtocolUrlBasedTicketValidator.java:33)
    org.jasig.cas.client.validation.AbstractUrlBasedTicketValidator.validate(AbstractUrlBasedTicketValidator.java:178)
    org.jasig.cas.client.validation.AbstractTicketValidationFilter.doFilter(AbstractTicketValidationFilter.java:132)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.jasig.cas.client.authentication.AuthenticationFilter.doFilter(AuthenticationFilter.java:102)
    au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:167)
    org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
    org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
 Labels: -Priority-Medium Priority-Critical Jul 8, 2013 Project Member #41 moyesyside 
this is a SSL  certificate issue that happened when the certificate expired 40 
mins ago. Affects more the the dashboard tooll....
 Jul 10, 2013 Project Member #42 [email protected] 
OK, the certificate issue is now fixed and the original problems remain. 
Lowering for now as there are higher priorities.
 Labels: -Priority-Critical Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=538


Reported by [email protected], Jun 1, 2011 
Update the layers table so that entries link back to their respective 
geonetwork pages (where available).
 Jun 5, 2011 #1 [email protected] 
Just working out the kinks in dev now. Have had to ask Simon how we reference 
geonetwork metadata records via uuid - the protocol may have changed in the 
latest version of gn.

eg.

http://spatial-dev.ala.org.au/geonetwork/srv/en/metadata.show?uuid=ADE7BE26-A04A
-4DD5-894D-7354AF083844

Should (and used to) work.
 Status: Started Jun 6, 2011 #2 [email protected] 
Checked with simon, the uuid needs to be in lowercase - have updated layers 
table accordingly.
 Status: InTest Jun 7, 2011 Project Member #3 [email protected] 
Thanks Gavin but problems remain. Tried (i) on "Phosphorus - plant available 
pre-European" and after the summary page link to geonetwork, I got -

The requested operation could not be performed.

MetadataNotFoundEx : Metadata not found 

I also noted formatting problems with the links to BRS with for example 
"Natural resources management expenditure" metadata.

We are in the situation again where we need a check script to see if we can 
detect if there are problems with these links.

To "Started"
 Status: Started Jun 7, 2011 #4 [email protected] 
Yeah, this is  issue 543  (I raised it the other day when we were on skype), 
unrelated to this issue (the geonetwork links are fine). I have touched base 
with Ajay this morning to take a look at it.
 Status: InTest Jun 8, 2011 Project Member #5 [email protected] 
Then unsure what I am testing? 
http://spatial-dev.ala.org.au/geonetwork/srv/en/metadata.show?uuid=ADE7BE26-A04A
-4DD5-894D-7354AF083844 still doesn't work.
 Status: Started Jun 8, 2011 #6 [email protected] 
Geonetwork uuids will now all be in lowercase from the layer pages.

Try clicking through from a layer page (from a climate or substrate layer
page).

http://spatial.ala.org.au/layers/
http://spatial-dev.ala.org.au/layers/

Cheers,
Gav
 Jun 9, 2011 #7 [email protected] 
(No comment was entered for this change.)
 Status: InTest Jun 9, 2011 Project Member #8 [email protected] 
Mapped Clay%, clicked (i), then on geonetwork link and got error.

 Status: Started Jun 16, 2011 #9 [email protected] 
OK - fixed up substrate records on dev (turns out I had to upload via anzmet 
lite - the geonetwork batch import process didn't index the uuid). All linked 
records can now be accessed (wget output logs attached).
 dev_metadata.sh 12.8 KB   View   Download output_dev.txt 121 KB   View   Download prod_metadata.sh 12.3 KB   View   Download output_prod.txt 118 KB   View   Download Status: InTest Jun 21, 2011 Project Member #10 [email protected] 
Gavin: 121 records = all in geonetwork but what about 'external' metadata?
 Jun 22, 2011 Project Member #11 [email protected] 
This should be back to Started to include availability of non-Geonetwork 
metadata.
 Status: Started Jun 26, 2011 #12 [email protected] 
Update: we have some broken external metadata links.

Dev: 9 broken URLs

http://adl.brs.gov.au/FindIt/php/full_internal.php?fileidentifier=http://adl.brs
.gov.au/findit/metadata_files/pa_daaslr9abd_00111a01.xml
http://adl.brs.gov.au/mapserv/intveg/index.html
http://www.ga.gov.au/nmd/products/digidat/dem_9s.jsp
http://gisca.adelaide.edu.au/products_services/ariav2_about.html
http://adl.brs.gov.au/anrdl/php/full.php?fileidentifier=http://adl.brs.gov.au/fi
ndit/metadata_files/pa_masocr9cl__01111a00.xml
http://adl.brs.gov.au/anrdl/php/full.php?fileidentifier=http://adl.brs.gov.au/fi
ndit/metadata_files/pa_sphaar9nnd_01611a00.xml
http://www.anra.gov.au/topics/soils/erosion/index.html,
http://www.ga.gov.au/nmd/products/digidat/dem_9s.jsp
http://www.ga.gov.au/nmd/products/digidat/dem_9s.jsp

Prod: 9 broken URLs

http://www.ga.gov.au/nmd/products/digidat/dem_9s.jsp
http://gisca.adelaide.edu.au/products_services/ariav2_about.html
http://adl.brs.gov.au/anrdl/php/full.php?fileidentifier=http://adl.brs.gov.au/fi
ndit/metadata_files/pa_masocr9cl__01111a00.xml
http://adl.brs.gov.au/anrdl/php/full.php?fileidentifier=http://adl.brs.gov.au/fi
ndit/metadata_files/pa_sphaar9nnd_01611a00.xml
http://adl.brs.gov.au/FindIt/php/full_internal.php?fileidentifier=http://adl.brs
.gov.au/findit/metadata_files/pa_daaslr9abd_00111a01.xml
http://www.anra.gov.au/topics/soils/erosion/index.html,
http://www.ga.gov.au/nmd/products/digidat/dem_9s.jsp
http://www.ga.gov.au/nmd/products/digidat/dem_9s.jsp
http://adl.brs.gov.au/mapserv/intveg/index.html


 external_metadata_test_dev.sh 12.8 KB   View   Download external_metadata_test_prod.sh 12.8 KB   View   Download wget_output_dev.txt 119 KB   View   Download wget_output_prod.txt 118 KB   View   Download Jun 26, 2011 #13 [email protected] 
Bryn has been emailed is going to take a look at these.

(the following relate to the name field in the layers table).

    slope
    aspect
    elevation
    aria
    soil_carbon
    ph
    sodicity
    landcover

These links are broken in both the dev and the prod environments (both 
environments will need to be fixed with an update sql script).

 Jul 13, 2011 #14 [email protected] 
Assigning to Bryn for metadata update.
 Owner: [email protected] Oct 6, 2011 Project Member #15 [email protected] 
Lowering non-biocache to High for now
 Cc: [email protected] Labels: -Priority-Critical Priority-High Jan 2, 2012 Project Member #16 [email protected] 
Allocating to myself. I'll try and track down broken metadata links and amend 
Layers Table.
 Owner: [email protected] Cc: [email protected] [email protected] [email protected] Jun 21, 2012 Project Member #17 [email protected] 
Post June.
 Labels: -Priority-High Priority-Medium Jul 8, 2013 Project Member #18 [email protected] 
land cover: 
http://adl.brs.gov.au/anrdl/metadata_files/pb_dpk09g9abl_01411a02.xml
ph: http://adl.brs.gov.au/anrdl/metadata_files/pb_dpk09g9abl_01411a02.xml
Sodicity: http://adl.brs.gov.au/anrdl/metadata_files/pb_dpk09g9abl_01411a02.xml
Carbon - organic: 
http://adl.brs.gov.au/anrdl/metadata_files/pb_dpk09g9abl_01411a02.xml
Remoteness index: 
http://adl.brs.gov.au/anrdl/metadata_files/pb_dpk09g9abl_01411a02.xml
Aspect: http://adl.brs.gov.au/anrdl/metadata_files/pb_dpk09g9abl_01411a02.xml

topographic slope (degrees) is ok (CMAR dataset)

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1067


Project Member Reported by [email protected], Jun 5, 2013 
What steps will reproduce the problem?

1. Add to Map | Areas | Gazetteer polygon

2. Enter "open alpine" and select the DLC class

3. Compare Lake Eyre DLC (attached) which is "brine" with mapped "open alpine 
class" (attached).

This is an URGENT (not "Medium") problem as some may not detect an error more 
subtle than this! It could be very embarassing.

 DLC.gif 184 KB   View   Download Alpine.gif 117 KB   View   Download Jun 5, 2013 Project Member #1 [email protected] 
(Copied from issue 632)

Hi Lee,

This problem is caused due to a problem with the special ingestion process that 
Adam developed to generate a contextual layer from a large gridded dataset. The 
only two layers that have been ingested using this process are Dynamic Land 
Cover and the new Land Cover Type layer that I got from AusCover.

For layers loaded via this process, a lot of data is read straight off files on 
disk where for other contextual layers it would be read from the layers 
database.

Because of this disk vs database difference, it is not possible to render 
gazetter areas for these layers in the ordinary way. So what Adam has done is 
display the entire layer that the layer belongs to, and then render it with a 
custom style to (in theory) only highlight the relevant area from the gazetter 
search. 

A problem with the generation of the custom style means that an incorrect area 
is highlighted.

I can fix the problem with the custom style, however there are a few other 
problems here:

1. The legend for the corresponding layer is displayed. e.g. the DLC legend is 
displayed when a gazetter search is done for "open alpine". This does not 
happen when a gazetteer area from other layers is displayed.

2. The hover tool displays values for the corresponding layer, even in 
non-highlighted areas. This does not happen when a gazeteer area from other 
layers is displayed.

3. The gazetteer area cannot be exported, used in an add to map/species etc. 
E.g. display "open alpine" and then try add to map/species.

I can fix the aforementioned style problem to get areas to display correctly, 
but as you can see this is only part of the problem.

Thoughts Lee and Dave?
 Jul 9, 2013 Project Member #2 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-High Jul 29, 2013 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Summary: Add to Map | Areas | Gazetteer polygon not working for some layers (dynamic land cover, surface geology) (was: Add to Map | Areas | Gazetteer polygon no working for some layers)

[deleted issue]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=565


Reported by [email protected], Jun 9, 2011 
Need to arrange with IM&T to open up the z3950 ports on ala-maps. Then need to 
contact John Hockaday to arrange ASDD harvesting of map metadata.
 Nov 22, 2011 #1 [email protected] 
ZReassigning to Chris - when you get back from China, touch base with Simon 
Pigot and Dave Matthews to find out what is required to get our geonetwork 
instance talking to a central index (I think it used to be called 
mymaps.gov.au).
 Owner: [email protected] Apr 24, 2012 Project Member #2 [email protected] 
Dependent on Simon Pigot update session TBA

 Apr 25, 2012 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-Critical Dec 3, 2012 Project Member #4 [email protected] 
This one is back high on the agenda after discussions with Helen Owen (OSP). We 
do need to facilitate access to our GeoNetwork metadata externally.
 Jun 5, 2013 Project Member #5 moyesyside 
I dont know what the progress is on this. Are we in active contact with anyone? 
if not suggest downgrading or closing. Im trying to build up a clearer picture 
of what issues we current have that need tackling ASAP.
 Status: WontFix Jun 5, 2013 Project Member #6 [email protected] 
I would rather see this issue as at least Low rather than WontFix as we need to 
ensure that we are corporate good citizens when it comes to exposing our 
metadata to the ASDD and other similar metadata aggregators. We have achieved a 
first in regards the environmental and contextual layers so not to have this 
exposed through our metadata doesn't do our profile justice.
 Status: Accepted Jun 5, 2013 Project Member #7 moyesyside 
Agreed.
 Labels: -Priority-Critical Priority-Low

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=829


Project Member Reported by [email protected], Jan 5, 2012 
GA_distance_to_coast
 Jan 5, 2012 Project Member #1 [email protected] 
provider: GA_distance_to_coast
 Apr 24, 2012 Project Member #2 [email protected] 
Delete layer dist_coast - this is in decimal degrees and not useful. Use 
dist_coast_me in its place.
 Apr 25, 2012 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-Critical Apr 25, 2012 Project Member #4 [email protected] 
There is a problem with the source data for this layer - no prj file is 
supplied, and the listed datum on the website (GDA94) results in a warped 
geotiff. Will need to contact GA about this.
 Labels: -Priority-Critical Priority-Low Jul 10, 2013 Project Member #5 [email protected] 
This needs a fix or two, namely (as above and more)

1. Remove layer ID=819  (substrate_distcoast) as it is useless as is and 
superceeded by ID=946

2. Layer ID=946 (dist_coast) is actually distance (km)/100 so we either need to 
change the legend or x 100 (latter better)

3. Classification of ID=946 is incorrect as "Marine | Distance". It should be 
Classification 1 = "Distance" 




 Cc: [email protected] moyesyside Labels: -Priority-Low Priority-High

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=566


Reported by [email protected], Jun 9, 2011 
Need to load Beards Province shapefile into postgis (on dev and prod), create 
geoserver vector layers and index in gazetteer.
 Aug 7, 2011 #1 [email protected] 
Loaded into dev and currently indexing within gazetteer

skel layer metadata record created

Over to Bryn to update
 Owner: [email protected] Mar 15, 2012 Project Member #2 [email protected] 
This one fell down the cracks. To Chris. Hopefully the file is still around. 
Was called Ben.zip (Ben Richardson request - WA). As Beard did an early 
bioregionalization, it would make sense to have this contextual loaded (gaz 
entries included).
 Owner: [email protected] Mar 15, 2012 Project Member #3 [email protected] 
edit title to fit Chris' scheme
 Summary: LOAD LAYER: Beards Province data of WA Apr 25, 2012 Project Member #4 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-Low Jul 10, 2013 Project Member #5 [email protected] 
Low hanging fruit and of high biodiversity relevance to WA - to medium
 Cc: moyesyside Labels: -Priority-Low Priority-Medium

[deleted issue]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=972


Project Member Reported by [email protected], May 8, 2012 
Hi, all - I've been referring to this myself as "experimental" as I would think 
the medium/longer term goal is to be able to, in a more advanced way do the 
following:
    1) Find sites/plots/survey areas 
    2) Find the above that have images over time
    3) Have a tool that enables comparison of these images over time (perhaps a timeline + ability to select some for side by side viewing) - I'm sure your ideas will be better than mine...

Associated with the above, I assume we'll need new data structures to support 
this - including aggregating images from a range of sources (ie: we may get 
nicely arranged images from TREND in an area but there will also others) + 
allow users to submit a photo of a site rather than a species etc etc...


 Jul 11, 2013 Project Member #1 [email protected] 
Fully agree Peter: 

The current Panoramio application in the SP support site-based images but these 
are totally unstructured: It is a suite of images taken by anybody at any time 
and any location. The minimal data is author, image, date/time, latitude and 
longitude. ANY image uploaded to Panoramio IS available in the SP. There is no 
search ability in the SP but that would be a terrific idea, if it is possible. 
All that can be done currently is zoom/pan to area of interest and after 
clicking the 'Panoramio button' (under zoom slider), images will appear.

In principle, it would be a great idea to have a more systematic approach to 
site-based images. Mind you, there is nothing stopping anyone from uploading 
high-quality, systematic site images to Panoramio, e.g., TERN images!

 Cc: moyesyside [email protected] Labels: -Priority-Low Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=994


Project Member Reported by [email protected], May 29, 2012 
Need to source a gridded version of this dataset - the only copy I can find of 
the raw data consists of extremely large shape files.

The layer then needs to be re-loaded using the GridClassBuilder


 Jun 18, 2012 Project Member #1 [email protected] 
Emailed Leo Lymburner to see if he can get a copy in grid format.
 Labels: -Priority-Medium Priority-High Jun 6, 2013 Project Member #2 [email protected] 
Hi Lee,

This one has fallen through the cracks - did you ever hear back about it? We 
had also discussed this with Kristen. Is it still a high priority?

Cheers,
Chris
 Cc: [email protected] moyesyside Jun 6, 2013 Project Member #3 [email protected] 
I've emailed Leo again about this. If no response, I'll ask Kristen as I know 
she will have this as a soil surrogate, but format - who knows.
 Jul 8, 2013 Project Member #4 [email protected] 
Kristen Williams has these data and could supply a 250m gridded version. Please 
pursue, via Miles?

NOTE: The reason the gridded data is needed is for processing for Tabulation 
and I suspect, Add to Map | Areas | Gazetteer polygon.

Remains a high priority as the layer is available to map but not to use in 
analyses. Inconsistent. Handed to Chris.
 Owner: [email protected] Cc: [email protected] [email protected]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=304


Project Member Reported by [email protected], Nov 22, 2010 
Code and documentation received from Glenn Manion. Slot in integration with the 
Spatial Portal
 Mar 17, 2011 Project Member #1 [email protected] 
Upping to HIGH as we need something basic running for meeting with Simon, 
Glenn, Kristen probably during the week of April 4.
 Labels: -Priority-Medium Priority-Critical May 12, 2011 Project Member #2 [email protected] 
Lowering priority till UI done.
 Cc: [email protected] Labels: -Priority-Critical Priority-High May 24, 2011 Project Member #3 [email protected] 
Started
 Status: Started Jan 2, 2012 Project Member #4 [email protected] 
Now to critical due to NPEI project that must be completed by June 30.
 Labels: -Priority-High Priority-Critical Feb 2, 2012 Project Member #5 [email protected] 
Ran all of Acacia on Tasmanian extent with equal site weight and first 5 test 
layers and didn't perceive that I got any GDM output other than the input-

http://spatial-dev.ala.org.au/output/gdm/1328233963170/

[DIR] Parent Directory                             -   
[   ] domain.grd              03-Feb-2012 12:52  311   
[   ] domain.gri              03-Feb-2012 12:52    0   
[TXT] gdm_params.txt          03-Feb-2012 12:52  673   
[TXT] species_points.csv      03-Feb-2012 12:52   33K  

 Feb 6, 2012 #6 ajay.ranipeta 
There was some code reverted. Process should now generate the species file with 
Longitude, Latitude, Species_name. 

Currently working on generating graphs and including them in the metadata file. 
 Feb 8, 2012 Project Member #7 [email protected] 
1. Need to swap over to import/paste assemblage code (which is seems to tap 
anyway)

2. Keeps cycling back to step 2 after mapping assemblage. Doesn't get to ask 
about environmental layers

3. Restrict mapped species to an area. Seems redundant as the area is defined 
in step 1? (So the answer is always "yes".


 Mar 1, 2012 #8 ajay.ranipeta 
latest code from Glenn now generates a segmentation fault.

metadata and charts should however be done (hopefully) now.
 Mar 13, 2012 #9 ajay.ranipeta 
In test.
 Status: InTest Mar 14, 2012 Project Member #10 [email protected] 
Looking good Ajay! A few comments

1. After designating layers should "working..." be replaced by a progress bar?

2. GDM options
Generate quantile from: Data                 [this is a statement, not an 
option?]
Use geographic distance as additional predictor: yes no
Use all site pairs  [this is also a statement as there is no option?]

3a. Naming prediction layers should default to something like "My GDM 
prediction"

3b. List of environmental layers is blank even though I selected the best 5. I 
can't get past Step 4






 Status: Started Mar 14, 2012 #11 ajay.ranipeta 
1. Leaving it as "Processing... ", I think. There is really one step which 
generates the domain grid and figures out the site pairs and should give you 
the option. I could randomly set it to, say a minute but it should take less 
than a minute to process

2.
a) it was meant to be an option, but now a default is set as recommended by 
Simon/Kristen. Now I've left it there for more as an information for the end 
users

b) this is fine.

c) No, not a statement. You should be able to uncheck the box which gives you 
more parameters to play with.

3a/b. Yea, so step 1 didn't really work, which might have not really finished 
off the whole process. This default layer name should come up as "My GDM".

testing and fixing the GDM issue now.
 Mar 14, 2012 #12 ajay.ranipeta 
somehow whoever updated the GDM code on dev didn't grab the latest from SVN. 
Have done that now and should all be fine. 

test again Lee.
 Status: InTest Mar 14, 2012 Project Member #13 [email protected] 
Thanks Ajay: A lot better.

1. The html looks good, but suggest the file be called gdm.html

2. ala.properties should be gdmparameters.txt.  Not sure how you want to 
differentiate this from gdm_params.txt

3. We need the transform grids as layers for further analysis (hover, sampling, 
scatterplot, classification, prediction). These I guess will just be scaled 0-1 
or 0-100. At the moment, there is nothing mapped from the run.

4. We need a Readme.txt file to describe all the files in the zip, as ever.

5. Would be good to substitute scientific name for species code in output 
(e.g., species frequency table)

6. Name for 'prediction layer' requested but not used?


 Status: Started Mar 14, 2012 #14 ajay.ranipeta 
1. ok

2. no, i generate the ala.properties so i can keep track of something to help 
generate the html page.

3. umm.. 

4. waiting for a final confirmation from Kristen/Simon/Glenn to get back to us 
about the current implementation and if there are any changes and any final 
file generations.

5. I'll need to generate a csv file that provides an index for species code to 
scientific name/lsid

6. huh? the file prompted for the download has the layer name set. 
 Mar 27, 2012 #15 ajay.ranipeta 
updated dev to include the output transformed grids as layer on SP. This will 
them to be available for:

- hover tool
- sampling
- other analysis tools

 Mar 27, 2012 #16 ajay.ranipeta 
(No comment was entered for this change.)
 Status: InTest Apr 1, 2012 Project Member #17 [email protected] 
No output layers mapped at the moment.
 Status: Started Apr 3, 2012 #18 ajay.ranipeta 
(No comment was entered for this change.)
 Status: InTest Apr 3, 2012 Project Member #19 [email protected] 
If Acacia + Eucalyptus are used for Tasmanian extent, GDM step 1 reports 0 
records per cell. It used to report a more realistic range.
 Status: Started Apr 12, 2012 Project Member #20 [email protected] 
Thanks Ajay. A lot better. The output transformed layers are all however called 
"Transformed null"


 Apr 12, 2012 #21 ajay.ranipeta 
(No comment was entered for this change.)
 Status: InTest Apr 12, 2012 Project Member #22 [email protected] 
Looks great! I'll get Kristen to have a play now.

 Apr 19, 2012 Project Member #23 [email protected] 
Kristen (April 19): Summary – issues with running more than default number of 
site pairs, classification of transformed grids didn’t work, additional 
outputs needed in zip file, HTML file needs a bit more work. 

1.  “records per cell” – this may be explained when we have the help files 
(when we write them) but intuitively “records” to me means the number of 
species by locations within a grid cell (I’m assuming this is a 1km grid 
cell). I think it would be more transparent to label this “taxa per cell” 
(do we mean species? are these matched-species, is there an option to choose 
matched species? it is important to know what the taxonomic unit is for GDM). 
I’m assuming the table represents the number of taxa per cell, rather than 
the number of records per cell. We had this conversation before and checked 
with Glenn. Even if Glenn uses the label “records per cell” and assuming 
the data is actually “taxa per cell” we should present the label as “taxa 
per cell”. 
2.   “Select a threshold to help generate the site pairs” this should be 
changed to something like: “Select the minimum number of taxa in a single 
grid-cell representing an assemblage to include”. The choice of threshold is 
designed to improve the quality of the data toward a “presence-absence” 
sample by removing grid cell (sites) from consideration, not so much to help 
with generating the site-pairs, but does reduce the number of sites considered 
in generating site-pairs. I used a threshold of ‘8’. 
3.  The bar for using all site pairs should also show the % site pairs (if easy 
to calculate on the fly)
4.  The button for “use all site pairs” – should say “choose the number 
of site pairs to use” or “use default number of site pairs”. I entered a 
number but it is not clear what would happen if I switched the button on or 
left it off. Are the button and bar interchangeable – one or the other, does 
one supersede the other? The default appears to be 1% (what was the rationale 
for the default?). The default should probably be set around 1 million site 
pairs or the number of available site pairs whichever is the lowest. For my 
random example the total site pairs is 4096000. The default is 40960. This 
wouldn’t be a big enough sample to model, so I chose 1045070. My analysis is 
for Corymbia with the 5 standard predictors. I choose weight by number of 
species. 
5.  Processing: after a short time a message comes back saying the server is 
temporarily out of services, and stops the analysis although one has to 
physically close the window. Seems to say something about a bad gateway…(is 
this a problem at my end related to my network and internet settings or 
software – I’m using Google Chrome - or at the ALA server end?) 
6.  I then had to start again. Perhaps the prelim analysis could be kept and 
become a set of assemblage points in then I could start again where I left off 
and try a different number of site pairs? This time I try 539391 site-pairs, 
and note that the bar is not present until I switch off the “default”… 
again the server out of service message came up… and the result below appeared
7.  GDM processing can take a while, it might be better if it went into the 
background on the server and returned the user to the ALA interface and then 
produced an email or pop-up when the processing is complete? 
8.  The user may undertake several iterations with GDM in order to find the best 
set of variables to include in the model. Typically, I iterate in using the 
fitting function of the model and when I’m satisfied I produce the 
transformed grids. 
9.  I try again, this time using the default number of site pairs….this time 
it worked…and I have a look through the outputs, the transformed grid are 
also available for further analysis (or modelling)
10. I now create a classification based on my transformed predictors using 20 
groups…but I received a failed message – in working through the steps of 
the classification, on the last page, the layer set is not listed? Is this an 
indicator of why the classification is not working with the transformed grids? 
I tried twice and the classification step failed each time…
HTTP Status 404 - /webportal//error/HTTP_NOT_FOUND.html.var

 Apr 19, 2012 #24 ajay.ranipeta 
Kristen (April 19): Metadata info

Comments on HTML report:

Under “your options” at the top of the HTML file need to include additional 
information about the parameters used in the analysis, please include:
-          Assemblage: (e.g. Corymbia) (plus include the records for the 
assemblage in the download; add the assemblage to the map in the spatial 
portal) I was able to create my own download but have no idea what the 
taxonomic unit in the GDM analysis is. Nor do I know what the list of species 
aggregated by grid cell is?

-          Number of unique taxa: # (include a list of taxa that can be related 
to the “code” in the species_points.csv file – we’ve talked through 
this before, the need to be able to identify the taxa used in the analysis – 
exactly what were these.)

-          Taxa resolution: subtaxa (i.e., is the cut-point of the taxa set at 
matched species or are all levels of taxa included?)

-          Grid-cell resolution: 0.01

-          Minimum number of taxa per grid cell: # (e.g. 8) (This is described 
as the cut point in GDM_parameters.txt)

-          Number of grid cells with taxa included in the model: #

-          Total number of site-pairs: # (e.g., 4096000)

-          Number of site-pairs used in the analysis: # (e.g. 40960)

-          Number of predictors used in the analysis: # (e.g. 5)

-          Number of I-splines per predictor: 3 (this is a default that is hard 
wired into this version of GDM)


Create a new section: “Model Summary” (this can be drawn from the file 
gdm_parameters.txt)
-          Intercept=0.612189

-          Null Deviance=70125.728738

-          GDM Deviance=54905.896804

-          Deviance Explained=21.703635

-          All Coefficients Summed=12.193876


Charts and text:
-          The cut-point.csv table could be presented first along with 
explanatory text so that users understand how to apply this parameter.

-          Observed versus predicted compositional dissimilarity (raw data 
plot): x-axis should not be labeled after a value of 1.0 (predicted values do 
not extend this far) and red line should end at a value of 1.0

-          “site pairs” or “site-pairs” inconsistent – I would prefer 
we used hyphenated “site-pairs”

-          Observed compositional dissimilarity vs predicted ecological 
distance (link function applied to the raw data plot): “The line represents 
the perfect 1:1 fit.” Not red curve and change to “The red curve represents 
the perfect 1:1 fit.”

-          Instead of “The scatter of points signifies noise in the 
relationship between the response and predictor variables.” Say “The 
scatter of points signifies residual variation and noise in the relationship 
between the response and predictor variables.” Not all of the scatter will be 
noise, some may be systematically correlated with variables not included in the 
model.

-          The plots of each predictor variable are not correctly linked into 
the HTML file…and links to the full plots as well as thumbnails would be 
handy – same as for maxent, from memory I think you can open the full plots 
by clicking on the thumb nails

-          Data list – need to include a list at the end of the HTML file 
describing each of the datasets provided in the zip file and what they mean. If 
Ajay could start with a list, I could draft the commentary and Glenn could 
check this is right (see attached spreadsheet for starters). I guess this is 
the objective of the “readme.html” which is presently blank.

-          Need lookup table relating “species code” to the actual taxon 
name used in the GDM analysis that would enable these to be matched to an ALA 
identifier in the data downloaded for an assemblage

-          Need a lookup table relating “EnvGrid#” to the layer name.  This 
can be inferred from the gdm_params.txt

 May 27, 2012 Project Member #25 [email protected] 
Kristen: I think it would be worth making step 4 GDM Options that produces the 
summary of species available with an Analysis ID. If the analysis fails (which 
it almost always does for me because I pick too large an extent or too many 
site pairs), one has to go back to scratch. If the entries can be saved at Step 
4, then one can make a small modification to the # site pairs and try again? 
Better still, run the GDM as a background job…so that most analyses produce a 
result. 

Lee: Ajay is currently working on background processing (#722).
 Status: Started Aug 21, 2012 Project Member #26 moyesyside 
Lee - to my knowledge this is all done and in production. Is this correct?
 Owner: [email protected] Cc: [email protected] [email protected] Aug 21, 2012 Project Member #27 [email protected] 
No, GDM isn't complete. Kristen and I still have to discuss what may be 
required to at least tidy GDM up. Kristen has her head down on NPEI and 
probably a heap of other work so I'm leaving it till she pops her head up. 
Needless to say, I'm busier than I'd like to be at this stage as well.
 Cc: [email protected] moyesyside Labels: -Priority-Critical Priority-High Jul 8, 2013 Project Member #28 [email protected] 
Lowering (Medium) until we can get some of Kristen's time. Issues:

1. GDM help review/edit
2. GDM case study

Updates to GDM will need to wait for higher priority issues to be addressed.
 Owner: [email protected] Cc: [email protected] [email protected] Labels: -Type-Enhancement -Priority-High Type-Task Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1029


Project Member Reported by [email protected], Aug 20, 2012 
What steps will reproduce the problem?

When producing a map for publications, it appears that the screen map extent 
can differ considerably from the image map extent. If you try and adjust the 
zoom level on the map window and try again with the export | map, it can 
overshoot the desired extent.

It looks like at least the high resolution (print) option has a series of zoom 
level that are coarsely quantized?

The size of the dots on the map also look to be larger than those on the 
exported image. This may howver be due to the zoom quantization effect?

The key issue is that the result is not WYSIWYG.
 Jul 8, 2013 Project Member #1 [email protected] 
Lowering this considering more critical issues
 Labels: -Priority-Critical Priority-Medium

[deleted issue]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=736


Project Member Reported by [email protected], Oct 19, 2011 
Allow 2 way use with sandbox.ala.org.au
 Oct 19, 2011 Project Member #1 [email protected] 
Adding Dave: We would really like to be able to use the Sandbox for the CSV 
uploads. Currently forget it. A good test set is "Demo_Random_100x9v.csv" at 
http://spatial.ala.org.au/files. 
 Cc: moyesyside Oct 20, 2011 Project Member #2 moyesyside 
Cheers Lee.

We need to integrate the biocache-store code with the new layers-index, so that 
this is the API  instead of the old gazetteer which is what we are currently 
using)  Need to catch up with Adam/Ajay/Gav about the possiblities here to make 
the point lookups as fast as possible.

We also need to add in support for dynamic fields - done using SOLR's dynamic 
index fields.



 Cc: [email protected] Mar 15, 2012 Project Member #3 [email protected] 
Current thoughts on the utility of this, given time left? 

My 5c - given other priorities, set to LOW
 Cc: [email protected] Labels: -Priority-Medium Priority-Low Mar 15, 2012 Project Member #4 moyesyside 
I think the one thing the sandbox is missing is the ability to handle and facet 
on arbitrary data fields including continuous variables. This is all possible 
but I agree with setting it as a low priority at this stage.

The benefit to the SP would be the ability to handle a richer data upload that 
included all the DwC terms that we handle/parse/process/cleanup.



 Cc: [email protected] Jul 10, 2013 Project Member #5 [email protected] 
Re-assign to Dave but still Low priority. The SP Facet on CSV import fields is 
still a deal breaker? In the SP, ANY point data can be imported (not just 
biological records) as with the wind farm case study and faceted on any import 
field (other than id, lat, long).
 Owner: moyesyside Cc: -ajay.ranipeta -moyesyside [email protected] [email protected] Jul 10, 2013 Project Member #6 moyesyside 
thanks Lee. Integration is done from sandbox to SP, it just requires the user 
to start at http://sandbox.ala.org.au.
Support is in the sandbox for faceting on any field.

e.g. 
http://sandbox.ala.org.au/hubs-webapp/occurrences/search?q=data_resource_uid:drt
1407

see http://www.ala.org.au/blogs-news/data/upload-your-data/

So we just need the UI integration on the SP
 Jul 10, 2013 Project Member #7 [email protected] 
OK, given this, I reckon it's worth a another integration step? Locations of 
change are

1. Add to map | Species | Import points
2. Tools | Points to grid | Import points
3. Tools | Scatterplot | Import points
4. Tools | Scatterplot list | Import points
5. Tools | GDM | Import points
6. Import | Import points
6. Tools predict | Import points

(Basically the same as the required alignment of Species List in 1064. It may 
therefore be expedient to do both at the same time.


 Labels: -Priority-Low Priority-High

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1072


Project Member Reported by [email protected], Jul 2, 2013 
Currently when importing own data points into Spatial Portal, the ordering of 
data columns is strictly defined. 

This means that people need to change their data sets for importing into 
different parts of ALA (For example Sandbox can accept DwC fields in arbitrary 
order)

Can Spatial Portal allow for arbitrarily ordered fields?

Note that this may cause a problem in that all data uploaded will need to have 
DwC or similarly labelled fields. Currently the upload demands are pretty 
simple - it doesn't matter what the column label is, as long as the data is in 
the right place.
 Today (44 minutes ago) Project Member #1 moyesyside 
(No comment was entered for this change.)
 Owner: moyesyside Today (44 minutes ago) Project Member #2 moyesyside 
(No comment was entered for this change.)
 Labels: Type-Enhancement Priority-Medium

[deleted issue]

[deleted issue]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=991


Project Member Reported by [email protected], May 27, 2012 
From Kristen Williams:

Hi Lee,



Here’s the LF7RUP datasets. It is a categorical dataset. I’ve included this 
as a float grid which is the format required by GDM.  However, GDM doesn’t 
work with categorical data – only continuous and ordinal…I don’t use this 
in GDM modelling, but it may be effective in Maxent modelling. This is the 0.01 
grid version. I’m still working on the 250m grid data. 



As in all the data I provide, the coastline of the 1km grid has been expanded a 
few cells to ensure full coverage and nodata cells have been filled to ensure 
consistency in data/nodata and modelling extent (a requirement for GDM 
analysis). 



The custodian is ANU, but Brenda Mackey was the contact – Brendan is now 
based with Griffith at the Gold Coast. 



I haven’t yet generated metadata also for this version of the layer, and will 
put that task on my to-do list. 



Cheers,

Kristen


 lf7rupw_1ke.zip 3.3 MB   Download Jun 6, 2013 Project Member #1 [email protected] 
(No comment was entered for this change.)
 Cc: moyesyside Jun 6, 2013 Project Member #2 [email protected] 
Hi Lee,

Are we still interested in this layer and is it priority critical?

Cheers,
Chris
 Jun 6, 2013 Project Member #3 [email protected] 
Let's lower the priority until we hear about any requests for it. Topographic 
position will certainly be more relevant at the 250m grid that 1km (0.01 
degree) - particularly for vegetation where this data can highly influence the 
species composition.
 Jun 6, 2013 Project Member #4 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Critical Priority-Medium Jun 6, 2013 Project Member #5 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-Low Jul 11, 2013 Project Member #6 [email protected] 
Kristen: I assume the categories are something like 'ridge', 'upper 
slope','mid-slope', 'lower slope' and 'valley'? Certainly could be useful in 
Sampling, MaxEnt and tabulation.

This dataset would only be of use at the 250m resolution (and with metadata :)) 

 Cc: [email protected]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=898


Project Member Reported by [email protected], Feb 27, 2012 
Load this layer, then set the opacity to around 33%. Notice that the country 
borders do not always line up with the google base map.
 Apr 25, 2012 Project Member #1 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-Low Jul 11, 2013 Project Member #2 [email protected] 
What is the date on the version of GADM? Metadata is 2011. There is a January 
2012 version of GADM and there is also http://geocommons.com/maps/185224 which 
may be handy with the standard country codes.

The boundaries seem to be ok in our area but agree, there are some anomalies

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=632


Project Member Reported by [email protected], Aug 30, 2011 
When we are onto the new BioCache...

Leo Lymburner would appreciate a species list for the Alpine and Sedges classes 
in the Dynamic Landcover layer. 
 Oct 13, 2011 Project Member #1 [email protected] 
Waiting on dynamic land cover layer on dev/prod. Upping to high as this layer 
is one of the most valuable we have.
 Owner: [email protected] Labels: -Priority-Medium Priority-High Oct 13, 2011 Project Member #2 [email protected] 
adding self
 Cc: [email protected] Oct 30, 2011 Project Member #3 [email protected] 
Added support for grid files as contextual layers.  dlcmv1 now operates 
correctly in layers-service on dev.
1. shape/ services are used to download an object area.  This needs a size 
limit and a message instead of the shape.  It is unreasonable to allow access 
to 500MB+ shapes.
2. Shapes produced from the grid file are accessed by a constructed id.  I do 
not think individual polygons generated from a grid require a pid.  

 Status: Started Oct 30, 2011 Project Member #4 [email protected] 
Dev: DLC currently reports "Layer unavailable"
 Apr 11, 2012 Project Member #5 [email protected] 
Update.  Only absent from tabulation and Add to map | gazetteer polygon.
 Cc: [email protected] Apr 11, 2012 Project Member #6 [email protected] 
Attempting to select alpine area (Add to Map | Areas | Select from mapped 
contextual | DLC. Got

The server is temporarily out of service.
Would you like to try again?

(404: Not Found)
 Apr 11, 2012 Project Member #7 [email protected] 
It did map after error reported. Assumed classes would be in gaz but appears 
not. Would be very useful if they were - otherwise can't answer Leo's question.

"Primarily Vegetated Natural & Semi-Natural Terrestrial Vegetation Herbaceous 
Graminoids Open Alpine"
 Cc: -ajay.ranipeta [email protected] Apr 11, 2012 Project Member #8 [email protected] 
Just noted comment 5. Sorry.
 Apr 20, 2012 Project Member #9 [email protected] 
Changing to InTest for the gaz polygon functionality.  e.g. search for 'open 
alpine'.

These areas are as functional as environmental envelopes.  They do require the 
sampling in biocache for operations on biocache occurrence records.  This will 
be in the next batch.
 Status: InTest Apr 25, 2012 Project Member #10 [email protected] 
This is still busted. Use gaz search on "alpine open" and multi-polygon is 
created by Area report won't work due to layer not indexed in BioCache. Adding 
Natasha. I'd like this done asap as Leo has been a fantastic supporter for the 
Atlas - and it has been on the books since August 2011!

The Dynamic Land Cover layer is one of the most important in the SP. We need it 
fully operational asap. ToCritical.

Also have a problem if I attempt an area from polygonal layer option on one 
alpine area. Spins wheels then produces error 404. Adam's problem.
 Status: Started Cc: [email protected] Labels: -Priority-High Priority-Critical Apr 25, 2012 Project Member #11 [email protected] 
What is the id for this layer?  Has it been released into production/synced to 
ala-macropus?
 May 2, 2012 Project Member #12 [email protected] 
Natasha the layer is cl1918.  layers-store sampling (for class names instead of 
numbers) and ala-maps data (for offset) updated today.  The class number 
instead of name was identified from the handful of biocache records with cl1918 
values with &fl, but that does not appear to be working now.
 May 2, 2012 Project Member #13 [email protected] 
Adam,

It looks as if the layer is in biocache:

http://biocache.ala.org.au/ws/occurrences/search?q=cl1918:[*%20TO%20*]&facets=cl
1918&facets=data_resource_uid&pageSize=0

Although there are only 858745 records that have values. I am not sure if this 
is correct for the layer.

Is there any action that I need to take?

 May 2, 2012 Project Member #14 [email protected] 
Could the 858745 records be the new/updated records since the last full 
refresh?  

If ala-macropus data sync is still daily then from tomorrow a full resampling 
for this layer will fix it.

Is there a way to test that the sampling is working for biocache, given the 
problems so far on our end?

 May 2, 2012 Project Member #15 [email protected] 
Not all the records have bee reprocessed since the last time I performed a 
complete resample/reprocess (on the 2012-04-14).

You can see this by inspecting the values for the last_processed_date:
http://biocache.ala.org.au/ws/occurrences/search?q=cl1918:[*%20TO%20*]%20&facets
=last_processed_date&facets=cl1918&pageSize=0

    "label": "2012-04-14T12:11:11Z",
    "count": 4853


The total number of records does seem a little low. But I am not sure about the 
coverage for the layer.

When the layer is available I will sample it and re run the processing on these 
858745 records. 

It will be applied to all records the next time we perform a complete 
reprocess.  

Is this OK?

 May 2, 2012 Project Member #16 [email protected] 
Perfect.  Can test it then.

Coverage is terrestrial Australia.  Similar but not the same number of records 
as the  others e.g. el874 26485514.  
 May 21, 2012 Project Member #17 [email protected] 
Re-assign to Lee and prod Natasha to inform me post BioCache re-index, then 
I'll get data to Leo
 Owner: [email protected] Cc: [email protected] [email protected] May 15, 2013 Project Member #18 moyesyside 
can this issue be closed ?
 May 15, 2013 Project Member #19 [email protected] 
No, but I'll work on the lists now.
 May 15, 2013 Project Member #20 [email protected] 
We have a problem. If I do the following:

1. Add to Map | Layers | DLC - it maps the layer

2. Add to Map | Area | Gazetteer polygon | primarily ........open alpine

The alpine areas do NOT match. A worry. (2) is MUCH larger than it should be 
(not restricted to the Alpine class).
 Cc: [email protected] May 15, 2013 Project Member #21 [email protected] 
(No comment was entered for this change.)
 Cc: [email protected] moyesyside May 16, 2013 Project Member #22 moyesyside 
Added Chris.

I've just  tested this i think and it seems ok to me. See screenshot attached.

Lee - can you attach a screenshot or add further detail ?
 Screen Shot 2013-05-16 at 4.59.07 PM.png 324 KB   View   Download Cc: [email protected] [email protected] May 16, 2013 Project Member #23 [email protected] 
I am 100% that the gazetteer class for alpine (and probably all others) is not 
correct. Images are of the alpine class for all Australia and a zoom in on Lake 
Eyre which is reported as part of alpine class in gazetteer but is BRINE class 
on DLC.
 DLC_Alpine_Class.gif 301 KB   View   Download DLC_Alpine_Class_Lake Eyre.gif 44.0 KB   View   Download DLC_Brine_Class_Lake Eyre.gif 236 KB   View   Download Jun 5, 2013 Project Member #24 [email protected] 
Hi Lee,

This problem is caused due to a problem with the special ingestion process that 
Adam developed to generate a contextual layer from a large gridded dataset. The 
only two layers that have been ingested using this process are Dynamic Land 
Cover and the new Land Cover Type layer that I got from AusCover.

For layers loaded via this process, a lot of data is read straight off files on 
disk where for other contextual layers it would be read from the layers 
database.

Because of this disk vs database difference, it is not possible to render 
gazetter areas for these layers in the ordinary way. So what Adam has done is 
display the entire layer that the layer belongs to, and then render it with a 
custom style to (in theory) only highlight the relevant area from the gazetter 
search. 

A problem with the generation of the custom style means that an incorrect area 
is highlighted.

I can fix the problem with the custom style, however there are a few other 
problems here:

1. The legend for the corresponding layer is displayed. e.g. the DLC legend is 
displayed when a gazetter search is done for "open alpine". This does not 
happen when a gazetteer area from other layers is displayed.

2. The hover tool displays values for the corresponding layer, even in 
non-highlighted areas. This does not happen when a gazeteer area from other 
layers is displayed.

3. The gazetteer area cannot be exported, used in an add to map/species etc. 
E.g. display "open alpine" and then try add to map/species.

I can fix the aforementioned style problem to get areas to display correctly, 
but as you can see this is only part of the problem.

Thoughts Lee and Dave?

 Jun 5, 2013 Project Member #25 [email protected] 
Thanks Chris. I remember Adam telling me about this. We do need a mechanism for 
generating polygons based on a class of what I called a 'non-unique (polygon) 
contextual layer' (e.g., States and Territories, DLC etc. 'Unique polygon 
contextual layers' are for example LGAs (I presume) or drainage catchments.

The gazetteer in the SP is one of the most powerful tools, mainly due to the 
integration of a wide range of location information, not just the traditional 
Australian point gazetteer. 

The power of 'Add to Map | Areas | Gazetteer polygon' is extreme. I suspect the 
biggest use will be for 'Tools | Area analysis' (and the Tools | Tabulation of 
course). This was the context of the request from Leo (and this will be a VERY 
common request!). Also, as you probably know, I'm EXTREMELY keen to beef up the 
Area Report. There are a number of easily added measures that would be great to 
see. This feature would be a game-changer.

We can certainly live with your 1 and 2 but the export bit of 3 is a pity (that 
we may have to live with). I've had about 10 requests for the ability to export 
the polygons from one class of a contextual map - mainly because this info is 
not available by other means.

 Jun 14, 2013 Project Member #26 [email protected] 
I have fixed the display of the gazetteer areas for DLC and also the Auscover 
land type layer. Note that these areas still can't be used for export, add to 
map species etc.
 Jun 18, 2013 Project Member #27 [email protected] 
NOPE: Problems remain.

Scenario-

1. Go to http://spatial.ala.org.au/
2. Add to Map | Area | Gazetteer polygon
3. Enter "open alpine" (for example) and select that class from the DLC layer
4. Tools | Area report - and use the default selected area  (Primarily 
Vegetated Natural & Semi-Natural Terrestrial Vegetation )
5. Download species list
6. Map all occurrences

Problems:

IThe area is mapped fine but the species list doesn't make sense with the Area 
report saying

1. Area is 0 sq km!
2. 3 species which map out at lat/long 0/0 with 4 occurrences...


 Jun 18, 2013 Project Member #28 [email protected] 
I should have expanded on my comment "Note that these areas still can't be used 
for export, add to map species etc." - it is now possible to correctly display 
classes from the DLC and Auscover land cover type layers via a gazetter search. 
That was the bug fix that I made.

However the resulting "area" cannot be used in further operations. Export, add 
species to map, area report all will not work or will not work correctly. It 
appears that the support for contextual layers derived from large grids was not 
completed. This is not a bug but an incomplete feature.
 Jul 9, 2013 Project Member #29 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Critical Priority-Medium

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=954


Project Member Reported by [email protected], Apr 29, 2012 
New version of this layer has been supplied by Kristen. See below. Also, the 
metadata for this layer needs to be loaded into getnetwork - see attached file.

Hi Lee,


I have created a corrected wii layer which applies a different resampling
method:
ftp://ftp.csiro.au/wil00p/ wii_1km.zip

The data is in geographics wgs84, projected from the lamberts (90m) to
geographics (0.01 degrees) using bilinear resampling. Lakes and water bodies
appear as nodata. The  version ending in 'e' has values assigned to nodata
areas based on a Euclidean allocation (nearest) and masked by the domain we
have been using Nationally as a seamless coverage for modelling.


regards,
Kristen
 1kmGDMsubstrateparent_NationalGeophysicsData_WII.xml 40.3 KB   Download Dec 3, 2012 Project Member #1 [email protected] 
This would be good to get loaded, but as High priority
 Labels: -Priority-Critical Priority-High Jul 8, 2013 Project Member #2 [email protected] 
Reason for update? I presume new/improved data. Changing to 'Medium' for now 
given other priorities.
 Labels: -Priority-High Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1071


Project Member Reported by [email protected], Jul 2, 2013 
Spatial Portal. When exporting own data, if a layer is not chosen, export 
fails. MESSAGE: Unknown error

What steps will reproduce the problem?
1. Import own dataset
Add to Map - Species - Import points
2. Export that dataset
Export - Point Sample
Area=current extent
Select species=MyData
Sampling - DO NOT CHOOSE A LAYER (if you choose a layer, this export will not 
fail)
3. Message=Unknown error

What is the expected output? 
Download of my own data

What do you see instead?
Error message, Message=Unknown error

What version of the product are you using? On what operating system?
FF21 on Win7

Please provide any additional information below.
Probably not a serious error. Why would anyone want to export their own data 
without adding any layers, etc?
However, I had a problem with the operation of the SP and was trying to check 
whether it was my data (had ALA corrupted it) or something else.
 Jul 8, 2013 Project Member #1 [email protected] 
Verified error. Thanks John.

We need to at least produce a reasonable message that says something like "No 
sampled layers have been selected" when an "Export | Point sample" is attempted 
on an "Import | Points" - illogical as it is.
 Status: Accepted Owner: [email protected] Cc: [email protected] moyesyside [email protected]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=922


Project Member Reported by [email protected], Mar 25, 2012 
gdalwarp by default uses "nearest neighbour" sampling. This is not desirable. 
Any layers that have been generated from gridded data need to be resampled 
using the "cublicspline" sampling method


 Apr 24, 2012 Project Member #1 [email protected] 
Cubic spline resampling should be used for environmental layers that need to be 
downscaled (i.e. 250m to 1km)

Same issue will occur with contextual layers but cannot use cublic spline 
resampling - will need to use a different method.
 Apr 25, 2012 Project Member #2 [email protected] 
Lowering. Acacdemic for now.
 Labels: -Priority-Medium Priority-Low Apr 25, 2012 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Low Priority-Critical Apr 25, 2012 Project Member #4 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Critical Priority-Low Jul 11, 2013 Project Member #5 [email protected] 
Please discuss and then we will revise issue. Can we batch up the processing? 
What are we doing with new additions?
 Cc: [email protected]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1022


Project Member Reported by [email protected], Jun 21, 2012 
It would be extremely useful to have a basic scatterplot web service. Supply 
species and 2 layers and return image.

Also add to /ws doco
 Dec 3, 2012 Project Member #1 [email protected] 
(No comment was entered for this change.)
 Owner: moyesyside Cc: [email protected] Labels: -Priority-Critical Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=631


Project Member Reported by [email protected], Aug 29, 2011 
We have had a number of failures on Prod where we have had no warnings leading 
up to the failure.

Once we know what issues have caused the failures (#629), we need a monitoring 
system that provides advance warning of potential failure on any vulnerable 
parts of our systems and processes. That way, we can take action or better tune 
the system to reduce the probability of failure.
 Aug 29, 2011 #1 [email protected] 
xymon has been configured for all of the spatial hosts.

Dave, could we (adam, ajay, and myself) get added to the xymon notification
list for these hosts:


   - ala-devmaps.vm.csiro.au
   - ala-devmaps-db.vm.csiro.au
   - ala-testmaps.vm.csiro.au
   - ala-maps.vic.csiro.au
   - ala-maps-db.vic.csiro.au


Also, could you please specify what the alert thresholds are for the
following xymon monitors:

   - conn
   - cpu
   - disk
   - diskio
   - http
   - info
   - memory
   - msgs
 Sep 8, 2011 #2 [email protected] 
Reassigning to Dave for action
 Owner: [email protected] Mar 4, 2012 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-High Priority-Low Jul 11, 2013 Project Member #4 [email protected] 
Raising this back up given the failure yesterday of the layers service and that 
I seem to be the one mostly detecting the failures.
 Cc: -ajay.ranipeta [email protected] [email protected] moyesyside Labels: -Priority-Low Priority-High

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=971


Project Member Reported by [email protected], May 8, 2012 
Organisation: Berkeley University
Contact: John Wiezorek
Link: http://www.gdam.org
Type: Contextual
 May 21, 2012 Project Member #1 [email protected] 
(No comment was entered for this change.)
 Labels: Type-Enhancement

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1069


Project Member Reported by [email protected], Jun 9, 2013 
Dynamic land cover is one of the most valuable layers in the SP. There has been 
a release of a standardized set of annual estimates of dynamic land cover by 
Leo Lymburner of Geoscience Australia.

There will also be an ongoing commitment by GA to add annual updates.

There is very high ecological value in looking at the changes in land cover 
between years.

I'd consider these layers as having the highest priority among potential 
additions to the layers library.
 image001.png 712 KB   View   Download Jun 9, 2013 Project Member #1 moyesyside 
Sounds good to me.

Lee - can you comment on their availability? Got a link?
 Jun 12, 2013 Project Member #2 [email protected] 
Talking with Leo, these data will probably be available at the end of 2013.

 Jul 8, 2013 Project Member #3 [email protected] 
Waiting on Leo. TBA: Expect December 2013. Lowering
 Labels: -Priority-High Priority-Low Today (44 minutes ago) Project Member #4 moyesyside 
(No comment was entered for this change.)
 Labels: Type-Enhancement

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1075


Project Member Reported by [email protected], Jul 11, 2013 
While users can send compute intensive tasks to background processing, there is 
no management of the number and intensity of tasks. It is highly likely (and 
desirable) that the number of 'hard' tasks increase over time. These can be ALA 
tasks (e.g., processing layers) or user-tasks. 

It would therefore be wise to setup a way to shuffle such tasks off to a 
pipeline that could schedule and manage compute-intensive tasks and notify 
authors when complete. In this way, we could better manage impact on servers. 
Obviously a separate server for the pipeline would be neat.

[deleted issue]

[deleted issue]

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=767


Reported by [email protected], Nov 1, 2011 
Upgrade geoserver on dev and prod to the latest trunk release (Simon has been 
busy fixing bugs).

 Nov 22, 2011 #1 [email protected] 
Chris and I will start this today
 Status: Started Cc: [email protected] Nov 22, 2011 #2 [email protected] 
Upgrade of Geonetwork (not Geoserver!)
 Summary: Upgrade Geonetwork Mar 15, 2012 Project Member #3 [email protected] 
Moved from Gavin to Chris. This could be tricky before outstanding layers are 
processed. Given no leverage over Simon Pigot, we may have problems here.
 Owner: [email protected] Cc: [email protected] moyesyside Labels: -Priority-High Priority-Medium Apr 25, 2012 Project Member #4 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-Medium Priority-Critical May 12, 2013 Project Member #5 moyesyside 
Need to know why this is critical. Is someone actively trying to integrate with 
our GeoNetwork install?

Downgrading to  medium for now.
 Labels: -Priority-Critical Priority-Medium May 15, 2013 Project Member #6 [email protected] 
We have had longstanding requests from http://asdd.ga.gov.au/asdd/, ANDS and 
iMOS (and TERN??) to tap our metadata via GeoNetwork and if I remember 
correctly, our version was not up to date nearly two years ago. 

As a general principle, it would seem wise to keep GeoNetwork up to date as 
this is rapidly developing (and universally accepted) metadata software.

We also need to maintain some knowledge about this system.

[deleted issue]

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=717


Project Member Reported by [email protected], Oct 16, 2011 
Ran a broad test on Prod using the iPad and here are the issues I found. I 
realize that it is probably not designed for the type of heavy browser load the 
SP can involve-

1. Difficulties in tapping on small icons such as remove menu (LHS) and restore 
menu

2. Next button on species upload won't activate (not selectable) 

3. No support for map or scatterplot digitizing. Unsure how we could address 
this.

4. Sampling seems to cycle through steps 1-3

5. Sliders don't work that well. What seems to work is to click on slider 
position.

6. No point select for Hover Tool support
 Nov 22, 2011 #1 [email protected] 
Reassigning to Ajay for consideration.
 Owner: ajay.ranipeta Feb 22, 2012 Project Member #2 [email protected] 
 Issue 896  has been merged into this issue.
 Cc: [email protected] [email protected] Apr 11, 2012 Project Member #3 [email protected] 
Fix for main menu now seems to work fine. Thanks Adam.

Still odd 'selection' function occurs when using auto-completes.
 Status: Started Apr 25, 2012 Project Member #4 [email protected] 
(No comment was entered for this change.)
 Owner: [email protected] Cc: [email protected] -ajay.ranipeta Labels: -Priority-Medium Priority-Critical Jun 5, 2012 Project Member #5 [email protected] 
Lowered
 Labels: -Priority-Critical Priority-Low Jul 10, 2013 Project Member #6 [email protected] 
Reassigning and to Medium. Given the rise of the tablet, this is an issue that 
needs to be at least evaluated in the next 3 months. 

Adam did some work-arounds on species selections that worked well, but at this 
stage, I have no idea how tricky some of the 6 issues above would be.
 Owner: [email protected] Cc: moyesyside Labels: -Priority-Low Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=737


Project Member Reported by [email protected], Oct 19, 2011 
With Adam's new "layer-memory" strategy, the shortnames (for entry) are looking 
more cryptic and confusing. For example, it is Bioclim_bio15, not Bio15.

As shortnames are an efficient way of entering layers, it may be wise to 
consider a systematic renaming that would make shortnames more intuitive? 

For example, bio15, wbio15. "rhu215_i" doesn't strike me as natively intuitive.

Gavin: Can you have a think about this?

BTW: I have asked maragert, Kristen and Renee to provide more layer keywords.

 Nov 22, 2011 #1 [email protected] 
Reassigning to Chris - I think Lee wants to rationalise the layer shortnames 
that are currently used (stored as name in layers table).
 Owner: [email protected] Mar 15, 2012 Project Member #2 [email protected] 
probably not time for this before June 30,2012 (but a good idea anyway).
 Labels: -Priority-Medium Priority-Low

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1070


Project Member Reported by [email protected], Jun 19, 2013 
Shape files of type "Polygon 3D" cause errors during sampling such as the 
following:

loading shape records error: /data/ala/data/layers/ready/shape/tams_reserves: 
java.nio.BufferUnderflowException
java.nio.BufferUnderflowException
 at java.nio.Buffer.nextGetIndex(Buffer.java:478)
 at java.nio.HeapByteBuffer.getInt(HeapByteBuffer.java:336)
 at org.ala.layers.intersect.PolygonZ.<init>(SimpleShapeFile.java:913)
 at org.ala.layers.intersect.ShapeRecord.<init>(SimpleShapeFile.java:664)
 at org.ala.layers.intersect.ShapeRecords.<init>(SimpleShapeFile.java:585)
 at org.ala.layers.intersect.SimpleShapeFile.<init>(SimpleShapeFile.java:94)
 at org.ala.layers.intersect.SamplingThread.intersectShape(SamplingThread.java:178)
 at org.ala.layers.intersect.SamplingThread.sample(SamplingThread.java:93)
 at org.ala.layers.intersect.SamplingThread.run(SamplingThread.java:67)


A workaround is exporting the shape file from the database using pgsql2shp, see 
:http://code.google.com/p/alageospatialportal/wiki/ContextualLayerLoadProcess#3d
_polygons

the intent of the PolygonZ class is to handle 3d polygons. Either this class 
should be fixed, or it should be removed and a more appropriate error message 
should be thrown when a 3d polygon is found during the sampling process.
 Jul 8, 2013 Project Member #1 [email protected] 
Can we check for a 3d polygon on import (which I presume is the only way a 3d 
can occur?) and generate 2d version as above?

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=1076


Project Member Reported by [email protected], Jul 31, 2013 
What steps will reproduce the problem?

1. Tools | Points to Grid 
2. Australia (current) extent | Acacia paradoxa | defaults (0.05 x 9 x 9)

Error message:

Too many potential output grid cells.  Decrease area or increase resolution.

SHOULD READ

Too many output grid cells: Decrease area or increase grid size.

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=575


Project Member Reported by [email protected], Jun 16, 2011 
Backups are occurring but for peace of mind, it would be good to do a test 
restore of the production system to the test vm. There is currently nothing 
happening on test that will be affected.

Dave: Can this be organized??
 Aug 9, 2011 #1 [email protected] 
(No comment was entered for this change.)
 Status: Started Oct 6, 2011 Project Member #2 [email protected] 
reset non-biocache issues to High
 Labels: -Priority-Critical Priority-High May 6, 2012 Project Member #3 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-High Priority-Low Jul 11, 2013 Project Member #4 [email protected] 
Is this still an issue? I suspect so.
 Summary: Test restore Prod - Test (was: Test restore Prod to Test) Cc: -ajay.ranipeta [email protected] moyesyside [email protected] Labels: -Priority-Low Priority-Medium

Original Issue  - 
https://code.google.com/p/alageospatialportal/issues/detail?id=801


Reported by [email protected], Nov 29, 2011 
load "layers->political->Australia States and Territories"  and then look at 
border area. I looked at the border between Canberra and Queanbeyan and also 
Cameron Corner http://en.wikipedia.org/wiki/Cameron_Corner.  The Google 
supplied borders matched the base layers but "layers->political->Australia 
States and Territories" matched neither. 
The end result is confusing if you are trying to work out visually which state 
a point close to the border is in. Important for understanding the operation of 
Sensitive data rules.

In addition the "layers->political->Australia States and Territories" shows a 
dog leg in the border near Cameron Corner that I have not been able to see on 
other maps.
Unfortunately the "View metadata for Australian States .." page 
http://spatial.ala.org.au/alaspatial/layers/22  has broken links.

The same issues apply to the LGA Boundaries layer as well
 Nov 29, 2011 #1 [email protected] 
I have just tested "layers->Marine->boundaries->States including coastal 
waters" and the State boundaries it includes match very closely with the google 
boundaries and base layers.
This layer also has excellent metadata associated with it and appears 
authoritative.  
 Nov 29, 2011 #2 ajay.ranipeta 
setting to Lee for triage 
 Owner: [email protected] Nov 29, 2011 Project Member #3 [email protected] 
It boils down to a need for a better States and Territories layer and fixing 
the broken links in the layer table. Meanwhile, the states/territories with 
coastal waters will need to suffice.

There is a 2011 states/territories shapefile at 
http://abs.gov.au/AUSSTATS/[email protected]/DetailsPage/1270.0.55.001July%202011?OpenDoc
ument. Metadata? Who knows.
 Status: Accepted Owner: [email protected] Cc: [email protected] Nov 29, 2011 Project Member #4 [email protected] 
(No comment was entered for this change.)
 Cc: [email protected] Feb 15, 2012 #5 ajay.ranipeta 
Should this be done by Chris as he is set to update the LGA boundaries?  Issue 
670  
 Feb 15, 2012 Project Member #6 [email protected] 
Yes. Over to Chris to lead. Added the updated states/territories to the 
ListOfOutstandingLayersToBeIngested spreadsheet on Google Docs.
 Owner: [email protected] Labels: -Priority-Medium Priority-High Apr 24, 2012 Project Member #7 [email protected] 
Changing title to reflect that this layer needs to be loaded.
 Summary: LOAD LAYER: States and Territories Polygons 2011 Apr 25, 2012 Project Member #8 [email protected] 
(No comment was entered for this change.)
 Labels: -Priority-High Priority-Low Jul 10, 2013 Project Member #9 [email protected] 
This is a basic layer used in many applications and there appears to be an 
offset of up to 1km on the ACT boundary so it would be a good idea to update 
this layer asap. Agree with Doug that the layer "States and territories 
including coastal waters" is far more accurate
 Cc: [email protected] moyesyside Labels: -Priority-Low Priority-High