atlasoflivingaustralia / biocache-service Goto Github PK

From @djtfmartin on August 19, 2014 10:31

migrated from: https://code.google.com/p/ala/issues/detail?id=98
date: Thu Aug 8 16:27:28 2013
author: moyesyside

Original Issue reported by Reported by [email protected], Today (16 hours ago) - https://code.google.com/p/ala-portal/issues/detail?id=300

Reported by [email protected], Today (16 hours ago)
I have been told that when we refer to 'fish' as a lifeform we should use the word 'fishes'
See http://australianmuseum.net.au/fish-and-fishes

The word 'fish' should be changed to 'fishes' when referring to a lifeform.

What steps will reproduce the problem?
An example:
Australian Museum Ichthyology collection. in the graph of records by higher level group:
Axis is Arthropods Fish Insects Reptiles

What is the expected output? What do you see instead?
Axis is Arthropods _Fishes_ Insects Reptiles

What version of the product are you using? On what operating system?
2013

Please provide any additional information below.
The term 'fish' is probably incorrectly used in a bunch of places.

This is a low priority fix.
fish or fishes.png 4.7 KB   View   Download

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#14

Externalise i18n files so they can be configured outside of the biocache-service.war

From @Tasilee on August 19, 2014 13:4

migrated from: https://code.google.com/p/ala/issues/detail?id=634
date: Wed Apr 9 23:58:26 2014
author: [email protected]

1. The ORDERING of geospatial facets appears random (=dog's breakfast):
   Uncertainty (in metres)
   Sensitive
   State conservation
   State conservation (unprocessed)
   IMCRA (meso-scale)
   Local Gov. Area
   State/Territory
   Country
   Biogeographic region
   IBRA
   IMCRA
   Dynamic land cover
   Vegetation types - native
   Vegetation types - present
   Spatial validity
2. NAMING of facets is inconsistent, e.g., the IBRA layers in the SP are named (Add to Map | Layers)-

IBRA 6 Regions
IBRA 6 Sub Regions
IBRA 7 Regions
IBRA 7 Subregions

but in the facets, you have

IBRA

So which IBRA is it? You could find out by mapping all the IBRA layers and checking alignment of points, but this is obtuse.

1. If the IBRA noted above is actually IBRA 6 Regions or Sub Regions, why is it still there when IBRA 7 supersedes it? Therefore, what is the process for deprecating facets? What is the process of identifying and 'loading' a new facet from a new contextual layer?
2. Ideally, a user should be able to facet on non-trivial (e.g., not single polygons of small extent, e.g., GER polygons) CONTEXTUAL non-trivial layers as this is a powerful filtering mechanism.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#69

API described here: http://api.ala.org.au/#ws98

Example URL in API docs:

http://biocache.ala.org.au/ws/occurrence/facets?flimit=10&q=data_resource_uid:dr359&facets=taxon_name

Facet results should be able to be paginated via the foffset param. E.g. http://biocache.ala.org.au/ws/occurrence/facets?flimit=10&q=data_resource_uid:dr359&facets=taxon_name&foffset=10

but this gives the same result set as the first URL. I also tried using the param startIndex mentioned in the API docs but this gave the same result set also.

From @sadeghim on December 23, 2014 2:10

Does the spatial portal export taxonomic lists in different levels through Export Checklist?

Here is the related request asked by an Atlas user:

I have found a major fault that has crept in since the last time I did a
search in Spatial Portal on organisms in a defined area. All the
infraspecific information (eg subspecies, variety) has been deleted from
the result of the search.

Taxonomists regularly move organisms from being a full species to a
subspecies or variety of another species and back again. Governments
gazette particular infraspecies of an organism as Threatened Species or
Noxious Weeds. Other infraspecies of the same species are not so
gazetted. This information is important.

Copied from original issue: AtlasOfLivingAustralia/spatial-portal#55

From @Tasilee on August 19, 2014 13:7

migrated from: https://code.google.com/p/ala/issues/detail?id=650
date: Sun Apr 27 15:59:51 2014
author: [email protected]

In developing the R library (ALA4R) for interfacing with ALA data, inconsistencies in the assertions have been detected.

The assertions developed by the ALA are the most significant value-add to the records available - particularly for the research community. 'Data Quality' has remained one of the most significant issues raised by the research community so it is vital that we communicate the assertions in a comprehensive and consistent manner. The intent in ALA4R is to enable users to visualize the assertions associated with a record set. For this to happen, assertions need to be comprehensive and consistent.

There are at least three sources of information related to record assertions in the ALA

1. http://biocache.ala.org.au/ws/assertions/codes
2. http://bit.ly/peFILi
3. Downloaded records from spatial portal, biocache, ALA4R etc

There needs to be one location where the list of assertions are, and (extremely important), their definitions can be found. This location should be linked to wherever assertions are exposed. There are currently missing assertions from the list in (2) above and others are not defined.

Assertions need to be a consistently named. At the moment, there are two different sets of names (and maybe more). I'd suggest that the names at http://biocache.ala.org.au/ws/assertions/codes be used throughout the systems.

As far as I can tell, the assertions appended to downloads are a consistent subset. If it was decided to remove assertions for which ALL records are "FALSE" (as was suggested happens by Dave M), fine - but this may conflict (at least by default) with Issue #489. There is a current maximum of 87 assertions so there is probably a case for removal of 'non applicable' assertions from the records downloads to reduce data volume.

The attached spreadsheet is a summary of the assertions from the three locations noted above. Highlighted cells in the spreadsheet represent missing information, as far as I can tell - without comprehensive definitions.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#74

From @nickdos on August 19, 2014 13:3

migrated from: https://code.google.com/p/ala/issues/detail?id=632
date: Wed Apr 9 19:13:44 2014
author: nickdos

E.g. http://biocache.ala.org.au/ws/webportal/bounds.json?q=lizard

returns

[
-175.333,
-322.35,
955.95,
54.083333
]

NE lng value is 955 but should not be more than 180.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#68

JSONP is being phased out in preference to using CORS and jQuery has much better support for error handling and POST requests when using CORS over JSONP.

I've aleady added it to bie-service here:

AtlasOfLivingAustralia/bie-service@347e998

So it should be straight forward to add a similar servlet or Spring filter to do the same thing.

From @djtfmartin on August 19, 2014 10:34

migrated from: https://code.google.com/p/ala/issues/detail?id=128
date: Thu Aug 8 16:38:03 2013
author: moyesyside

Original Issue reported by Reported by [email protected], Apr 16, 2012 - https://code.google.com/p/ala-portal/issues/detail?id=220

Reported by [email protected], Apr 16, 2012
All the values of the type_status facet are singular except for paratypes.

Screen shot 2012-04-17 at 8.38.16 AM.png 22.6 KB   View   Download

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#23

From @mbohun on August 19, 2014 13:5

migrated from: https://code.google.com/p/ala/issues/detail?id=638
date: Mon Apr 14 22:42:36 2014
author: [email protected]

This is a regression issue since String getQueryHash(HttpServletRequest request) method has been used to get the name of the map file.

This is because the hash of the normal query string will be different to the hash that includes forceRefresh=true.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#71

From @djtfmartin on August 19, 2014 10:31

migrated from: https://code.google.com/p/ala/issues/detail?id=112
date: Thu Aug 8 16:34:11 2013
author: moyesyside

Original Issue reported by Project Member Reported by [email protected], Aug 4 (3 days ago) - https://code.google.com/p/ala-portal/issues/detail?id=299

Project Member Reported by [email protected], Aug 4 (3 days ago)
Attached to this issue is the patch required to upgrade to SOLR4.4.0. This code base will not be committed into the trunk until we are ready to release biocache-service at SOLR 4.4 level.
Aug 4 (3 days ago) Project Member #1 [email protected]
(No comment was entered for this change.)
Labels: SOLR Aug 5 (2 days ago) Project Member #2 [email protected]
I didn't realise that there was a bug in one of my files. Here is that works
SOLR4.4-integration.patch 31.1 KB   View   Download

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#15

From @pbrenton on August 19, 2014 12:21

migrated from: https://code.google.com/p/ala/issues/detail?id=489
date: Wed Dec 18 17:02:01 2013
author: [email protected]

Reported by user wanting to do periodic manual exports from ALA to import into a local system for mapping and analysis.

The sequence of columns for DQ test results is inconsistent in the CSV output between different download events. Client is finding this makes processing on his end difficult.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#54

From @chrisala on August 19, 2014 11:56

migrated from: https://code.google.com/p/ala/issues/detail?id=283
date: Tue Nov 5 21:59:40 2013
author: [email protected]

Requested via support email on 6/11.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#51

From @nickdos on August 19, 2014 13:0

migrated from: https://code.google.com/p/ala/issues/detail?id=607
date: Wed Mar 12 18:58:16 2014
author: nickdos

E.g. http://biocache.ala.org.au/ws/occurrences/search?q=flower&fq=taxon_name%3A%22Lomandra+longifolia%22&fq=raw_taxon_name%3A%22Lomandra+longifolia%22&fq=-basis_of_record%3AHumanObservation&fq=-(month:04%20OR%20month:05%20OR%20month:06)

see ->

"activeFacetMap" : {
"-basis_of_record" : {
"displayName" : "-basis_of_record:HumanObservation",
"name" : "-basis_of_record",
"value" : "HumanObservation"
},
"month" : {
"displayName" : "-Month:April OR Month:May OR Month:June",
"name" : "month",
"value" : "04 OR month:05 OR month:06"
},
"raw_taxon_name" : {
"displayName" : "Scientific name (unprocessed):Lomandra longifolia",
"name" : "raw_taxon_name",
"value" : ""Lomandra longifolia""
},
"taxon_name" : {
"displayName" : "Scientific name:Lomandra longifolia",
"name" : "taxon_name",
"value" : ""Lomandra longifolia""
}
}

The issue is with the "name" attribute when an "exclude" filter is applied with multiple (OR'ed) values. In this case (month) the name attribute is missing the leading minus sign. The JSON key for the group should also have a leading minus sign (see basis_of_record).

Also, the "displayName" attribute should include the surrounding braces from the original "fq" param.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#64

webservice like the one below are not jsonp compatible. If enhanced, it will benefit applications like phylojive.

http://sandbox.ala.org.au/ala-hub/occurrence/legend

From @aruizca on June 16, 2015 3:22

Can any of you @nickdos or @djtfmartin help me to find out why the following is happening:
In the bug report that I fixed today the user gave us the following url: http://regions.ala.org.au/Major%20drainage%20divisions/DARLING%2520RIVER#group=Crustaceans&subgroup=&from=1850&to=2015&tab=speciesTab with a total of 861 records. How come if you select the next subgroup "Fairy shrimp, Clam shrimp" we get 964 records -> http://regions.ala.org.au/Major%20drainage%20divisions/DARLING%2520RIVER#group=Crustaceans&subgroup=Fairy+shrimp,+Clam+shrimp&from=1850&to=2015&tab=speciesTab

• In the first instance the following URL generated and executed: http://biocache.ala.org.au/ws/occurrences/search?q=cl1059%3A%22DARLING+RIVER%22&facets=names_and_lsid&fsort=taxon_name&pageSize=0&flimit=50&foffset=0&fq=rank%3A%28species+OR+subspecies%29+AND+species_group%3A%22Crustaceans%22
• When subgroup is selected the following URL is generated: http://biocache.ala.org.au/ws/occurrences/search?q=cl1059%3A%22DARLING+RIVER%22&facets=names_and_lsid&fsort=taxon_name&pageSize=0&flimit=50&foffset=0&fq=rank%3A%28species+OR+subspecies%29+AND+species_subgroup%3A%22Fairy+shrimp%2C+Clam+shrimp%22

Copied from original issue: AtlasOfLivingAustralia/regions#46

1. If I ask for "matched_name" or "lsid" in my list of fields to be returned, I don't get them back.

(try e.g. http://biocache.ala.org.au/ws/occurrences/index/download?reasonTypeId=10&q=data_resource_uid:dr356&fields=longitude,lsid,matched_name&qa=none)

1. If I leave the requested fields as their default values, I get the scientific name in a column called scientificName - all good. But if I actually specify the field "scientificName", I get something with all-lower case names and abbreviated genus:

http://bie.ala.org.au/ws/download?q=genus:Aptenodytes&fields=scientificName

scientificName
"aptenodytes"
"a. forsteri"
"a. patagonicus"

If I ask for "nameComplete", I get what appears to be the correct scientific name.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#86

From @djtfmartin on August 19, 2014 10:32

migrated from: https://code.google.com/p/ala/issues/detail?id=113
date: Thu Aug 8 16:34:23 2013
author: moyesyside

Original Issue reported by Reported by [email protected], Jul 9, 2013 - https://code.google.com/p/ala-portal/issues/detail?id=298

Reported by [email protected], Jul 9, 2013
User flagged an issue on 9 July 2013
http://biocache.ala.org.au/occurrences/4e9cbb3d-c152-4971-b9b3-f0724820e89c#userAnnotations

Comment: Lat and Long are correct for this but Lat should be SOUTHERN hemisphere. i.e. -29.93... Does anyone check this stuff??

Note that this is a fish, and so may be a cause for not checking for marine/non-marine

What steps will reproduce the problem?

1. Citizen Science data is entered. Lat-long is given wrong hemisphere.
   (I know that Google Maps will show you where you are on the planet, but for some reason, this didn't work properly this time. The location given was too descriptive for Google Maps, so the marker would have had to be manually moved. Probably where the first error came in.)
2. ALA Data quality tests do not detect any problems
   Failed quality tests: 0
   Data warnings: 0
   Passed quality tests: 24
   Missing record properties: 11
   Test not ran (lack of data): 42

Some of the tests not run include
Latitude is negated Unchecked (lack of data)
Coordinates dont match supplied country Unchecked (lack of data)

What is the expected output?
A validity check that picks up wrong hemisphere, or out-of-country.

What do you see instead?
All tests passed.

What version of the product are you using? On what operating system?
N/a

Please provide any additional information below.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#16

Moved from AtlasOfLivingAustralia/biocache-hubs#91.

https://www.dropbox.com/s/putc8k4zz594x3k/Screenshot%202014-08-21%2016.13.24.png

label occurrence_status_s becomes occurrencetatus

Can be seen here:
http://biocache.ala.org.au/ws/occurrences/search?q=*:*&fq=occurrence_status_s:present&facet=false&pageSize=0

2014-12-12 07:52:28,330 [LocationProcessor] Problem processing using the SDS for record drt0|02663a3b-1d09-4b19-91bf-64e7a9e07a0f
java.lang.NullPointerException
at au.org.ala.sds.model.SensitivityInstance.equals(SensitivityInstance.java:89)
at java.util.ArrayList.indexOf(ArrayList.java:298)
at java.util.ArrayList.contains(ArrayList.java:281)
at au.org.ala.sds.model.SensitiveTaxonStore.verifyAndInitialiseSpeciesList(SensitiveTaxonStore.java:106)
at au.org.ala.sds.model.SensitiveTaxonStore.(SensitiveTaxonStore.java:58)
at au.org.ala.sds.SensitiveSpeciesFinderFactory.getStoreFromUrl(SensitiveSpeciesFinderFactory.java:103)
at au.org.ala.sds.SensitiveSpeciesFinderFactory.getSensitiveSpeciesFinder(SensitiveSpeciesFinderFactory.java:61)
at au.org.ala.sds.SensitiveSpeciesFinderFactory.getSensitiveSpeciesFinder(SensitiveSpeciesFinderFactory.java:44)
at au.org.ala.biocache.Config$.sdsFinder$lzycompute(Config.scala:68)
at au.org.ala.biocache.Config$.sdsFinder(Config.scala:66)
at au.org.ala.biocache.processor.LocationProcessor.sdsFinder$lzycompute(LocationProcessor.scala:33)
at au.org.ala.biocache.processor.LocationProcessor.sdsFinder(LocationProcessor.scala:33)
at au.org.ala.biocache.processor.LocationProcessor.processSensitivity(LocationProcessor.scala:823)
at au.org.ala.biocache.processor.LocationProcessor.process(LocationProcessor.scala:125)
at au.org.ala.biocache.processor.RecordProcessor$$anonfun$processRecord$1.apply(RecordProcessor.scala:96)
at au.org.ala.biocache.processor.RecordProcessor$$anonfun$processRecord$1.apply(RecordProcessor.scala:95)
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.MapLike$DefaultValuesIterable.foreach(MapLike.scala:206)
at au.org.ala.biocache.processor.Processors$.foreach(Processors.scala:10)
at au.org.ala.biocache.processor.RecordProcessor.processRecord(RecordProcessor.scala:95)
at au.org.ala.biocache.tool.Consumer$$anonfun$act$1$$anonfun$apply$1$$anonfun$applyOrElse$1.apply(ProcessRecords.scala:332)
at au.org.ala.biocache.tool.Consumer$$anonfun$act$1$$anonfun$apply$1$$anonfun$applyOrElse$1.apply(ProcessRecords.scala:327)
at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33)
at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:108)
at au.org.ala.biocache.tool.Consumer$$anonfun$act$1$$anonfun$apply$1.applyOrElse(ProcessRecords.scala:327)
at scala.runtime.AbstractPartialFunction$mcVL$sp.apply$mcVL$sp(AbstractPartialFunction.scala:33)
at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:33)
at scala.runtime.AbstractPartialFunction$mcVL$sp.apply(AbstractPartialFunction.scala:25)
at scala.actors.ReactorTask.run(ReactorTask.scala:31)
at scala.actors.Reactor$class.resumeReceiver(Reactor.scala:129)
at au.org.ala.biocache.tool.Consumer.scala$actors$InternalReplyReactor$$super$resumeReceiver(ProcessRecords.scala:303)
at scala.actors.InternalReplyReactor$class.resumeReceiver(InternalReplyReactor.scala:59)
at au.org.ala.biocache.tool.Consumer.resumeReceiver(ProcessRecords.scala:303)
at scala.actors.InternalActor$class.searchMailbox(InternalActor.scala:76)
at au.org.ala.biocache.tool.Consumer.searchMailbox(ProcessRecords.scala:303)
at scala.actors.Reactor$$anonfun$startSearch$1$$anonfun$apply$mcV$sp$1.apply$mcV$sp(Reactor.scala:117)
at scala.actors.Reactor$$anonfun$startSearch$1$$anonfun$apply$mcV$sp$1.apply(Reactor.scala:114)
at scala.actors.Reactor$$anonfun$startSearch$1$$anonfun$apply$mcV$sp$1.apply(Reactor.scala:114)
at scala.actors.ReactorTask.run(ReactorTask.scala:33)
at scala.actors.ReactorTask.compute(ReactorTask.scala:63)
at scala.concurrent.forkjoin.RecursiveAction.exec(RecursiveAction.java:160)
at scala.concurrent.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at scala.concurrent.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at scala.concurrent.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at scala.concurrent.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

We have to stop SPAM queries as early in the system as possible, otherwise even if they are not causing any error per say, they are basically wasting resources, putting genuine valid queries on hold. Although to be considered that the SPAM queries are being run by a script, meaning that there is a big number of them hitting the system at highest possible speed (compared to a genuine user query)

example (re-formatted for clarity):

2015-01-08 10:51:12,372 [org.ala.biocache.dao.SearchDAOImpl] Error executing query with requestParams: 

q=text:

In conclusion,

http://www.carfuelpumpmodule.com/94-1994-Mercury-Topaz-Radiator-23L-V4-140
Cid 94 1994 Mercury Topaz Radiator 2.3L V4 140Cid
Thus you gas tank can ensure effective heating without any harm to your health. 

http://www.carfuelpumpmodule.com/89-1989-Honda-Civic-Radiator-16L-V4-97
Cid 89 1989 Honda Civic Radiator 1.6L V4 97Cid 
Apart from these kind of, there are several items that should be window regulator  taken into account although acquiring the used parts. 

http://www.carfuelpumpmodule.com/81-1981-Pontiac-Firebird-All-Aluminum-Radiator-49L-V8-301
Cid 81 1981 Pontiac Firebird All Aluminum Radiator 4.9L V8 301Cid 
You can join an online forum fuel pump module about collecting rare cars or reconstructing junk cars. 

http://www.carfuelpumpmodule.com/09-2009-Toyota-Tundra-Radiator-57L-V8-345
Cid 09 2009 Toyota Tundra Radiator 5.7L V8 345Cid 
Try to determine that absolutely nothing on the car door mirror  has been unduly tampered with.

http://www.carfuelpumpmodule.com/96-1996-Buick-Roadmaster-Radiator-57L-V8-350
Cid 96 1996 Buick Roadmaster Radiator 5.7L V8 350Cid
Tial wastegates offer you the reliability along with the functionality of door mirror  some of the higher priced brands at a more economical price. . 

raw_name:Jbuppnvb 
species_group:Crustaceans 
ibra:"South East Corner" 
imcra:"Northeast Shelf Province" 
cl959:"Beverley (S)" 
type_status:allotype 
basis_of_record:LivingSpecimen 
catalogue_number:86085 
record_number: http://www.carfuelpumpmodule.com/96-1996-Toyota-Corolla-Radiator-18L-L4-Cid (
matched_name_children:lIEe4 OR 
matched_name_children:yxgrU OR 
matched_name_children:APMeS OR 
matched_name_children:VO2Iu) 
occurrence_date:[10121985T00:00:00Z TO 10121985T00:00:00Z]

&fq=
&fq=data_hub_uid:dh3
&start=0
&pageSize=20
&sort=first_loaded_date
&dir=desc
&qc=data_hub_uid:dh3
&facets=taxon_name
&facets=raw_taxon_name
&facets=common_name
&facets=subspecies_name
&facets=species
&facets=genus
&facets=family
&facets=order
&facets=class
&facets=phylum
&facets=kingdom
&facets=species_group
&facets=rank
&facets=interaction
&facets=species_habitats
&facets=uncertainty
&facets=sensitive
&facets=state_conservation
&facets=raw_state_conservation
&facets=cl966
&facets=cl959
&facets=state
&facets=country
&facets=ibra
&facets=imcra
&facets=cl1918
&facets=cl617
&facets=cl620
&facets=geospatial_kosher
&facets=month
&facets=year
&facets=decade
&facets=basis_of_record
&facets=type_status
&facets=multimedia
&facets=collector
&facets=occurrence_status_s
&facets=alau_user_id
&facets=data_resource_uid
&facets=institution_uid
&facets=collection_uid
&facets=provenance
&facets=assertions
&facets=assertion_user_id
&facets=outlier_layer
&facets=outlier_layer_count
&facets=taxonomic_issue
&facets=ViabilitySummary_d_RNG
&facets=AdjustedSeedQuantity_i_RNG
&formattedQuery=text:In conclusion, http:\/\/www.carfuelpumpmodule.com\/94\-1994\-Mercury\-Topaz\-Radiator\-23L\-V4\-140Cid 94 1994 Mercury Topaz Radiator 2.3L V4 140Cid Thus you gas tank can ensure effective heating without any harm to your health. http:\/\/www.carfuelpumpmodule.com\/89\-1989\-Honda\-Civic\-Radiator\-16L\-V4\-97Cid 89 1989 Honda Civic Radiator 1.6L V4 97Cid Apart from these kind of, there are several items that should be window regulator  taken into account although acquiring the used parts. http:\/\/www.carfuelpumpmodule.com\/81\-1981\-Pontiac\-Firebird\-All\-Aluminum\-Radiator\-49L\-V8\-301Cid 81 1981 Pontiac Firebird All Aluminum Radiator 4.9L V8 301Cid You can join an online forum fuel pump module about collecting rare cars or reconstructing junk cars. http:\/\/www.carfuelpumpmodule.com\/09\-2009\-Toyota\-Tundra\-Radiator\-57L\-V8\-345Cid 09 2009 Toyota Tundra Radiator 5.7L V8 345Cid Try to determine that absolutely nothing on the car door mirror  has been unduly tampered with. http:\/\/www.carfuelpumpmodule.com\/96\-1996\-Buick\-Roadmaster\-Radiator\-57L\-V8\-350Cid 96 1996 Buick Roadmaster Radiator 5.7L V8 350Cid Tial wastegates offer you the reliability along with the functionality of door mirror  some of the higher priced brands at a more economical price. . 

raw_name:Jbuppnvb 
species_group:Crustaceans 
ibra:"South\ East\ Corner" 
imcra:"Northeast\ Shelf\ Province" 
cl959:"Beverley\ \(S\)" 
type_status:allotype 
basis_of_record:LivingSpecimen 
catalogue_number:86085 
record_number:http\:\/\/www.carfuelpumpmodule.com\/96\-1996\-Toyota\-Corolla\-Radiator\-18L\-L4\-Cid (
taxon_name:lIEe4 OR 
taxon_name:yxgrU OR 
taxon_name:APMeS OR 
lft:[179321 TO 179322]) 
occurrence_date:[10121985T00:00\:00Z TO 10121985T00:00\:00Z] 

EXCEPTION: undefined field http

other (semi-raw) examples:

2015-02-01 00:10:37,033 [org.ala.biocache.dao.SearchDAOImpl] Error executing query with requestParams: 
q=text:RoylRU 
raw_name:"generic cialis fast" species_group:Molluscs state:Queensland country:France ibra:"Darling Riverine Plains" imcra:"Norfolk Island Province" cl959:"Warrumbungle Shire (A)" catalogue_number:39206 record_number:http://www.cialisonlineshop2015.com/ (matched_name_children:PbATF OR matched_name_children:lcHSbF OR matched_name_children:b2vP7 OR matched_name_children:SSnjCA) institution_uid:in52 occurrence_date:[10121985T00:00:00Z TO 10121985T00:00:00Z]&fq=&fq=data_hub_uid:dh5&start=0&pageSize=20&sort=first_loaded_date&dir=desc&qc=data_hub_uid:dh5&facets=taxon_name&facets=raw_taxon_name&facets=common_name&facets=subspecies_name&facets=species&facets=genus&facets=family&facets=order&facets=class&facets=phylum&facets=kingdom&facets=species_group&facets=rank&facets=interaction&facets=species_habitats&facets=uncertainty&facets=sensitive&facets=state_conservation&facets=raw_state_conservation&facets=cl966&facets=cl959&facets=state&facets=country&facets=ibra&facets=imcra&facets=cl1918&facets=cl617&facets=cl620&facets=geospatial_kosher&facets=month&facets=year&facets=decade&facets=basis_of_record&facets=type_status&facets=multimedia&facets=collector&facets=occurrence_status_s&facets=alau_user_id&facets=data_resource_uid&facets=institution_uid&facets=collection_uid&facets=provenance&facets=assertions&facets=assertion_user_id&facets=outlier_layer&facets=outlier_layer_count&facets=taxonomic_issue&formattedQuery=text:RoylRU raw_name:"generic\ cialis\ fast" species_group:Molluscs state:Queensland country:France ibra:"Darling\ Riverine\ Plains" imcra:"Norfolk\ Island\ Province" cl959:"Warrumbungle\ Shire\ \(A\)" catalogue_number:39206 record_number:http\:\/\/www.cialisonlineshop2015.com\/ (taxon_name:PbATF OR taxon_name:lcHSbF OR taxon_name:b2vP7 OR taxon_name:SSnjCA) institution_uid:in52 occurrence_date:[10121985T00:00\:00Z TO 10121985T00:00\:00Z] EXCEPTION: Invalid Date in Date Math String:'10121985T00:00:00Z'

2015-02-01 00:10:37,082 [org.ala.biocache.dao.SearchDAOImpl] Error executing query with requestParams: 
q=text:RoylRU 
raw_name:"generic cialis fast" species_group:Molluscs state:Queensland country:France ibra:"Darling Riverine Plains" imcra:"Norfolk Island Province" cl959:"Warrumbungle Shire (A)" catalogue_number:39206 record_number:http://www.cialisonlineshop2015.com/ (matched_name_children:PbATF OR matched_name_children:lcHSbF OR matched_name_children:b2vP7 OR matched_name_children:SSnjCA) institution_uid:in52 occurrence_date:[10121985T00:00:00Z TO 10121985T00:00:00Z]&fq=&fq=data_hub_uid:dh5&start=0&pageSize=0&sort=first_loaded_date&dir=desc&qc=data_hub_uid:dh5&facets=multimedia&formattedQuery=text:RoylRU raw_name:"generic\ cialis\ fast" species_group:Molluscs state:Queensland country:France ibra:"Darling\ Riverine\ Plains" imcra:"Norfolk\ Island\ Province" cl959:"Warrumbungle\ Shire\ \(A\)" catalogue_number:39206 record_number:http\:\/\/www.cialisonlineshop2015.com\/ (taxon_name:PbATF OR taxon_name:lcHSbF OR taxon_name:b2vP7 OR taxon_name:SSnjCA) institution_uid:in52 occurrence_date:[10121985T00:00\:00Z TO 10121985T00:00\:00Z] EXCEPTION: Invalid Date in Date Math String:'10121985T00:00:00Z'

2015-02-01 00:11:45,394 [org.ala.biocache.dao.SearchDAOImpl] Error executing query with  requestParams: 
q=text:JCrQYG 
raw_name:"generic viagra counterfeit" species_group:Insects country:"New Caledonia" type_status:allotype basis_of_record:MachineObservation catalogue_number:67136 record_number:http://www.viagratr2015.com/ (matched_name_children:3hg3k OR matched_name_children:IOEGK0 OR matched_name_children:kEwS9B OR matched_name_children:LEEir) occurrence_date:[10121985T00:00:00Z TO 10121985T00:00:00Z]&fq=&fq=data_hub_uid:dh7&start=0&pageSize=20&sort=first_loaded_date&dir=desc&qc=data_hub_uid:dh7&facets=taxon_name&facets=raw_taxon_name&facets=common_name&facets=subspecies_name&facets=species&facets=genus&facets=family&facets=order&facets=class&facets=phylum&facets=kingdom&facets=species_group&facets=rank&facets=interaction&facets=species_habitats&facets=uncertainty&facets=sensitive&facets=state_conservation&facets=raw_state_conservation&facets=cl966&facets=cl959&facets=state&facets=country&facets=ibra&facets=imcra&facets=cl1918&facets=cl617&facets=cl620&facets=geospatial_kosher&facets=month&facets=year&facets=decade&facets=basis_of_record&facets=type_status&facets=multimedia&facets=collector&facets=occurrence_status_s&facets=alau_user_id&facets=data_resource_uid&facets=institution_uid&facets=collection_uid&facets=provenance&facets=assertions&facets=assertion_user_id&facets=outlier_layer&facets=outlier_layer_count&facets=taxonomic_issue&facets=ViabilitySummary_d_RNG&facets=AdjustedSeedQuantity_i_RNG&formattedQuery=text:JCrQYG raw_name:"generic\ viagra\ counterfeit" species_group:Insects country:"New\ Caledonia" type_status:allotype basis_of_record:MachineObservation catalogue_number:67136 record_number:http\:\/\/www.viagratr2015.com\/ (taxon_name:3hg3k OR taxon_name:IOEGK0 OR taxon_name:kEwS9B OR taxon_name:LEEir) occurrence_date:[10121985T00:00\:00Z TO 10121985T00:00\:00Z] EXCEPTION: Invalid Date in Date Math String:'10121985T00:00:00Z'

2015-02-01 00:11:45,444 [org.ala.biocache.dao.SearchDAOImpl] Error executing query with requestParams: 
q=text:JCrQYG 
raw_name:"generic viagra counterfeit" species_group:Insects country:"New Caledonia" type_status:allotype basis_of_record:MachineObservation catalogue_number:67136 record_number:http://www.viagratr2015.com/ (matched_name_children:3hg3k OR matched_name_children:IOEGK0 OR matched_name_children:kEwS9B OR matched_name_children:LEEir) occurrence_date:[10121985T00:00:00Z TO 10121985T00:00:00Z]&fq=&fq=data_hub_uid:dh7&start=0&pageSize=0&sort=first_loaded_date&dir=desc&qc=data_hub_uid:dh7&facets=multimedia&formattedQuery=text:JCrQYG raw_name:"generic\ viagra\ counterfeit" species_group:Insects country:"New\ Caledonia" type_status:allotype basis_of_record:MachineObservation catalogue_number:67136 record_number:http\:\/\/www.viagratr2015.com\/ (taxon_name:3hg3k OR taxon_name:IOEGK0 OR taxon_name:kEwS9B OR taxon_name:LEEir) occurrence_date:[10121985T00:00\:00Z TO 10121985T00:00\:00Z] EXCEPTION: Invalid Date in Date Math String:'10121985T00:00:00Z'

in a log from 2015-01-08 08:19:38,625 to 2015-02-04 17:29:16,071:

sudo grep '\[org\.ala\.biocache\.dao\.SearchDAOImpl\]' /var/log/tomcat7/biocache-service.log|grep viagra|wc -l
2268

# out of 21942 logged EXCEPTIONs
sudo grep '\[org\.ala\.biocache\.dao\.SearchDAOImpl\]' /var/log/tomcat7/biocache-service.log|wc -l
21942

the string viagra is present 2268 times (although a single query may contain the string multiple, usually 2-3 times) it is still apx. 700 separate SPAM viagra queries wasting the resources, and slowing down the system.

Date ranges are common in survey data e.g. a trap put out for week
incomplete dates (common in historical records) can be considered a date range e.g. 03-2015 can be interpreted as 01-03-2015/31-03-2015

Searching on date should include return records if any part of the date range is include in the target date/date range

e.g.
a search on 15-03-2015 would return the record with a date 03-2015 or 01-03-2015/31-03-2015

a search on records between 01-01-2015 and 30-06-2015 would also return the record with a date 03-2015 or 01-03-2015/31-03-2015

From @djtfmartin on August 19, 2014 11:23

migrated from: https://code.google.com/p/ala/issues/detail?id=244
date: Sun Aug 18 18:42:16 2013
author: moyesyside

Support shape file friendly spreadsheet export

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#41

From @mbohun on August 19, 2014 13:3

migrated from: https://code.google.com/p/ala/issues/detail?id=624
date: Mon Mar 31 22:15:03 2014
author: [email protected]

The CS records do not have the license information attached to them. This is because they are reporting the value in a non DWC field.

I have modified the DataLoader to map this field to the correct DWC one. This change has been performed in biocache-store 1.1. In order for the fix to be applied to the data:

1. biocache-service 1.1 needs to be deployed on macropus
2. all the citzen science records need to be reloaded onto the jms queue

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#67

From @sadeghim on December 4, 2014 0:6

On the "Original versus Processed" Comparison Table in occurrence view, Class is misspelled as Classs .

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#110

Transferred from AtlasOfLivingAustralia/ALA4R#9

http://biocache.ala.org.au/ws/assertions/codes: look for "decimalLatLongConverionFailed" (should be "conversion" not "converion")

When displaying images show creator, rights, rightsHolder and license with information drawn from the image metadata (rather than the occurrence record)

From @djtfmartin on August 19, 2014 11:54

migrated from: https://code.google.com/p/ala/issues/detail?id=271
date: Wed Oct 2 21:36:30 2013
author: moyesyside

Additional download fields to indicate the presence of user provided annotations.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#46

From @Tasilee on August 20, 2014 3:32

migrated from: https://code.google.com/p/ala/issues/detail?id=616
date: Thu Mar 20 16:52:14 2014
author: [email protected]

At the moment, the record details don't state what the UNIT is when reporting "Distance outside expert range". It appears to be metres? I'd suggest km.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#87

From @djtfmartin on August 19, 2014 13:20

migrated from: https://code.google.com/p/ala/issues/detail?id=697
date: Thu Jun 12 18:33:27 2014
author: moyesyside

1. Take out duplicate from messages.properties & download.properties (with download.properties being the primary source).
2. Take out all references to EL and CL layers from both.
3. Support darwin core fields in downloads with a dwcHeaders=true request params - leaving the default as is.
4. Add the description into the /search/grouped/facets service.
5. Move i18n properties in message.properties into download.properties (e.g. http://biocache.ala.org.au/ws/index/fields)
6. If dwcHeaders=true, then use cl### field for headers for sampled fields.
7. Provide dwc.***** mapping in download.properties for index fields and include a dwcTerm field in /index/fields and /search/grouped/facets
8. Add sorts values (index or count).
9. Rename download.properties to fields.properties
10. Consider merging message.properties and download.properties and adding doco.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#83

From @nickdos on January 20, 2015 2:50

From @mbohun on August 19, 2014 11:16

migrated from: https://code.google.com/p/ala/issues/detail?id=230
date: Mon Aug 12 03:24:21 2013
author: [email protected]

Records downloaded through the BioCache come with a README file which contains a link to information about the Download Fields:
https://docs.google.com/spreadsheet/ccc?key=0AjNtzhUIIHeNdHhtcFVSM09qZ3c3N3ItUnBBc09TbHc#gid=0

Some of the fields have explanations that are not helpful. For example:
Coordinate Precision The precision of the coordinates
Coordinate Uncertainty In Meters Distance from the occurrence

Although there is a link to the Darwin Core Terms for the fields, the description could be more helpful for a person needing to understand what they have downloaded.

Other editing requirements
ACRONYMS need explaining eg GUID, IBRA, IMCRA
Spelling
Links to further assistance
Some issue flags missing definitions

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#39

Copied from original issue: AtlasOfLivingAustralia/bie-service#2

Cross domain queries are not supported as the server rejects them. It will be nice to have this feature since it can help standalone web applications.

More recent ALA sightings in biocache display with an Observer field of the ALA user ID (numeric) and lack a recordedBy field in the JSON output. E.g.

http://biocache.ala.org.au/occurrences/b963e1dd-5cf7-4a14-8335-38a709fbe746

In older records, this field shows the user's name and is indicated by text in the recordedBy field in the JSON output. E.g.

http://biocache.ala.org.au/occurrences/46a77fd8-1d27-49e4-a7db-2056ddf9e679

So this suggests there has been some change to AUTH or security somewhere that has resulted in this difference.

References to auth.ala.org.au were recently updated in config file to use HTTPS, which fixed some related problems (like showing ALA user's name) but this issue is still outstanding.

Currently in the biocache-hubs, autocomplete is tied to the ALA BIE service.

With more external users running biocache, there is a need to provide the autocomplete service for just the data coming from biocache-service. biocache-service is already doing names lookups via the lucene index, so it should be possible to produce an aucomplete lookup service, similar to that provided by the BIE.

APPD would benefit from this.

E.g. http://biocache.ala.org.au/ws/occurrences/search.json?q=*%3A*&fq=species_group%3AMammals&fq=rank_id%3A%5B7000+TO+*%5D&facets=common_name_and_lsid&flimit=30&foffset=0&start=0&pageSize=0&lat=-35.27717398771344&lon=149.11247491836548&radius=5

returns the facet values:

{  
    fieldResult:[  
        {  
            label:"Eastern Grey Kangaroo|Macropus giganteus|urn:lsid:biodiversity.org.au:afd.taxon:43639327-3bc9-43ae-861b-e0f982b1a8b2|Eastern Grey Kangaroo|ANIMALIA|MACROPODIDAE",
            count:14
        },
        {  
            label:"Short-beaked Echidna|Tachyglossus aculeatus|urn:lsid:biodiversity.org.au:afd.taxon:0d4c9c0c-51d3-44e0-a365-fe0f8b791c66|Short-beaked Echidna|ANIMALIA|TACHYGLOSSIDAE",
            count:13
        },
        {  
            label:"Common Brushtail Possum|Trichosurus vulpecula|urn:lsid:biodiversity.org.au:afd.taxon:00b1b9a2-70c9-45be-8019-9c7fd755afc8|Common Brushtail Possum|ANIMALIA|PHALANGERIDAE",
            count:8
        },
        {  
            label:"Fox|Vulpes vulpes|urn:lsid:biodiversity.org.au:afd.taxon:ba8d0c3b-9753-46cf-87b4-a1b9ec290634|Fox|ANIMALIA|CANIDAE",
            count:6
        },
        {  
            label:"Smaller Horseshoe Bat|Rhinolophus megaphyllus megaphyllus|urn:lsid:biodiversity.org.au:afd.taxon:1da83fac-7b55-4a39-b23c-d1843c72eff8|Smaller Horseshoe Bat|ANIMALIA|RHINOLOPHIDAE",
            count:5
        },
        {  
            label:"Grey-headed Flying-fox|Pteropus poliocephalus|urn:lsid:biodiversity.org.au:afd.taxon:a2553aed-383a-4c9b-9534-c6058bcee81b|Grey-headed Flying-fox|ANIMALIA|PTEROPODIDAE",
            count:4
        },
        {  
            label:"Common Wombat|Vombatus ursinus|urn:lsid:biodiversity.org.au:afd.taxon:e079f94d-3d7f-4deb-ae29-053fec4d1b53|Common Wombat|ANIMALIA|VOMBATIDAE",
            count:2
        },
        {  
            label:"Sugar Glider|Petaurus breviceps breviceps|urn:lsid:biodiversity.org.au:afd.taxon:6c373938-06c9-4e82-8326-1f6a5b10ef45|Sugar Glider|ANIMALIA|PETAURIDAE",
            count:2
        },
        {  
            label:"Yellow-footed Antechinus|Antechinus flavipes|urn:lsid:biodiversity.org.au:afd.taxon:b58b9afe-8499-425c-9dae-ce392c4f673f|Yellow-footed Antechinus|ANIMALIA|DASYURIDAE",
            count:2
        },
        {  
            label:"African Lion|Panthera leo|urn:lsid:catalogueoflife.org:taxon:df159870-29c1-102b-9a4a-00304854f820:col20120124|African Lion|ANIMALIA|FELIDAE",
            count:1
        },
        {  
            label:"Bindjulang|Dasyurus maculatus|urn:lsid:biodiversity.org.au:afd.taxon:33d1cf65-5c15-4864-8ce1-88bc483f713e|Bindjulang|ANIMALIA|DASYURIDAE",
            count:1
        },
        {  
            label:"Eastern Bent-wing Bat|Miniopterus schreibersii oceanensis|urn:lsid:biodiversity.org.au:afd.taxon:e261aeb0-b757-4627-afbf-fa3a91b7e844|Eastern Bent-wing Bat|ANIMALIA|MINIOPTERIDAE",
            count:1
        },
        {  
            label:"Gould's Wattled Bat|Chalinolobus gouldii|urn:lsid:biodiversity.org.au:afd.taxon:225f3d82-6177-46b4-8b52-d591eee8f015|Gould's Wattled Bat|ANIMALIA|VESPERTILIONIDAE",
            count:1
        },
        {  
            label:"Platypus|Ornithorhynchus anatinus|urn:lsid:biodiversity.org.au:afd.taxon:ac61fd14-4950-4566-b384-304bd99ca75f|Platypus|ANIMALIA|ORNITHORHYNCHIDAE",
            count:1
        },
        {  
            label:"Rabbit|Oryctolagus cuniculus|urn:lsid:biodiversity.org.au:afd.taxon:692effa3-b719-495f-a86f-ce89e2981652|Rabbit|ANIMALIA|LEPORIDAE",
            count:1
        },
        {  
            label:"Swamp Wallaby|Wallabia bicolor|urn:lsid:biodiversity.org.au:afd.taxon:0c826b9b-6863-4845-b851-35864ec2ebb5|Swamp Wallaby|ANIMALIA|MACROPODIDAE",
            count:1
        }
    ],
    fieldName:"common_name_and_lsid"
}

So inly 15 results returned but if you modify the query to ask for species_subgroup:Diprotodont+Marsupials, then you get another 15 results, many of which are missing from the first results set.

http://biocache.ala.org.au/ws/occurrences/search.json?q=*%3A*&fq=species_subgroup%3ADiprotodont+Marsupials&fq=rank_id%3A%5B7000+TO+*%5D&facets=common_name_and_lsid&flimit=30&foffset=0&start=0&pageSize=0&lat=-35.27717398771344&lon=149.11247491836548&radius=5&_=1433306605934

Also note in this set, there are (effectively) duplicate entries for species, one without a common name and the other with a common name but they both have the same LSID. E.g.

{
  label: "|Macropus giganteus|urn:lsid:biodiversity.org.au:afd.taxon:43639327-3bc9-43ae-861b-e0f982b1a8b2||ANIMALIA|MACROPODIDAE",
  count: 162
},
{
  label: "Eastern Grey Kangaroo|Macropus giganteus|urn:lsid:biodiversity.org.au:afd.taxon:43639327-3bc9-43ae-861b-e0f982b1a8b2|Eastern Grey Kangaroo|ANIMALIA|MACROPODIDAE",
  count: 14
}

So these appear to be data errors.

Do a review of the group and sub group labels and improve them.

E.g. Insects -> ants

should be ants, wasps, sawflies and bees - see Wikipedia page.

both production and test env biocache-service log (and most likely other services) ansible-playbook-s should make sure that biocache-serice.log (and all other important log files: tomcat, solr, etc.) are properly preserved/archived (i found out accidentally on the 2015-02-20 when the /var/log/tomcat7/biocache-service.log i was working with was deleted, resp. replaced/reset and all the existing log messages starting from early January 2015 were lost)

NOTE: it is very likely that this applies to all ALA production vm-s/services

Support for non-zipped downloads + citation service.

The decade facet is non-standard as it appears to be a synonym or "special" facet name (not sure exactly). the WMS service will not show any dots for a search when "decade" is used.

E.g. the equivilent "year" colormode gives:

http://biocache.ala.org.au/ws/webportal/wms/reflect?q=lsid%3Aurn%3Alsid%3Abiodiversity.org.au%3Aafd.taxon%3Ae9e7db31-04df-41fb-bd8d-e0b0f3c332d6&fq=family%3AEQUIDAE&fq=state%3A%22Victoria%22&SERVICE=WMS&REQUEST=GetMap&VERSION=1.1.1&LAYERS=ALA%3Aoccurrences&STYLES=&FORMAT=image%2Fpng&TRANSPARENT=true&HEIGHT=256&WIDTH=256&BGCOLOR=0x000000&OUTLINE=true&ENV=colormode%3Ayear%3Bname%3Acircle%3Bsize%3A4%3Bopacity%3A1&STYLE=opacity%3A0.8&SRS=EPSG%3A3857&BBOX=15967389.460660176,-4383204.9499851465,16280475.52851626,-4070118.8821290643

but change it to decade and it returns no dots:

http://biocache.ala.org.au/ws/webportal/wms/reflect?q=lsid%3Aurn%3Alsid%3Abiodiversity.org.au%3Aafd.taxon%3Ae9e7db31-04df-41fb-bd8d-e0b0f3c332d6&fq=family%3AEQUIDAE&fq=state%3A%22Victoria%22&SERVICE=WMS&REQUEST=GetMap&VERSION=1.1.1&LAYERS=ALA%3Aoccurrences&STYLES=&FORMAT=image%2Fpng&TRANSPARENT=true&HEIGHT=256&WIDTH=256&BGCOLOR=0x000000&OUTLINE=true&ENV=colormode%3Adecade%3Bname%3Acircle%3Bsize%3A4%3Bopacity%3A1&STYLE=opacity%3A0.8&SRS=EPSG%3A3857&BBOX=15967389.460660176,-4383204.9499851465,16280475.52851626,-4070118.8821290643

This is breaking the biocache search map when colour_by = decade.

From @Tasilee on August 19, 2014 12:58

migrated from: https://code.google.com/p/ala/issues/detail?id=597
date: Tue Feb 25 19:13:40 2014
author: [email protected]

Add to Map | Species | Mogurnda clivicola

This species is listed as "Vulnerable" (AU) in the species page but not in the facets.

State conservation
State conservation status (unprocessed)

This seems to imply that a species listed under the EPBC act will not reflect in either of the two conservation status facets? If so, not nice.

This issue was raised by a user from SA (via Robyn Lawrence) who was attempting to find out what fish species in SA had a conservation status.

Apparently there are 16 fish species in SA with some conservation status while the ALA reports 2 as far as I can tell. If I use the SP to facet on lifeform=fish, area=SA with coastal zone, conservation=some status I get 2.

I assume it is a biocache issue.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#60

Or add a case-insensitive copyField.

As reported by a user:

On 9 Sep 2014, at 6:23 pm, Gioia, Paul [email protected] wrote:

species download - http://bie.ala.org.au/ws/download?q={q}&fq={fq} - If you search on kingdom, Plantae works fine, but Animalia doesn’t until you realise the searches are case sensitive, and Plantae, Fungi are in title case while ANIMALIA is upper case. Either the data should be consistent or the querying case-insensitive, otherwise you don’t know what you can query for.

This is caused by SOLR going down and coming up, but biocache -service not recovering the available download fields.

2014-09-16 10:27:48,214 [org.ala.biocache.service.DownloadService] 
java.lang.NullPointerException
    at au.org.ala.biocache.dao.SearchDAOImpl.writeResultsFromIndexToStream(SearchDAOImpl.java:562)
    at sun.reflect.GeneratedMethodAccessor834.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)
    at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:309)
    at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:196)
    at com.sun.proxy.$Proxy25.writeResultsFromIndexToStream(Unknown Source)
    at au.org.ala.biocache.service.DownloadService.writeQueryToStream(DownloadService.java:164)
    at au.org.ala.biocache.service.DownloadService.writeQueryToStream(DownloadService.java:134)
    at au.org.ala.biocache.service.DownloadService.writeQueryToStream(DownloadService.java:225)
    at au.org.ala.biocache.web.OccurrenceController.occurrenceIndexDownload(OccurrenceController.java:798)
    at sun.reflect.GeneratedMethodAccessor826.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:606)

From @djtfmartin on August 19, 2014 12:59

migrated from: https://code.google.com/p/ala/issues/detail?id=605
date: Wed Mar 12 17:48:06 2014
author: moyesyside

QID issues for creating alerts from specieslists

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#63

From @mbohun on August 19, 2014 11:55

migrated from: https://code.google.com/p/ala/issues/detail?id=277
date: Tue Oct 15 21:17:05 2013
author: [email protected]

At the moment the metadata for the download is based on the default fields that are included in the download. It would be nice if it could include all the fields that were requested in the download.

Very apparent when users are constructing the download URL using customised field lists.

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#48

We are missing the definitions for

mediaRepresentative
mediaUnrepresentative
recordByUnparsable
resourceTaxonomicScopeMismatch

on http://biocache.ala.org.au/ws/assertions/codes

https://github.com/AtlasOfLivingAustralia/biocache-service/blob/master/src/main/java/au/org/ala/biocache/util/RangeBasedFacets.java

Convert to i18n values for terms such as "less than" and "between".

Download assertions - include all in the downloads.
Currently the assertion columns are filtered to only return the column if at least one record has failed.

Allow users to flag an issue for duplicate records including adding an identifier for the duplicate UUID or a full path to the record plus notes and/or reason it's a duplicate

E.g.

http://biocache.ala.org.au/ws/occurrences/search?q=qid%3A1434072315708
vs
http://biocache.ala.org.au/ws/occurrences/search?q=qid%3A1434072315708&qc=&wkt=POLYGON((143.13262939453122+-32.472695022061494,149.10919189453125%20-32.472695022061494,149.10919189453125%20-34.81380331711314,143.13262939453122%20-34.81380331711314,143.13262939453122%20-32.472695022061494))

both return the same number of hits (55694) and results. Thus wkt filter is being ignored.

Second URL should have a much smaller results set.

From @djtfmartin on August 19, 2014 12:59

migrated from: https://code.google.com/p/ala/issues/detail?id=602
date: Tue Mar 4 20:36:05 2014
author: moyesyside

http://biocache.ala.org.au/ws/occurrences/download?q=red+kangaroo&fields=institution_name,collection_name&reasonTypeId=1

Copied from original issue: AtlasOfLivingAustralia/biocache-hubs#62