From 1adf2369062c886a94ecd6a8d7947aaae1f700c2 Mon Sep 17 00:00:00 2001 From: utas-raymondng Date: Mon, 21 Oct 2024 09:53:01 +1100 Subject: [PATCH] Fix missing enum, refactor test to follow correct naming --- .../aodn/esindexer/model/GeoNetworkField.java | 2 +- .../esindexer/service/IndexerServiceImpl.java | 4 +- ...iceTests.java => GeoNetworkServiceIT.java} | 2 +- ...erviceTests.java => IndexerServiceIT.java} | 7 +- .../esindexer/service/IndexerServiceTest.java | 58 + ...erviceTests.java => RankingServiceIT.java} | 6 +- ...a => StacCollectionMapperServiceTest.java} | 19 +- ...abServiceTest.java => VocabServiceIT.java} | 2 +- .../canned/sample_geoenum_publication.xml | 1584 +++++++++++++++++ .../sample_geoenum_publication_stac.json | 177 ++ pom.xml | 16 + 11 files changed, 1861 insertions(+), 16 deletions(-) rename indexer/src/test/java/au/org/aodn/esindexer/service/{GeoNetworkServiceTests.java => GeoNetworkServiceIT.java} (99%) rename indexer/src/test/java/au/org/aodn/esindexer/service/{IndexerServiceTests.java => IndexerServiceIT.java} (99%) create mode 100644 indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java rename indexer/src/test/java/au/org/aodn/esindexer/service/{RankingServiceTests.java => RankingServiceIT.java} (96%) rename indexer/src/test/java/au/org/aodn/esindexer/service/{StacCollectionMapperServiceTests.java => StacCollectionMapperServiceTest.java} (95%) rename indexer/src/test/java/au/org/aodn/esindexer/service/{VocabServiceTest.java => VocabServiceIT.java} (99%) create mode 100644 indexer/src/test/resources/canned/sample_geoenum_publication.xml create mode 100644 indexer/src/test/resources/canned/sample_geoenum_publication_stac.json diff --git a/indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java b/indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java index 12ff968e..7da75110 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/model/GeoNetworkField.java @@ -6,5 +6,5 @@ public enum GeoNetworkField { creation, revision, - ; + publication, } diff --git a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java index 0d1e3dbe..c64c4a23 100644 --- a/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java +++ b/indexer/src/main/java/au/org/aodn/esindexer/service/IndexerServiceImpl.java @@ -482,10 +482,10 @@ public BulkResponse executeBulk(BulkRequest.Builder bulkRequest, Callback callba } } - protected BulkResponse reduceResponse(BulkResponse in) { + protected static BulkResponse reduceResponse(BulkResponse in) { List errors = in.items() .stream() - .filter(p -> p.status() != HttpStatus.CREATED.value() || p.status() != HttpStatus.OK.value()) + .filter(p -> !(p.status() == HttpStatus.CREATED.value() || p.status() == HttpStatus.OK.value())) .toList(); return errors.isEmpty() ? diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceTests.java b/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java similarity index 99% rename from indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceTests.java rename to indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java index 8d4619a5..713ac89d 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceTests.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/GeoNetworkServiceIT.java @@ -36,7 +36,7 @@ @ActiveProfiles("test") @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @TestInstance(TestInstance.Lifecycle.PER_CLASS) -public class GeoNetworkServiceTests extends BaseTestClass { +public class GeoNetworkServiceIT extends BaseTestClass { // Must use the impl to access protected method for testing @Autowired protected GeoNetworkServiceImpl geoNetworkService; diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTests.java b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java similarity index 99% rename from indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTests.java rename to indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java index 698b3e00..bedad339 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTests.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceIT.java @@ -3,6 +3,8 @@ import au.org.aodn.esindexer.BaseTestClass; import au.org.aodn.esindexer.configuration.GeoNetworkSearchTestConfig; import co.elastic.clients.elasticsearch.ElasticsearchClient; +import co.elastic.clients.elasticsearch.core.BulkResponse; +import co.elastic.clients.elasticsearch.core.bulk.BulkResponseItem; import co.elastic.clients.elasticsearch.core.search.Hit; import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; @@ -15,6 +17,7 @@ import org.springframework.beans.factory.annotation.Qualifier; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.http.HttpStatus; import org.springframework.test.context.ActiveProfiles; import java.io.IOException; @@ -26,7 +29,7 @@ @ActiveProfiles("test") @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @TestInstance(TestInstance.Lifecycle.PER_CLASS) -public class IndexerServiceTests extends BaseTestClass { +public class IndexerServiceIT extends BaseTestClass { @Autowired protected GeoNetworkServiceImpl geoNetworkService; @@ -250,7 +253,7 @@ public void verifyThumbnailLinkNullAdbbdedOnIndex() throws IOException { String test = String.valueOf(Objects.requireNonNull(objectNodeHit.source())); String expected = indexerObjectMapper.readTree(expectedData).toPrettyString(); String actual = indexerObjectMapper.readTree(test).toPrettyString(); -logger.info("{}", actual); + JSONAssert.assertEquals(expected, actual, JSONCompareMode.STRICT); } catch (JSONException e) { throw new RuntimeException(e); diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java new file mode 100644 index 00000000..9bdaa981 --- /dev/null +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/IndexerServiceTest.java @@ -0,0 +1,58 @@ +package au.org.aodn.esindexer.service; + +import co.elastic.clients.elasticsearch._types.ErrorCause; +import co.elastic.clients.elasticsearch.core.BulkResponse; +import co.elastic.clients.elasticsearch.core.bulk.BulkResponseItem; +import co.elastic.clients.elasticsearch.core.bulk.OperationType; +import lombok.extern.slf4j.Slf4j; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; +import org.springframework.http.HttpStatus; + +/** + * Unit test that do not require other dependent software running goes here + */ +@Slf4j +public class IndexerServiceTest { + /** + * Verify this function, it should only return error if items contains status no CREATED or OK + */ + @Test + public void verifyReduceResponse() { + BulkResponse bulkResponse = BulkResponse.of(b -> + b.items( + BulkResponseItem.of(i -> i + .status(HttpStatus.CREATED.value()) + .operationType(OperationType.Create) + .index("A") + ), + BulkResponseItem.of(i -> i + .status(HttpStatus.OK.value()) + .operationType(OperationType.Update) + .index("A") + )) + .errors(false).took(1) + ); + + bulkResponse = IndexerServiceImpl.reduceResponse(bulkResponse); + Assertions.assertFalse(bulkResponse.errors(), "Should not contain error"); + + bulkResponse = BulkResponse.of(b -> + b.items( + BulkResponseItem.of(i -> i + .status(HttpStatus.CREATED.value()) + .operationType(OperationType.Create) + .index("B") + ), + BulkResponseItem.of(i -> i + .status(HttpStatus.NOT_EXTENDED.value()) + .operationType(OperationType.Index) + .index("B") + )) + .errors(false).took(1) + ); + + bulkResponse = IndexerServiceImpl.reduceResponse(bulkResponse); + Assertions.assertTrue(bulkResponse.errors(), "Should contain error"); + } +} diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/RankingServiceTests.java b/indexer/src/test/java/au/org/aodn/esindexer/service/RankingServiceIT.java similarity index 96% rename from indexer/src/test/java/au/org/aodn/esindexer/service/RankingServiceTests.java rename to indexer/src/test/java/au/org/aodn/esindexer/service/RankingServiceIT.java index f0c8565d..f1f54287 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/RankingServiceTests.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/RankingServiceIT.java @@ -1,12 +1,9 @@ package au.org.aodn.esindexer.service; import au.org.aodn.esindexer.BaseTestClass; -import au.org.aodn.esindexer.utils.SummariesUtils; import au.org.aodn.stac.model.*; import org.junit.jupiter.api.*; -import org.mockito.InjectMocks; import org.mockito.Mockito; -import org.mockito.Spy; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.beans.factory.annotation.Value; import org.springframework.boot.test.context.SpringBootTest; @@ -16,7 +13,6 @@ import static org.mockito.Mockito.*; import java.io.IOException; -import java.math.BigDecimal; import java.util.ArrayList; import java.util.List; @@ -24,7 +20,7 @@ @ActiveProfiles("test") @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @TestInstance(TestInstance.Lifecycle.PER_CLASS) -class RankingServiceTests extends BaseTestClass { +class RankingServiceIT extends BaseTestClass { @Value("${elasticsearch.index.name}") protected String INDEX_NAME; diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTests.java b/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java similarity index 95% rename from indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTests.java rename to indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java index ba332ac7..954ba909 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTests.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/StacCollectionMapperServiceTest.java @@ -13,14 +13,12 @@ import co.elastic.clients.elasticsearch.core.search.TotalHits; import co.elastic.clients.json.JsonData; import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.node.ObjectNode; import jakarta.xml.bind.JAXBException; import lombok.extern.slf4j.Slf4j; import org.json.JSONException; import org.junit.jupiter.api.AfterEach; -import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.mockito.Mockito; @@ -47,7 +45,7 @@ */ @Slf4j @SpringBootTest(classes = {StacCollectionMapperServiceImpl.class}) -public class StacCollectionMapperServiceTests { +public class StacCollectionMapperServiceTest { protected ObjectMapper objectMapper = new ObjectMapper(); protected JaxbUtils jaxbUtils = new JaxbUtils<>(MDMetadataType.class); @@ -88,7 +86,7 @@ protected void verify(String expected) throws JsonProcessingException, JSONExcep ); } - public StacCollectionMapperServiceTests() throws JAXBException { + public StacCollectionMapperServiceTest() throws JAXBException { GeometryUtils.setExecutorService(Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors())); GeometryUtils.init(); } @@ -397,6 +395,19 @@ public void verifyNonNodedIntersectionsWorks() throws IOException, JSONException String expected = readResourceFile("classpath:canned/sample_non_noded_intersections_stac.json"); indexerService.indexMetadata(xml); + verify(expected); + } + /** + * There is a missing enum publication, this case is check if we works after fix + * @throws IOException - Not expect to throw + * @throws JSONException - Not expect to throw + */ + @Test + public void verifyNoMissingGeonetworkFieldEnum() throws IOException, JSONException { + String xml = readResourceFile("classpath:canned/sample_geoenum_publication.xml"); + String expected = readResourceFile("classpath:canned/sample_geoenum_publication_stac.json"); + indexerService.indexMetadata(xml); + verify(expected); } } diff --git a/indexer/src/test/java/au/org/aodn/esindexer/service/VocabServiceTest.java b/indexer/src/test/java/au/org/aodn/esindexer/service/VocabServiceIT.java similarity index 99% rename from indexer/src/test/java/au/org/aodn/esindexer/service/VocabServiceTest.java rename to indexer/src/test/java/au/org/aodn/esindexer/service/VocabServiceIT.java index e06839a8..86d73999 100644 --- a/indexer/src/test/java/au/org/aodn/esindexer/service/VocabServiceTest.java +++ b/indexer/src/test/java/au/org/aodn/esindexer/service/VocabServiceIT.java @@ -31,7 +31,7 @@ @ActiveProfiles("test") @TestMethodOrder(MethodOrderer.OrderAnnotation.class) @TestInstance(TestInstance.Lifecycle.PER_CLASS) -public class VocabServiceTest extends BaseTestClass { +public class VocabServiceIT extends BaseTestClass { @Autowired VocabService vocabService; diff --git a/indexer/src/test/resources/canned/sample_geoenum_publication.xml b/indexer/src/test/resources/canned/sample_geoenum_publication.xml new file mode 100644 index 00000000..b9963819 --- /dev/null +++ b/indexer/src/test/resources/canned/sample_geoenum_publication.xml @@ -0,0 +1,1584 @@ + + + + + + cffa7269-5d95-486b-9b2e-77316e808398 + + + urn:uuid + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Australian Institute of Marine Science (AIMS) + + + + + eAtlas Data Manager + + + + + + + +61 7 4753 4444 + + + + + + + + + + PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE + + + Townsville + + + Queensland + + + 4810 + + + Australia + + + e-atlas@aims.gov.au + + + + + + + https://eatlas.org.au + + + WWW:LINK-1.0-http--link + + + eAtlas portal + + + + + + + + + + + + + + + + + + 2024-03-17T03:07:01 + + + + + + + + + + 2023-08-08T05:28:21 + + + + + + + + + + 2023-08-22T03:02:00 + + + + + + + + + + ISO 19115-3.2018 + + + + + + + https://eatlas.org.au/data/uuid/cffa7269-5d95-486b-9b2e-77316e808398 + + + + + + + + + + https://doi.org/10.26274/V6K5-2F34 + + + + + + + + + + + + + + + + + + + + + WGS 1984 + + + + + + + + + + + Benthic habitats of Yanyuwa Sea Country, Barni - Wardimantha Awara Indigenous Protected Area, Gulf of Carpentaria, Northern Territory, Australia (NESP MaC Project 1.12, JCU & CDU) + + + + + 2023-08-08 + + + + + + + + + + 2023-08-22 + + + + + + + + + + https://doi.org/10.26274/V6K5-2F34 + + + Digital Object Identifier + + + + + + + + + + + + Charles Darwin University + + + + + + + Research Organization Registry + + + + + + + + + + + + Groom, Rachel, Dr + + + + + + + + + + + + + + + + + + + + Darwin + + + Northern Territory + + + + + + Australia + + + rachel.groom@cdu.edu.au + + + + + + + + + + + + + + + + + + + + + TropWATER, James Cook University + + + + + Carter, Alex, Dr + + + + + + + + + + + + + + + + + + + + Cairns + + + Queensland + + + + + + Australia + + + alexandra.carter@jcu.edu.au + + + + + + + + + + + + + + + + + + + + + TropWATER, James Cook University + + + + + Collier, Catherine, Dr + + + + + + + + + + + + + + + + + + + + Cairns + + + Queensland + + + + + + Australia + + + catherine.collier@jcu.edu.au + + + + + + + + + + + + + + + + + + + + + TropWATER + + + + + Firby, Lauren, Ms + + + + + + + + + + + + + + + + + + + + Cairns + + + Queensland + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + li-Anthawirriyarra Sea Ranger Unit, Mabunji Aboriginal Resource Indigenous Corporation + + + + + Evans, Shaun, Mr + + + + + + + + + + + + + + + + + + + + Borroloola + + + Northern Territory + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + li-Anthawirriyarra Sea Ranger Unit, Mabunji Aboriginal Resource Indigenous Corporation + + + + + Barrett, Stephen, Mr + + + + + + + + + + + + + + + + + + + + Borroloola + + + Northern + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + TropWATER, James Cook University + + + + + Hoffman, Luke, Mr + + + + + + + + + + + + + + + + + + + + Cairns + + + Queensland + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + TropWATER, James Cook University + + + + + van der Wetering, Chris, Mr, Alex, Dr + + + + + + + + + + + + + + + + + + + + Cairns + + + Queensland + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + li-Anthawirriyarra Sea Ranger Unit, Mabunji Aboriginal Resource Indigenous Corporation + + + + + Evans, Shade, Mr + + + + + + + + + + + + + + + + + + + + Borroloola + + + Northern Territory + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + li-Anthawirriyarra Sea Ranger Unit, Mabunji Aboriginal Resource Indigenous Corporation + + + + + Simon, Steven, Mr + + + + + + + + + + + + + + + + + + + + Borroloola + + + Northern Territory + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + + + + Jungkayi for eastern Vanderlin Island + + + + + Anderson, Stephen, Mr + + + + + + + + + + + + + + + + + + + + + + + Northern Territory + + + + + + Australia + + + + + + + + + + + + + + + + + + + + + This dataset summarises benthic surveys in Yanyuwa Sea Country into 3 GIS shapefiles. + (1) A point (site) shapefile describes seagrass presence/absence at 3248 sites surveyed by small vessel and helicopter. + (2) The meadow shapefile describes attributes of 180 intertidal seagrass meadows. + (3) The interpolation GeoTiff describes variation in seagrass biomass across the seagrass meadows. + + This project is a partnership between li-Anthawirriyarra rangers, Charles Darwin University, James Cook University, and Mabunji Aboriginal Resource Indigenous Corporation to map the intertidal habitats of the Yanyuwa Indigenous Protected Area (IPA), an area of profound importance to the Marra and Yanyuwa people and to the marine ecosystem of the Gulf of Carpentaria. Benthic habitat maps of Yanyuwa Country were produced, with a focus on seagrass. + + Report reference: Groom R, Carter A, Collier C, Firby L, Evans S, Barrett S, Hoffmann L, van de Wetering C, Shepherd L, Evans S, Anderson S. (2023) Mapping Critical Habitat in Yanyuwa Sea Country. Report to the National Environmental Science Program. Charles Darwin University, pp. 40. Available at: https://www.nespmarinecoastal.edu.au/wp-content/uploads/2023/07/NESP-MaC-Hub-Project-1.12_Groom-et-al-FINAL-REPORT.pdf + + Methods: + The sampling methods used to study, describe and monitor seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater). + Geographic Information System (GIS) + + All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.8. Rectified colour satellite imagery of Yanyuwa Sea Country (Source: Allen Coral Atlas and ESRI), field notes and aerial photographs taken from the helicopter during surveys were used to identify geographical features, such as reef tops, channels and deep-water drop-offs, to assist in determining seagrass meadow boundaries. Three GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and a seagrass biomass interpolation layer. + + Seagrass site layer + This layer contains information on data collected at assessment sites. This layer includes: + 1. Temporal survey details – Survey date; + 2. Spatial position - Latitude/longitude; + 3. Survey location; + 4. Seagrass information including presence/absence of seagrass, above-ground biomass (total and for each species), percent cover of seagrass at each site and whether individual species were present/absent at a site; + 5. Benthic macro-invertebrate information including the percent cover of hard coral, soft coral, sponges and other benthic macro invertebrates (e.g. ascidian, clam) at a site; + 6. Algae information including percent cover of algae at a site and percent contribution of algae functional groups to algae cover at a site; + 7. Open substrate – the percent cover of the site that had no flora or habitat forming benthic invertebrates present; + 8. Dominant sediment type - Sediment type based on grain size visual assessment or deck descriptions. + 9. Survey method and vessel + 10. Relevant comments and presence/absence of megafauna and animals of interest (dugong, turtle, dolphin, evidence of dugong feeding trails); + 11. Data custodians. + + Seagrass meadow layer + Seagrass presence/absence site data, mapping sites, field notes, and satellite imagery were used to construct meadow boundaries in ArcGIS®. The meadow (polygon) layer provides summary information for all sites within each seagrass meadow, including: + 1. Temporal survey details – Survey month and year as individual columns and the survey date (the date range the survey took place); + 2. Spatial survey details – Survey location, meadow identification number that identifies the reef name and the meadow number. This allows individual meadows to be compared among years; + 3. Survey method; + 4. Meadow depth for subtidal meadows. Intertidal: meadow was mapped on an exposed bank during low tide; + 5. Species presence – a list of the seagrass species in the meadow; + 6. Meadow density – Seagrass meadows were classified as light, moderate, dense based on the mean biomass of the dominant species within the meadow. For example, a Thalassia hemprichii dominated meadow would be classed as “light” if the mean meadow biomass was <5 grams dry weight m-2 (g DW m-2), and “dense” if mean meadow biomass was >25 g DW m-2. + 7. Meadow community type – Seagrass meadows were classified into community types according to seagrass species composition within each meadow. Species composition was based on the percent each species’ biomass contributed to mean meadow biomass. A standard nomenclature system was used to categorize each meadow. + 8. Mean meadow biomass measured in g DW m-2 (+ standard error if available); + 9. Meadow area (hectares; ha) (+ mapping precision) of each meadow was calculated in the GDA 2020 Geoscience Australia MGA Zone 53 projection using the ‘calculate geometry’ function in ArcMap. Mapping precision estimates (R; in ha) were based on the mapping method used for that meadow. Mapping precision estimate was used to calculate an error buffer around each meadow; the area of this buffer is expressed as a meadow reliability estimate (R) in hectares; + 10. Any relevant comments; + 11. Data custodians. + + Seagrass biomass interpolation layer + An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in seagrass biomass within seagrass meadows. The interpolation was conducted in ArcMap 10.8. + Base map + The base map used is courtesy ESRI 2023. + + Format of the data: + This dataset consists of 1 point layer package, 1 polygon layer package and 1 raster file: + 1. Yanyuwa Sea Country sites 2021-2022.lpk + - Symbology representing seagrass presence/absence at each survey site + 2. Yanyuwa Sea Country seagrass meadows 2021-2022.lpk + - Symbology representing dominant species (in terms of biomass) for each intertidal meadow. + 3. Yanyuwa Sea Country seagrass biomass interpolation 2021-2022.lpk + - Symbology representing the spatial variation in seagrass biomass within each seagrass meadow. + + Data dictionary: + Yanyuwa Sea Country sites 2021-2022 (point data) + SITE (text) - Unique identifier representing a single sample site + MEADOW (text) - Unique identifier representing what meadow the sample site is located in. Blank if sample site is not located within a meadow + SURVEY_DATE (numeric) – survey date (day/month/year) + MONTH (text) – survey month + YEAR (numeric) – survey year + SURVEY_NAME (text) – Name of survey location + LOCATION (text) – Name of survey location + LATITUDE (numeric) – Site location in decimal degrees south + LONGITUDE (numeric) – Site location in decimal degrees east + TIME (numeric) – sample time (24 hours; GMT +9:30) (NT time - subtidal sites only) + DEPTH (numeric) – depth recorded from vessel depth sounder (metres) for subtidal sites. Intertidal sites depth recorded as 0. + DBMSL (numeric) – depth below mean sea level (metres) for subtidal sites. Intertidal sites depth recorded as 0. + TIDAL (text) – identifying if the site was in an intertidal or subtidal location + SUBSTRATE (text) – tags identifying the types of substrates at the sample site. Possible tags are Mud, Sand, Coarse Sand, Silt, Shell, Rock, Reef, Rubble and various combinations. Listed in order from most dominant substrate to least dominant. + SEAGRASS_P (numeric) – Absence (0) or Presence (1) of seagrass + SEAGRASS_C (numeric) - Estimated % of seagrass cover at sample site + SEAGRASS_B (numeric) - Estimated total biomass per square metre for sample site calculated from the mean of three replicate quadrats. Unit is gdw m-2. + SEAGRASS_SE (numeric) – standard error of biomass at sample site calculated from the three replicate quadrats used to estimate biomass at a sample site. Unit is gdw m-2. + EXCLUDE_B (numeric) – Include (0) or Exclude (1). Any site identified that needs to be excluded from contributing to the calculation of mean meadow biomass, e.g. where a visual estimate of biomass could not be optioned (i.e. no visibility at the site, only a van Veen sediment grab was used at the site) + C. rotundata (numeric) – Estimated biomass of Cymodocea rotundata at the sample site. Unit is gdw m-2. + C. serrulata (numeric) – Estimated biomass of Cymodocea serrulata at the sample site. Unit is gdw m-2. + E. acoroides (numeric) – Estimated biomass of Enhalus acoroides at the sample site. Unit is gdw m-2. + H. uninervis (narrow) (numeric) – Estimated biomass of Halodule uninervis (narrow leaf morphology) at the sample site. Unit is gdw m-2. + H. uninervis (wide) (numeric) – Estimated biomass of Halodule uninervis (wide leaf morphology) at the sample site. Unit is gdw m-2. + H. decipiens (numeric) – Estimated biomass of Halophila decipiens at the sample site. Unit is gdw m-2. + H. ovalis (numeric) – Estimated biomass of Halophila ovalis at the sample site. Unit is gdw m-2. + H. spinulosa (numeric) – Estimated biomass of Halophila spinulosa at the sample site. Unit is gdw m-2. + H. tricostata (numeric) – Estimated biomass of Halophila tricostata at the sample site. Unit is gdw m-2. + S. isoetifolium (numeric) – Estimated biomass of Syringodium isoetifolium at the sample site. Unit is gdw m-2. + T. ciliatum (numeric) – Estimated biomass of Thalassodendron ciliatum at the sample site. Unit is gdw m-2. + T. hemprichii (numeric) – Estimated biomass of Thalassia hemprichii at the + Z. muelleri (numeric) – Estimated biomass of Zostera muelleri at the sample site. Unit is gdw m-2. + ALGAE_COVER (numeric) - Estimated % of algae cover at sample site (all algae types grouped) + TURF_MAT (numeric) – (Turf mat algae % contribution to algae cover). Algae that forms a dense mat on the substrate + ERECT_MACROPHYTE (numeric) – (Erect macrophyte algae % contribution to algae cover). Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species + ENCRUSTING (numeric) – (Encrusting algae % contribution to algae cover). Algae that grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae. + ERECT_CALCAREOUS (numeric) – (Erect calcareous algae % contribution to algae cover). Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. + FILAMENTOUS (numeric) – (Filamentous algae % contribution to algae cover). Thin, thread-like algae with little cellular differentiation. + *Note: TURF_MAT + ERECT_MACROPHYTE + ENCRUSTING + ERECT_CALCAREOUS + FILAMENTOUS = 100% of algae cover + HARD_CORAL (numeric) – (Hard coral %). All scleractinian corals including massive, branching, tabular, digitate and mushroom + SOFT_CORAL (numeric) – (Soft coral %). All alcyonarian corals, i.e. corals lacking a hard limestone skeleton + SPONGE (numeric) – (Sponge %) + OTHER_BMI (numeric) – Any other benthic macro-invertebrates identified, e.g. oysters, ascidians, clams. Other benthic macro-invertebrates are listed in the “comments” attribute for intertidal and shallow subtidal camera drops, and listed as percent cover in the deepwater GIS. + OPEN_SUBSTRATE (numeric) – Open substrate, no seagrass, algae or benthic macro-invertebrates at site + DUGONG (numeric) - Absence (0) or Presence (1) of dugong/s at site + TURTLE (numeric) - Absence (0) or Presence (1) of turtle/s at site + DOLPHIN (numeric) - Absence (0) or Presence (1) of dolphin/s at site + DFT PRESENT (numeric) - Absence (0) or Presence (1) of dugong feeding trails at site. Only clearly visible and therefore assessed at intertidal sites. Subtidal sites not assessed for DFTs coded as -999 + METHOD (text) – e.g. helicopter, walking, hovercraft, boat-based including camera, free diving, scuba diving, van Veen grab, sled net + VESSEL (text) – Vessel name (if known) + COMMENTS (text) – Any comments for that site + CUSTODIAN (text) – Custodian/owner of the data set + UPDATED (text) - The date the shapefile was last updated + AUTHOR (text) – Creator of GIS from the data set + *Note: SEAGRASS_C + ALGAE_COVER + HARD_CORAL + SOFT_CORAL + SPONGE + OTHER_BMI + OPEN_SUBSTRATE = 100% of benthic cover + + Yanyuwa Sea Country seagrass meadows 2021-2022 (polygon data) + ID (numeric) - Unique identifier representing a single meadow + SURVEY_NAME (text) – Name of survey location + LOCATION (text) – Name of survey location + SURVEY_DATE (text) – Sample date (day/month/year) + MONTH (numeric) – Sample month + YEAR (numeric) – Sample year + PERSISTENCE (text) – Meadow form on three categories: enduring, transitory, unknown + DENSITY (text) – Meadow density categories (light, moderate, dense) + TYPE (text) - Meadow community type determined according to seagrass species composition within the meadow + SPECIES (text) – (Seagrass species): seagrass species found within the meadow. Species are recorded as abbreviated species names such as “E. acoroides” + TOT_SITES (numeric) – (Number of survey sites): the number of sample sites within the meadow + BIOMASS (numeric) – (Seagrass biomass (gdw m-2)): Mean biomass calculated from all sites (BIO_SITES) within an individual meadow + SE (numeric) – (Standard Error (gdw m-2)): The error is a calculation of standard error of biomass from all (BIO_SITES) sites within an individual meadow. Where only 1 site surveyed in the meadow, SE will be 0. Where two sites were surveyed and biomass was 0 at one site, mean biomass and SE are the same values when calculated; + AREA_HA (numeric) – (Meadow area (Ha)): Estimated meadow size (unit: hectares) + R_M (numeric) – (Meadow mapping precision (m)): Estimated mapping precision based on mapping method. + R_HA (numeric) - (Meadow reliability estimate (Ha)): Meadow reliability estimate (unit: hectares). Expressing the error buffer around each meadow as calculated from the mapping precision estimate + SURVEY METHOD (text) – e.g. helicopter, walking, hovercraft, boat-based including camera, free diving, scuba diving, van Veen grab, sled net + VESSEL (text) – Vessel name (if known) + COMMENTS (text) – Any relevant comments for that meadow + UPDATED (date) – The date the shapefile was last updated + CUSTODIAN (text) – Custodian/owner of the data set + AUTHOR (text) – Creator of GIS from the data set + + Yanyuwa biomass interpolation 2022 (interpolation layer) + Inverse Distance Weighted interpolation. + Band 1: Interpolated biomass in gdw m-2 + + Data Description: + This section provides an brief text description of the data. This data set shows that in Yanyuwa sea country in the Gulf of Carpentaria, that there is significant seagrass along the coastline. The inshore coastline seagrass continues from Rosie Creek to Robinson River, where King Ash Bay and Bing Bong has almost continuous, reasonably dense seagrass meadows. Seagrass cover is present around the north, east and southern intertidal areas of West Island. Around the northern side of Black Islet has seagrass as well as north areas of Skull Island. Watson Island has seagrass areas on the southern and eastern coastlines. Seagrass cover can be found on Centre Island on all sides, particularly on the east and western sides. Vanderlin Island has light seagrass cover mostly towards the southern tip. Species present in these regions include C. serrulate, E. acoroides, H. ovalis, H. uninervis. + + + eAtlas Processing: + The original data were provided as ArcGIS Layer Packages (lpk]. Data were converted to Shapefiles and + GeoTiff with no modifications to the underlying data. + + Location of the data: + This dataset is filed in the eAtlas enduring data repository at: data\\custodian\NESP-MaC-1\1.12_Yanyuwa-sea-country-seagrass + + + + + + The data collections described in this record are funded by the Australian Government Department of Climate Change, Energy the Environment and Water (DCCEEW) through the NESP Marine and Coastal Hub. In addition to NESP (DCCEEW) funding, this project is matched by an equivalent amount of in-kind support and co-investment from project partners and collaborators. + + + + + + + + + + + + + TropWATER, James Cook University + + + + + Carter, Alex, Dr + + + + + + + + + + + + + + + + + + + + Cairns + + + Queensland + + + + + + Australia + + + alexandra.carter@jcu.edu.au + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + environment + + + biota + + + + + Benthic habitats were surveyed in Yanyuwa Sea Country, Northern Territory, Australia. Survey sites and mapped seagrass meadows are provided as GIS shapefiles. + + + + + 136.1866 + + + 137.2787 + + + -16.0337 + + + -15.3817 + + + + + + + + + 2021-10-13 + 2022-10-05 + + + + + + + + + + + + + + + + + https://eatlas.org.au/geonetwork/srv/api/records/cffa7269-5d95-486b-9b2e-77316e808398/attachments/Yanyuwa_Sea_Country_sites_2021-2022.jpg + + + Yanyuwa Sea Country sites layer preview 2021-2022. + + + + + + + https://eatlas.org.au/geonetwork/srv/api/records/cffa7269-5d95-486b-9b2e-77316e808398/attachments/Yanyuwa_Sea_Country_seagrass_meadows_2021-2022.jpg + + + Yanyuwa Sea Country seagrass meadows layer preview, 2021-2022 + + + + + + + https://eatlas.org.au/geonetwork/srv/api/records/cffa7269-5d95-486b-9b2e-77316e808398/attachments/Yanyuwa_Sea_Country_seagrass_biomass_interpolation_2021-2022.jpg + + + Yanyuwa Sea Country seagrass biomass interpolation layer preview, 2021-2022 + + + + + + + marine + + + National Environmental Science Program (NESP) Marine and Coastal Hub + + + + + + + + + + MARINE + + + + + + + + theme.sciencekeywords-8.1_.rdf + + + + + 2022-05-09 + + + + + + + + + + geonetwork.thesaurus.external.theme.sciencekeywords-8.1_ + + + + + + + + + + + Coastal Waters (Australia) + + + + + + + + AODN Geographic Extents Vocabulary + + + + + 2022-05-09 + + + + + + + + + + geonetwork.thesaurus.external.place.aodn_aodn-geographic-extents-vocabulary_version-4-0(1) + + + + + + + + + + + TropWATER gives no warranty in relation to the data (including accuracy, reliability, completeness, currency or suitability) and accepts no liability (including without limitation, liability in negligence) for any loss, damage or costs (including consequential damage) relating to any use of the data. TropWATER reserves the right to update, modify or correct the data at any time. The limitations of some older data included need to be understood and recognised. TropWATER and other data custodians would appreciate the opportunity to review documents providing research, management, legislative or compliance advice based on this data. + + + + + + + + https://i.creativecommons.org/l/by/4.0/88x31.png + + + WWW:LINK-1.0-http--related + + + License Graphic + + + + + + + + + Creative Commons Attribution 4.0 International License + + + CC-BY + + + 4.0 + + + + + http://creativecommons.org/licenses/by/4.0/ + + + WWW:LINK-1.0-http--related + + + + + + + + + + Cite as: Groom, R., Carter, A. B., Collier, C., Firby, L., Evans, S., Barrett, S., Hoffman, L., van de Wetering, C., Evans, S., Simon, S., & Anderson, S. (2023). Benthic habitats of Yanyuwa Sea Country, Barni - Wardimantha Awara Indigenous Protected Area, Gulf of Carpentaria, Northern Territory, Australia (NESP MaC Project 1.12, JCU & CDU) [Data set]. eAtlas. https://doi.org/10.26274/V6K5-2F34 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Australian Institute of Marine Science (AIMS) + + + + + eAtlas Data Manager + + + + + + + +61 7 4753 4444 + + + + + + + + + + PRIVATE MAIL BAG 3, TOWNSVILLE MAIL CENTRE + + + Townsville + + + Queensland + + + 4810 + + + Australia + + + e-atlas@aims.gov.au + + + + + + + https://eatlas.org.au + + + WWW:LINK-1.0-http--link + + + eAtlas portal + + + + + + + + + + + + + + + + + + + + + + https://maps.eatlas.org.au/maps/ows + + + OGC:WMS + + + nesp-mac-1:NT_JCU_CDU_NESP-MaC-1-12_Yanyuwa-Seagrass-Sites_2021-2022 + + + Yanyuwa Seagrass Sites, 2021-2022 (NESP MaC 1-12, JCU & CDU) + + + + + + + + + + https://maps.eatlas.org.au/maps/ows + + + OGC:WMS + + + nesp-mac-1:NT_JCU_CDU_NESP-MaC-1-12_Yanyuwa-Seagrass-Meadows_2021-2022 + + + Yanyuwa Seagrass Meadows, 2021-2022 (NESP MaC 1-12, JCU & CDU) + + + + + + + + + + https://maps.eatlas.org.au/index.html?intro=false&z=9&ll=136.78606,-15.62248&l0=ea_nesp-mac-1%3ANT_JCU_CDU_NESP-MaC-1-12_Yanyuwa-Seagrass-Meadows_2021-2022,ea_ea-be%3AWorld_Bright-Earth-e-Atlas-basemap,google_HYBRID,google_TERRAIN,google_SATELLITE,google_ROADMAP,ea_nesp-mac-1%3ANT_JCU_CDU_NESP-MaC-1-12_Yanyuwa-Seagrass-Sites_2021-2022&s0=nesp-mac-1%3AYanyuwa-Seagrass_Type&v0=,,f,f,f,f + + + WWW:LINK + + + Interactive map of the resource + + + Interactive map of the resource: This dataset summarises benthic surveys in Yanyuwa Sea Country - meadow type and presence/absence of seagrass. + + + + + + + + + + https://maps.eatlas.org.au/maps/ows + + + OGC:WMS + + + nesp-mac-1:NT_JCU_CDU_NESP-MaC-1-12_Yanyuwa-Seagrass-Biomass-Interpolation_2021-2022 + + + Yanyuwa Seagrass Biomass Interpolation, 2021-2022 (NESP MaC 1.12, JCU & CDU) + + + + + + + + + + https://nextcloud.eatlas.org.au/apps/sharealias/a/1.12_Yanyuwa-sea-country-seagrass + + + WWW:DOWNLOAD-1.0-http--download + + + Download a copy of the dataset + + + Access the dataset [2 shapefiles, 1 geotiff & 3 preview images] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://i.creativecommons.org/l/by/4.0/88x31.png + + + WWW:LINK-1.0-http--related + + + License Graphic + + + + + + + + + Creative Commons Attribution 4.0 International License + + + CC-BY + + + 4.0 + + + + + http://creativecommons.org/licenses/by/4.0/ + + + WWW:LINK-1.0-http--related + + + License Text + + + + + + + + diff --git a/indexer/src/test/resources/canned/sample_geoenum_publication_stac.json b/indexer/src/test/resources/canned/sample_geoenum_publication_stac.json new file mode 100644 index 00000000..ab09df5f --- /dev/null +++ b/indexer/src/test/resources/canned/sample_geoenum_publication_stac.json @@ -0,0 +1,177 @@ +{ + "title" : "Benthic habitats of Yanyuwa Sea Country, Barni - Wardimantha Awara Indigenous Protected Area, Gulf of Carpentaria, Northern Territory, Australia (NESP MaC Project 1.12, JCU & CDU)", + "description" : "This dataset summarises benthic surveys in Yanyuwa Sea Country into 3 GIS shapefiles.\n (1) A point (site) shapefile describes seagrass presence/absence at 3248 sites surveyed by small vessel and helicopter.\n (2) The meadow shapefile describes attributes of 180 intertidal seagrass meadows.\n (3) The interpolation GeoTiff describes variation in seagrass biomass across the seagrass meadows.\n\n This project is a partnership between li-Anthawirriyarra rangers, Charles Darwin University, James Cook University, and Mabunji Aboriginal Resource Indigenous Corporation to map the intertidal habitats of the Yanyuwa Indigenous Protected Area (IPA), an area of profound importance to the Marra and Yanyuwa people and to the marine ecosystem of the Gulf of Carpentaria. Benthic habitat maps of Yanyuwa Country were produced, with a focus on seagrass.\n\n Report reference: Groom R, Carter A, Collier C, Firby L, Evans S, Barrett S, Hoffmann L, van de Wetering C, Shepherd L, Evans S, Anderson S. (2023) Mapping Critical Habitat in Yanyuwa Sea Country. Report to the National Environmental Science Program. Charles Darwin University, pp. 40. Available at: https://www.nespmarinecoastal.edu.au/wp-content/uploads/2023/07/NESP-MaC-Hub-Project-1.12_Groom-et-al-FINAL-REPORT.pdf\n\n Methods:\n The sampling methods used to study, describe and monitor seagrass meadows were developed by the TropWATER Seagrass Group and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater).\n Geographic Information System (GIS)\n\n All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.8. Rectified colour satellite imagery of Yanyuwa Sea Country (Source: Allen Coral Atlas and ESRI), field notes and aerial photographs taken from the helicopter during surveys were used to identify geographical features, such as reef tops, channels and deep-water drop-offs, to assist in determining seagrass meadow boundaries. Three GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and a seagrass biomass interpolation layer.\n\n Seagrass site layer\n This layer contains information on data collected at assessment sites. This layer includes:\n 1.\tTemporal survey details – Survey date;\n 2.\tSpatial position - Latitude/longitude;\n 3.\tSurvey location;\n 4.\tSeagrass information including presence/absence of seagrass, above-ground biomass (total and for each species), percent cover of seagrass at each site and whether individual species were present/absent at a site;\n 5.\tBenthic macro-invertebrate information including the percent cover of hard coral, soft coral, sponges and other benthic macro invertebrates (e.g. ascidian, clam) at a site;\n 6.\tAlgae information including percent cover of algae at a site and percent contribution of algae functional groups to algae cover at a site;\n 7.\tOpen substrate – the percent cover of the site that had no flora or habitat forming benthic invertebrates present;\n 8.\tDominant sediment type - Sediment type based on grain size visual assessment or deck descriptions.\n 9.\tSurvey method and vessel\n 10.\tRelevant comments and presence/absence of megafauna and animals of interest (dugong, turtle, dolphin, evidence of dugong feeding trails);\n 11.\tData custodians.\n\n Seagrass meadow layer\n Seagrass presence/absence site data, mapping sites, field notes, and satellite imagery were used to construct meadow boundaries in ArcGIS®. The meadow (polygon) layer provides summary information for all sites within each seagrass meadow, including:\n 1.\tTemporal survey details – Survey month and year as individual columns and the survey date (the date range the survey took place);\n 2.\tSpatial survey details – Survey location, meadow identification number that identifies the reef name and the meadow number. This allows individual meadows to be compared among years;\n 3.\tSurvey method;\n 4.\tMeadow depth for subtidal meadows. Intertidal: meadow was mapped on an exposed bank during low tide;\n 5.\tSpecies presence – a list of the seagrass species in the meadow;\n 6.\tMeadow density – Seagrass meadows were classified as light, moderate, dense based on the mean biomass of the dominant species within the meadow. For example, a Thalassia hemprichii dominated meadow would be classed as “light” if the mean meadow biomass was <5 grams dry weight m-2 (g DW m-2), and “dense” if mean meadow biomass was >25 g DW m-2.\n 7.\tMeadow community type – Seagrass meadows were classified into community types according to seagrass species composition within each meadow. Species composition was based on the percent each species’ biomass contributed to mean meadow biomass. A standard nomenclature system was used to categorize each meadow.\n 8.\tMean meadow biomass measured in g DW m-2 (+ standard error if available);\n 9.\tMeadow area (hectares; ha) (+ mapping precision) of each meadow was calculated in the GDA 2020 Geoscience Australia MGA Zone 53 projection using the ‘calculate geometry’ function in ArcMap. Mapping precision estimates (R; in ha) were based on the mapping method used for that meadow. Mapping precision estimate was used to calculate an error buffer around each meadow; the area of this buffer is expressed as a meadow reliability estimate (R) in hectares;\n 10.\tAny relevant comments;\n 11.\tData custodians.\n\n Seagrass biomass interpolation layer\n An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in seagrass biomass within seagrass meadows. The interpolation was conducted in ArcMap 10.8.\n Base map\n The base map used is courtesy ESRI 2023.\n\n Format of the data:\n This dataset consists of 1 point layer package, 1 polygon layer package and 1 raster file:\n 1.\tYanyuwa Sea Country sites 2021-2022.lpk\n -\tSymbology representing seagrass presence/absence at each survey site\n 2.\tYanyuwa Sea Country seagrass meadows 2021-2022.lpk\n -\tSymbology representing dominant species (in terms of biomass) for each intertidal meadow.\n 3.\tYanyuwa Sea Country seagrass biomass interpolation 2021-2022.lpk\n -\tSymbology representing the spatial variation in seagrass biomass within each seagrass meadow.\n\n Data dictionary:\n Yanyuwa Sea Country sites 2021-2022 (point data)\n SITE (text) - Unique identifier representing a single sample site\n MEADOW (text) - Unique identifier representing what meadow the sample site is located in. Blank if sample site is not located within a meadow\n SURVEY_DATE (numeric) – survey date (day/month/year)\n MONTH (text) – survey month\n YEAR (numeric) – survey year\n SURVEY_NAME (text) – Name of survey location\n LOCATION (text) – Name of survey location\n LATITUDE (numeric) – Site location in decimal degrees south\n LONGITUDE (numeric) – Site location in decimal degrees east\n TIME (numeric) – sample time (24 hours; GMT +9:30) (NT time - subtidal sites only)\n DEPTH (numeric) – depth recorded from vessel depth sounder (metres) for subtidal sites. Intertidal sites depth recorded as 0.\n DBMSL (numeric) – depth below mean sea level (metres) for subtidal sites. Intertidal sites depth recorded as 0.\n TIDAL (text) – identifying if the site was in an intertidal or subtidal location\n SUBSTRATE (text) – tags identifying the types of substrates at the sample site. Possible tags are Mud, Sand, Coarse Sand, Silt, Shell, Rock, Reef, Rubble and various combinations. Listed in order from most dominant substrate to least dominant.\n SEAGRASS_P (numeric) – Absence (0) or Presence (1) of seagrass\n SEAGRASS_C (numeric) - Estimated % of seagrass cover at sample site\n SEAGRASS_B (numeric) - Estimated total biomass per square metre for sample site calculated from the mean of three replicate quadrats. Unit is gdw m-2.\n SEAGRASS_SE (numeric) – standard error of biomass at sample site calculated from the three replicate quadrats used to estimate biomass at a sample site. Unit is gdw m-2.\n EXCLUDE_B (numeric) – Include (0) or Exclude (1). Any site identified that needs to be excluded from contributing to the calculation of mean meadow biomass, e.g. where a visual estimate of biomass could not be optioned (i.e. no visibility at the site, only a van Veen sediment grab was used at the site)\n C. rotundata (numeric) – Estimated biomass of Cymodocea rotundata at the sample site. Unit is gdw m-2.\n C. serrulata (numeric) – Estimated biomass of Cymodocea serrulata at the sample site. Unit is gdw m-2.\n E. acoroides (numeric) – Estimated biomass of Enhalus acoroides at the sample site. Unit is gdw m-2.\n H. uninervis (narrow) (numeric) – Estimated biomass of Halodule uninervis (narrow leaf morphology) at the sample site. Unit is gdw m-2.\n H. uninervis (wide) (numeric) – Estimated biomass of Halodule uninervis (wide leaf morphology) at the sample site. Unit is gdw m-2.\n H. decipiens (numeric) – Estimated biomass of Halophila decipiens at the sample site. Unit is gdw m-2.\n H. ovalis (numeric) – Estimated biomass of Halophila ovalis at the sample site. Unit is gdw m-2.\n H. spinulosa (numeric) – Estimated biomass of Halophila spinulosa at the sample site. Unit is gdw m-2.\n H. tricostata (numeric) – Estimated biomass of Halophila tricostata at the sample site. Unit is gdw m-2.\n S. isoetifolium (numeric) – Estimated biomass of Syringodium isoetifolium at the sample site. Unit is gdw m-2.\n T. ciliatum (numeric) – Estimated biomass of Thalassodendron ciliatum at the sample site. Unit is gdw m-2.\n T. hemprichii (numeric) – Estimated biomass of Thalassia hemprichii at the\n Z. muelleri (numeric) – Estimated biomass of Zostera muelleri at the sample site. Unit is gdw m-2.\n ALGAE_COVER (numeric) - Estimated % of algae cover at sample site (all algae types grouped)\n TURF_MAT (numeric) – (Turf mat algae % contribution to algae cover). Algae that forms a dense mat on the substrate\n ERECT_MACROPHYTE (numeric) – (Erect macrophyte algae % contribution to algae cover). Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species\n ENCRUSTING (numeric) – (Encrusting algae % contribution to algae cover). Algae that grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae.\n ERECT_CALCAREOUS (numeric) – (Erect calcareous algae % contribution to algae cover). Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species.\n FILAMENTOUS (numeric) – (Filamentous algae % contribution to algae cover). Thin, thread-like algae with little cellular differentiation.\n *Note: TURF_MAT + ERECT_MACROPHYTE + ENCRUSTING + ERECT_CALCAREOUS + FILAMENTOUS = 100% of algae cover\n HARD_CORAL (numeric) – (Hard coral %). All scleractinian corals including massive, branching, tabular, digitate and mushroom\n SOFT_CORAL (numeric) – (Soft coral %). All alcyonarian corals, i.e. corals lacking a hard limestone skeleton\n SPONGE (numeric) – (Sponge %)\n OTHER_BMI (numeric) – Any other benthic macro-invertebrates identified, e.g. oysters, ascidians, clams. Other benthic macro-invertebrates are listed in the “comments” attribute for intertidal and shallow subtidal camera drops, and listed as percent cover in the deepwater GIS.\n OPEN_SUBSTRATE (numeric) – Open substrate, no seagrass, algae or benthic macro-invertebrates at site\n DUGONG (numeric) - Absence (0) or Presence (1) of dugong/s at site\n TURTLE (numeric) - Absence (0) or Presence (1) of turtle/s at site\n DOLPHIN (numeric) - Absence (0) or Presence (1) of dolphin/s at site\n DFT PRESENT (numeric) - Absence (0) or Presence (1) of dugong feeding trails at site. Only clearly visible and therefore assessed at intertidal sites. Subtidal sites not assessed for DFTs coded as -999\n METHOD (text) – e.g. helicopter, walking, hovercraft, boat-based including camera, free diving, scuba diving, van Veen grab, sled net\n VESSEL (text) – Vessel name (if known)\n COMMENTS (text) – Any comments for that site\n CUSTODIAN (text) – Custodian/owner of the data set\n UPDATED (text) - The date the shapefile was last updated\n AUTHOR (text) – Creator of GIS from the data set\n *Note: SEAGRASS_C + ALGAE_COVER + HARD_CORAL + SOFT_CORAL + SPONGE + OTHER_BMI + OPEN_SUBSTRATE = 100% of benthic cover\n\n Yanyuwa Sea Country seagrass meadows 2021-2022 (polygon data)\n ID (numeric) - Unique identifier representing a single meadow\n SURVEY_NAME (text) – Name of survey location\n LOCATION (text) – Name of survey location\n SURVEY_DATE (text) – Sample date (day/month/year)\n MONTH (numeric) – Sample month\n YEAR (numeric) – Sample year\n PERSISTENCE (text) – Meadow form on three categories: enduring, transitory, unknown\n DENSITY (text) – Meadow density categories (light, moderate, dense)\n TYPE (text) - Meadow community type determined according to seagrass species composition within the meadow\n SPECIES (text) – (Seagrass species): seagrass species found within the meadow. Species are recorded as abbreviated species names such as “E. acoroides”\n TOT_SITES (numeric) – (Number of survey sites): the number of sample sites within the meadow\n BIOMASS (numeric) – (Seagrass biomass (gdw m-2)): Mean biomass calculated from all sites (BIO_SITES) within an individual meadow\n SE (numeric) – (Standard Error (gdw m-2)): The error is a calculation of standard error of biomass from all (BIO_SITES) sites within an individual meadow. Where only 1 site surveyed in the meadow, SE will be 0. Where two sites were surveyed and biomass was 0 at one site, mean biomass and SE are the same values when calculated;\n AREA_HA (numeric) – (Meadow area (Ha)): Estimated meadow size (unit: hectares)\n R_M (numeric) – (Meadow mapping precision (m)): Estimated mapping precision based on mapping method.\n R_HA (numeric) - (Meadow reliability estimate (Ha)): Meadow reliability estimate (unit: hectares). Expressing the error buffer around each meadow as calculated from the mapping precision estimate\n SURVEY METHOD (text) – e.g. helicopter, walking, hovercraft, boat-based including camera, free diving, scuba diving, van Veen grab, sled net\n VESSEL (text) – Vessel name (if known)\n COMMENTS (text) – Any relevant comments for that meadow\n UPDATED (date) – The date the shapefile was last updated\n CUSTODIAN (text) – Custodian/owner of the data set\n AUTHOR (text) – Creator of GIS from the data set\n\n Yanyuwa biomass interpolation 2022 (interpolation layer)\n Inverse Distance Weighted interpolation.\n Band 1: Interpolated biomass in gdw m-2\n\n Data Description:\n This section provides an brief text description of the data. This data set shows that in Yanyuwa sea country in the Gulf of Carpentaria, that there is significant seagrass along the coastline. The inshore coastline seagrass continues from Rosie Creek to Robinson River, where King Ash Bay and Bing Bong has almost continuous, reasonably dense seagrass meadows. Seagrass cover is present around the north, east and southern intertidal areas of West Island. Around the northern side of Black Islet has seagrass as well as north areas of Skull Island. Watson Island has seagrass areas on the southern and eastern coastlines. Seagrass cover can be found on Centre Island on all sides, particularly on the east and western sides. Vanderlin Island has light seagrass cover mostly towards the southern tip. Species present in these regions include C. serrulate, E. acoroides, H. ovalis, H. uninervis.\n\n\n eAtlas Processing:\n The original data were provided as ArcGIS Layer Packages (lpk]. 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