Load Layer - CAPAD 2018 Marine

[Tasilee]

http://www.environment.gov.au/fed/catalog/search/resource/details.page?uuid=%7BAF4EE98E-7F09-4172-B95E-067AB8FA10FC%7D. Latest update (retain prior versions). Priority-Hi.

Investigation and approval

Check the boxes below that apply, including comments where necessary, and then refer this issue to the appropriate person for approval:

• [ ] The information doesn’t already exist (e.g., IPAs are in CAPAD)
• [ ] Is it an AREA (single or multi-polygon that could be imported/saved) rather than a layer?
• [ ] National coverage, or international coverage where data helps place the Australian region in context
• [ ] Presents information that suggests spatial control of species distributions or would be use-ful in the interpretation or management of species and areas
• [ ] Data is from an authoritative source
• [ ] Spatial resolution of 1km or better preferred
• [ ] Fills a gap in or complements our layer collection (name, space, time, environmental factor)
• [ ] Anticipated broad usage by one or more of the following communities (research, area managers, environmental consultants, citizen scientists, education, public)
• [ ] Has quality metadata
• [ ] Data is in a form that is readily ingested into our systems
• [ ] Is up to date
• [ ] Supersedes an existing layer (deprecation or deletion)
• [ ] Anticipates future requirements
• [ ] Supports nationally significant projects (which themselves would need some evaluation, but GBR management given World Heritage status and threats would pass)
• [ ] Externally funded? This may relate to project support.
• [ ] Openly available (free and open source data).

Approval

• [ ] Obtain approval from ALA Management to load layer based on an evaluation

Loading the layer

Once layer loading has been approved, the following are the steps required to load, integrate, and test it.

• [ ] Download the original shapefile and metadata file
• [ ] Analyse the shapefile for field value expectations
• [ ] Select one or more fields from the shapefile to be included as fields in spatial/biocache
• [ ] Upload layer at: https://nectar-spatial-staging.ala.org.au/ws/manageLayers/uploads
• [ ] Once the shapefile upload is complete, choose Create layer
• [ ] Enter the layer metadata and choose create layer
• [ ] Once the layer is loaded, create one or more fields
• [ ] Once the fields are created, check that they are visible and correct on nectar-spatial-staging spatial-hub instance by adding the new Layer to a map
• [ ] If not visible, run https://nectar-spatial-staging.ala.org.au/ws/tasks/create?name=Thumbnails
• [ ] If still not visible, restart nectar-spatial-staging
• [ ] If still not visible, wait for 24 hours and check again
• [ ] If still not visible, give up and submit an issue on Github with the details for a spatial developer to look at
• [ ] Once the fields are visible, go to https://spatial.ala.org.au/ws/manageLayers/remote and choose Copy layer
• [ ] Once the copy is complete, check that the layer copy succeeded. The layer and the field should not be Enabled after the layer copy process completes, as a final safety if the copy failed to complete successfully.
• [ ] Copy the layer to ala-dylan.it.csiro.au based on running the following on ala-dylan:

  export LAYER_NAME=... # This is the short name for the layer
  export LAYER_ID=... # This is the numeric identifier for the layer
  export FIELD_ID=... # This is the cl/el identifier for the field
  export API_KEY= # Obtain API key from at https://auth.ala.org.au/apikey/
  /root/copy-layer-from-aws-spatial-prod.sh "${LAYER_NAME}" "${LAYER_ID}" "${FIELD_ID}" "${API_KEY}"

• [ ] Enable both the layer and the field on https://spatial.ala.org.au/ws/manageLayers/layers
• [ ] Check if the layer with LAYER_ID is enabled in https://spatial.ala.org.au/ws/layers
• [ ] Check if the field with FIELD_ID is enabled in https://spatial.ala.org.au/ws/fields
• [ ] Put a shutdown on the Jenkins queue on aws-scjenkins.ala.org.au and check that there are no jobs running. If there are jobs running, undo the shutdown and try again another time.
• [ ] Restart tomcat on ala-dylan.it.csiro.au using:

  sudo service tomcat7 restart

• [ ] Pick a suitable coordinate that is expected to have a value from the layer, and test intersection sampling is working using the following and then inspecting ~/${FIELD_ID}-intersection-output/sample.csv:

  export INTERSECTING_COORDINATES=-17,150;
  export FIELD_ID=... # This is the cl/el identifier for the field
  /root/check-intersection.py --field-id=${FIELD_ID} --intersecting-coordinates=${INTERSECTING_COORDINATES} --output-dir ~/${FIELD_ID}-intersection-output

• [ ] Remove the shutdown on the Jenkins queue on aws-scjenkins.ala.org.au
• [ ] Check the contents of the fieldsdb service on ala-dylan (https://sampling.ala.org.au/sampling-service/fieldsdb) and aws-spatial-prod (https://spatial.ala.org.au/ws/fieldsdb)

  Fetch 'https://sampling.ala.org.au/sampling-service/fieldsdb' and double-check that the field now exists and 'indb: true' is on the field that was added
  TODO: automate this using 'jq'.

• [ ] Run Complete Process and Sample jenkins job on aws-scjenkins http://aws-scjenkins.ala:9193/job/Complete%20Process%20and%20Sample/ (Or wait for the weekly automated job)
• [ ] Run the Complete Reindex on aws-scjenkins http://aws-scjenkins.ala:9193/job/Complete%20Indexing/job/MASTER%20-%20Complete%20Re-index/ (Or wait for the next automated job after the Complete Process and Sample)
• [ ] Check using biocache.ala.org.au that expected records have the new cl value (individual record displays are sourced from cassandra)
• [ ] Check using biocache.ala.org.au that searches on the new cl value succeed (search results are sourced from solr)
• [ ] Check that the new field exists in https://biocache-ws.ala.org.au/ws/index/fields