Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
322 changes: 322 additions & 0 deletions _episodes/30_near_real_time_qc_process.md

Large diffs are not rendered by default.

46 changes: 46 additions & 0 deletions _episodes/31_near_real_time_qc_how_to_WildlifeComputers.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
---
title: "Near Real Time (NRT) Animal Tagging Location Data Quality Control (QC) Process: Wildlife Computers"
teaching: 120
exercises: 0
questions:
- "How to receive metadata & data access from a researcher to set up satellite data harvesting"
- "How to use the metadata to create a config file"
- "How to push that config file somewhere so it can be processed regularly by the RT process"
- "How to process a dataset that is no longer real-time - delayed-mode"
---


## How to receive metadata & data access from a researcher to set up satellite data harvesting for Wildlife Computers tags
### Metadata
The minimum metadata required by the QC process is:

1. species common name.
2. species scientific name.
3. release site (e.g., Sable Island).
4. release country.
5. tag serial number(s) and PTT ID(s).

Use whatever method for obtaining these metadata from the researcher works for you.

### Data access
Ensure you have a Wildlife Computers (WC) Portal account & a security key pair set up (see 30_near_time_qc_process). Ask the researcher to setup sharing for their tag datasets via the WC Portal. The data owner(s) will need the email address the node manager used for their WC Portal user account. If the researcher does not know how to do this, refer them to the information on p. 19 in [document (p 19)](https://static.wildlifecomputers.com/Portal-and-Tag-Agent-User-Guide-2.pdf).

Once data sharing is setup, within R you can verify access to the researcher's data via the WC Portal API using the ArgosQC utility function `wc_get_collab_ids`:
```
ArgosQC:::wc_get_collab_ids((a.key = "...", s.key = "...")
```
Where the `a.key` and `s.key` values are your WC access and secret key pair. Executing this function with R returns a data.frame of all data owners' (collaborators) ID's and email addresses who have set up data sharing with the node manager:
![](../fig/wc_owner.ids.png){width=300}

If this function does not return a data.frame (or results in an error) then data sharing has not been setup correctly in the WC Portal and you will need to troubleshoot with the researcher.

## How to use the metadata to create a config file
All details for constructing `ArgosQC` config files are in this [Jupyter notebook](https://github.com/ocean-tracking-network/rt-sat-to-obis/blob/add_conda_env/ArgosQC_WildlifeComputers_Project_Config.ipynb).

## How to push that config file somewhere so it can be processed regularly by the RT process
Details on how to do this are in this [Jupyter notebook](https://github.com/ocean-tracking-network/rt-sat-to-obis/blob/add_conda_env/ArgosQC_WildlifeComputers_Project_Config.ipynb).

## How to process a dataset that is no longer real-time - delayed-mode
Tag datasets that are no longer real-time (deployments have ended) may be processed in the same manner as real-time datasets, except that the QC process only needs to be run once.


38 changes: 38 additions & 0 deletions _episodes/32_near_real_time_qc_how_to_SMRU.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
---
title: "Near Real Time (NRT) Animal Tagging Location Data Quality Control (QC) Process: SMRU"
teaching: 120
exercises: 0
questions:
- "How to receive metadata & data access from a researcher to set up satellite data harvesting"
- "How to use the metadata to create a config file"
- "How to push that config file somewhere so it can be processed regularly by the RT process"
- "How to process a dataset that is no longer real-time - delayed-mode"
---


## How to receive metadata & data access from a researcher to set up satellite data harvesting for SMRU tags
### Metadata
The minimum metadata required by the QC process is:

1. species common name.
2. species scientific name.
3. release site (e.g., Sable Island).
4. release country.
5. SMRU campaign id(s) (e.g., ct190).

Use whatever method for obtaining these metadata from the researcher works for you.

### Data access
Ensure you have the researcher's username and password to access the data on the [SMRU server](https://www.smru.st-andrews.ac.uk/protected/technical.html). The server page is accessible to anyone to view SMRU tag deployments by registered project, but access to data within individual deployment "campaigns" are behind a WAF.

Once you have the researcher's username and password, these can be entered in the config file `harvest` block.

## How to use the metadata to create a config file
All details for constructing `ArgosQC` config files are in this [Jupyter notebook](https://github.com/ocean-tracking-network/rt-sat-to-obis/blob/add_conda_env/ArgosQC_SMRU_Project_Config.ipynb)

## How to push that config file somewhere so it can be processed regularly by the RT process
Details on how to do this are in this [Jupyter notebook](https://github.com/ocean-tracking-network/rt-sat-to-obis/blob/add_conda_env/ArgosQC_SMRU_Project_Config.ipynb)

## How to process a dataset that is no longer real-time - delayed-mode
Tag datasets that are no longer real-time (deployments have ended) may be processed in the same manner as real-time datasets, except that the QC process only needs to be run once.

Binary file added fig/smru_config_harvest.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/smru_server.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_config_akey_skey.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_config_model_params.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_config_owner.id.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_config_tag.list.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_dataset_uuids.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_owner.ids.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_portal_account_settings.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_portal_create_account.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_portal_login.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_portal_security_keypair.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_qc_lat_ssmfit.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_qc_map1.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_qc_map12.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_qc_map3.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_qc_map6.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_qc_map_reroute.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added fig/wc_tag.list.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.