pysgcn

This package provides the necessary steps to assemble the Synthesized Species of Greatest Conservation Need database from source files in ScienceBase.

Workflow

The IPython Notebooks in the workflow folder provide a recipe for processing the SGCN source data using a combination of the pysgcn functions and pysppin modules.

1. Get Processable SGCN Items - The get_processable_items function from pysgcn provides the basic logic for querying ScienceBase and returning processable item metadata (simplified set of properties needed to process source data). The workflow step in the standalone package sends processable items to a data table as messages, and can be modified to send messages to an actual message queue.
2. Cache Metadata and Document Schemas - This workflow caches several metadata files needed for data processing in the local database for use and exercises a method to document schemas.
3. Extract Source Data - This workflow step includes functions to pull source data from ScienceBase files, add records to a queue for processing, and add taxa names to a queue for lookup against ITIS (next step with scientific names before additional information gathering steps).
4. Process Source Data - This workflow step can start executing as soon as there are source data messages in the queue. It processes the source records, validates them against a schema, and puts them into a database table.
5. ITIS - Runs the process to lookup species names and TSN identifiers and return records.
6. ITIS - Runs the process to lookup species names and TSN identifiers and return records.

Pipeline

The AWS pipeline interacts with the scripts through the pysgcn/bis_pipeline.py file.

Running Locally

Interactions with permanent infastructure in the AWS pipeline are replaced with sqlite for local runs. All of this functionality is in the local_pipeline_run.py file and can be modified if needed. Make sure the cache_root variable in local_pipeline_run.py points towards a sqlite db. The reults of the pipeline run will be stored in the cache table. Run python local_pipeline_run.py and the processing will start.

Provisional Software Statement

Under USGS Software Release Policy, the software codes here are considered preliminary, not released officially, and posted to this repo for informal sharing among colleagues.

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

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