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7yl4r / _tasks.md
Created November 17, 2022 18:40
MBON data management checklists

The bare minimum to register an MBON-facilitated dataset:

  • a unique dataset_id
  • supporting MBON node(s)
  • a contact email
  • a plain-text description of the dataset

Multiple google forms are used to collect different aspects of metadata.

MBON-facilitated dataset forms:

@7yl4r
7yl4r / DasDds_output.txt
Created October 26, 2022 17:58
no NFS but still failing
root@4c2b94c118bb:/usr/local/tomcat/webapps/erddap/WEB-INF# bash DasDds.sh OC_c7fe_e1ee_913d
////**** EDStatic Low Level Startup
localTime=2022-10-26T17:57:42+00:00
erddapVersion=2.18
Java 1.8.0_322 (64 bit, Oracle Corporation) on Linux (4.18.0-348.7.1.el8_5.x86_64).
MemoryInUse= 50 MB (highWaterMark= 50 MB) (Xmx ~= 958 MB)
logLevel=info: verbose=true reallyVerbose=false
got bigParentDirectory from ERDDAP_bigParentDirectory
got emailFromAddress from ERDDAP_emailFromAddress
@7yl4r
7yl4r / permissions_check.txt
Created October 26, 2022 16:53
sanity checks whilst debugging https://github.com/USF-IMARS/erddap-config/issues/22
root@302d01eec869:/erddapData/logs# ls -lah /test_local_data_dir/
total 64M
drwxr-xr-x. 2 root root 126 Oct 26 16:22 .
drwxr-xr-x. 1 root root 118 Oct 26 16:30 ..
-rwxr-xr--. 1 4747 4504 22M Oct 26 16:19 MODA_2002185_2002189_7D_FK_OC.nc
-rwxr-xr--. 1 4747 4504 22M Oct 26 16:19 MODA_2002190_2002196_7D_FK_OC.nc
-rwxr-xr--. 1 4747 4504 22M Oct 26 16:19 MODA_2002197_2002203_7D_FK_OC.nc
root@302d01eec869:/erddapData/logs# head -1 /test_local_data_dir/MODA_2002185_2002189_7D_FK_OC.nc
�HDF
@7yl4r
7yl4r / DasDds_output.txt
Last active October 26, 2022 17:56
NFS + Docker ERDDAP datasets.xml issues
root@302d01eec869:/usr/local/tomcat/webapps/erddap/WEB-INF# bash DasDds.sh OC_c7fe_e1ee_913c
////**** EDStatic Low Level Startup
localTime=2022-10-26T16:38:54+00:00
erddapVersion=2.18
Java 1.8.0_322 (64 bit, Oracle Corporation) on Linux (4.18.0-348.7.1.el8_5.x86_64).
MemoryInUse= 50 MB (highWaterMark= 50 MB) (Xmx ~= 958 MB)
logLevel=info: verbose=true reallyVerbose=false
got bigParentDirectory from ERDDAP_bigParentDirectory
got emailFromAddress from ERDDAP_emailFromAddress
@7yl4r
7yl4r / OC_c7fe_e1ee_913c_dasdds_log.txt
Created October 22, 2022 16:21
root@95c41cfa96c1:/usr/local/tomcat/webapps/erddap/WEB-INF# bash DasDds.sh OC_c7fe_e1ee_913c | tee OC_c7fe_e1ee_913c_dasdds_log.txt
////**** EDStatic Low Level Startup
localTime=2022-10-22T16:18:13+00:00
erddapVersion=2.18
Java 1.8.0_322 (64 bit, Oracle Corporation) on Linux (4.18.0-348.7.1.el8_5.x86_64).
MemoryInUse= 50 MB (highWaterMark= 50 MB) (Xmx ~= 958 MB)
logLevel=info: verbose=true reallyVerbose=false
got bigParentDirectory from ERDDAP_bigParentDirectory
got emailFromAddress from ERDDAP_emailFromAddress
@7yl4r
7yl4r / rebase-merge-walkthrough.md
Created July 20, 2022 20:51

This example demonstrates a rebase and how it differs from a merge. Understanding this is critical for working within most collaborative git workflows.

Example Setup

I have a local repo (named origin) which I have forked from an upstream remote (named upstream):

tylar@laptop:~/pyobis$ git remote -v
origin  git@github.com:7yl4r/pyobis.git (fetch)
origin  git@github.com:7yl4r/pyobis.git (push)
upstream git@github.com:iobis/pyobis.git (fetch)
@7yl4r
7yl4r / implementation-01.py
Created July 20, 2022 19:04
pyOBIS pagination implementations
def search(
scientificname=None,taxonid=None,nodeid=None,datasetid=None,startdate=None,enddate=None,
startdepth=None,enddepth=None,geometry=None,year=None,flags=None,fields=None,size=5000,
offset=0,mof=False,hasextensions=None,**kwargs
):
args = {
'taxonid': taxonid,'obisid': obisid,'datasetid': datasetid,
'scientificname': scientificname,'startdate': startdate,
'enddate': enddate,'startdepth': startdepth,'enddepth': enddepth,
'geometry': geometry,'year': year,'fields': fields,
@7yl4r
7yl4r / notes.md
Created May 12, 2022 19:45

next steps

  1. find funding for 2030 effort
  2. producing products (product = map layers in AWS)

product production details

  1. want to auto-update the layer when data submitted 2. crowd-source submission system goes to AWS then converted to xyz data files in AWS buckets 1. then can use VM in paperspace via parsec 4. not working in ArcGIS bc it is too big - too many polygons (300billion +).
  2. tried ArcOnline & Enterprise also. Enterprise could maybe do it w/ more cores.
@7yl4r
7yl4r / example.html
Created March 2, 2022 19:10
<!doctype html>
<html lang="en-gb" class="no-js">
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1">
<title>|7y|4r|</title>
<meta name="description" content="web portfolio">
<meta name="author" content="7yl4r">
<link rel="stylesheet" href="css/bootstrap.min.css" />
@7yl4r
7yl4r / python-r-tooling-map.md
Last active March 4, 2022 17:47
language package manager configuration file(s) Package index environment manager
R . DESCRIPTION cran packrat
python pip Pipfile, requirements.txt pypi pipenv
python conda environment.yml conda-forge .