Mark Servilla

Updating Zoom no worky

Nowhere on Zoom's company website does it tell you how to reinstall the Desktop Application on a Ubuntu client effectively. When updating to the latest version of Zoom and starting Zoom from the command line the first time, a transient error message appears that says something like "Zoom could not

Load high, who's hitting us?...

Operating a fairly large open environmental data repository seems to be a good target for scrapers. When they hit us, along with Google, our system loads begin to peak above our alarm threshold. When this happens, I am always curious about the source of the scraping, including count statistics to

The hidden newline

In many applications within our data repository, strings are converted to MD5 checksum hash values to preclude dealing with unsavory characters (e.g., non-UTF8, whitespace, etc...). It is not uncommon that these strings must be manually hashed when hunting down errors. For the longest time, I could never figure out

Validating XML with Python's LXML package

The most commonly used Python package IMO for managing (and parsing) XML is lxml (https://lxml.de/), but my experience with it for validating an XML instance document is limited. The basics are as follows (and you mileage may vary): from lxml import etree # XML DOM instance of EML document

Dissecting PASTA Audit event information

The PASTA Audit service collects information about user-related events that occur in PASTA, including data entity downloads. This information is stored in the Audit Manager's event database and is reported back to you through the PASTA Audit service "Get Audit Report [https://pasta.lternet.edu/audit/docs/api#GET%20:

PASTA

Amazon Corretto, the new OpenJDK 8 on the block

The time has finally come to abandon Ubuntu's OpenJDK 8 LTS for a new maintainer - enter Amazon Corretto [https://docs.aws.amazon.com/corretto/index.html], a Technology Compatibility Kit (TCK) drop-in replacement [https://medium.com/@javachampions/java-is-still-free-3-0-0-ocrt-2021-bca75c88d23b] for Ubuntu's version of the LTS Java runtime and development kit

Coding

Using a local XML Catalog file in Oxygen

Much of my day job requires a good technical understanding of XML files, including schema validation. I came across a recent GitHub post that briefly mentioned using the Oxygen XML Catalog file to bind a xsi:schemaLocation namespace declaration to a local schema file. I find the local schema files

Admin

PAN Global Protect VPN client, no thanks!

My institution recently transitioned from Juniper Networks VPN to PAN Global Protect. I do not have a burning opinion in this transition, but I am incredibly disappointed that my institution refuses to support the GP VPN client for Linux. VPN Request Description: Where do I obtain the GlobalProtect VPN client

Admin

"Certbot, help me..."

I love navigating the unknown, and dealing with SSL certificates for me falls into this category. The scenario I will describe involves flipping HTTPS sites from one server (read IP address) to another when unexpected outages requires DNS to stay alive. So when our primary and public facing website went

Life

I like...

"Dead fish are the only ones that go with the flow"

Python

All inclusive with importlib.resources

An issue I had to deal with recently was how to access a package resource (e.g., a JSON file) when you never know exactly where that named resource will wind up on the local file system, especially when installing into a virtual environment from a package index like PyPI.

Python

Python packaging for idiots (me)

I have now reached the need to package a Python package and publish it through PyPI for the world (albeit a very small world) to have unfettered access to it. The package is called "Metapype", and its purpose is to simplify generating and managing scientific metadata. This post, however, is

Python

Some quick Python 3 Unicode tips

Here are some quick tips for working wtih Python 3 unicode characters. Lets work with the the small delta Unicode character:  "δ". 1. Show the UTF-8 encoding: In []: "δ".encode("utf-8") Out[]: b'\xce\xb4' 2. Show the Unicode escape sequence (or code point value): In []: "δ".encode("unicode_escape"

Admin

Some Linux CLI tools for CSV table analysis

OK, so here is my task. I must verify that a set of files on portable disk drive (about 20,000 files) match a list of files (and their respective MD5 checksum values) found in an accompanying manifest document (CSV format). I could (and have) write a simple Python module

Admin

Non UTF-8 characters getting you down?

Need to identify non UTF-8 characters in a text file? Here's a fast and handy method using grep that highlights non UTF-8 characters with the "�" glyph: grep -axvn '.*' data.csv 491:2012-08-23 18:10:00,"Lovers_Leap","KD",28,1,3,3,2,3,1,NA,"very stagnant

PASTA

A few thoughts on PASTA+ and Tomcat8

The PASTA+ project uses Tomcat8 as it primary servlet container and interface for interactions with its REST-based API. Here are some thoughts on how tomcat8 is deployed and being used. 1. The default Tomcat8 does not include the manager application One way of examining memory usage by tomcat8 is to

PASTA

Tracking the elusive PASTA+ process tree

PASTA+ is a Java-based project (primarily servlets) that functions as a metadata-driven data repository. In short, metadata that is written in the Ecological Metadata Language (EML) standard is uploaded and parsed by PASTA+, which then initiates processes to download and evaluate individual data files before finally registering and archiving the

Python

A Conda workflow that, well, just works

Our project has been developing Python applications for almost 5 years now, including DevOp-based tools, full-stack websites, a bit of data science, and a bunch of one-off, use-once, toss away applications. Now overlay these Python applications on top of development and deployment systems running Windows 10, Mac OS X, and

Admin

A short guide to deleting a Solr document

After performing a major systems migration of our production environment to new hardware, we needed to perform a series of regression and integration tests to ensure all services, including Solr, were up-to-snuff. This included indexing a test document into Solr, which needed to be removed post-testing. Doing so can be

Admin

A few UFW tidbits

Here are some of the common UFW rule management commands that I seem to always forget... 1. View rules in numbered format: sudo ufw status numbered 2. Add an allow rule with comment: sudo ufw allow from to any port <#> comment "Comment goes here" 3. Add an deny rule

Coding

After thoughts of a recent Data Carpentry workshop...

I recently team instructed a Data Carpentry workshop with an awesome group of students. Interestingly, there were three students using laptops with Ubuntu Linux (or derivative) installed, which is both a first and just plain amazing! Unfortunately, there were issues with the SQLite Browser and either the R-base installation or

Life

Rostra Cruise Control on a 2007 Tacoma with a Manual Transmission - #@!!#!$

I've had my 2007 4x4 Toyota Tacoma now for about 8 years and lived without cruise control since then. It's about as basic a truck that you can own - manual transmission, manual windows, single-cab, but it did come with A/C (a must here in New Mexico). I've taken

Life

A Walk

https://photos.app.goo.gl/T7c9eUXwA1JP3Cav8Like You Like you I love love, life, the sweet smell of things, the sky-blue landscape of January days. And my blood boils up and I laugh through eyes that have known the buds of tears. I believe the world is beautiful and that poetry,

Google

Google Home Max growing pains

I've been in search of a decent wireless speaker system for both music and video (via my JVC not so smart TV). This quest has basically left me with two choices: the Sonos Play 5 or the Google Home Max [https://store.google.com/product/google_home_max?gclid=CjwKCAiA3OzvBRBXEiwALNKDP3G4LgxyB4s_

Google

Direct download links from Google Drive

Sometimes, you need to host or stage a file on Google Drive and make that file acessible to a non-human (um, another computer). Unfortunately, the “shareable” link that you can generate from the Google Drive interface requires a human to navigate via a web-browser to the Google Drive interface, and