Jim Allman jimallman
jimallman
/ chord-seq3-pachelbel.vcv
Created
February 7, 2020 06:40
Test patch (Pachelbel's Canon in D) for VCV Rack and Chord CV
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| { | |
| "version": "1.1.6", | |
| "modules": [ | |
| { | |
| "id": 1, | |
| "plugin": "Core", | |
| "version": "1.1.6", | |
| "model": "AudioInterface", | |
| "params": [], | |
| "leftModuleId": 2, |
jimallman
/ gather-curator-names.py
Created
September 21, 2019 17:35
Gather all unique OpenTree curator names from phylesystem
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| #!/usr/bin/env python3 | |
| # Scan all nearby studies for unique '^ot:curatorName' values | |
| import os | |
| import json | |
| studies_found = 0 | |
| unique_names = [ ] | |
| try: | |
| # look for "bundles" of studies with IDs ending in (e.g.) "99" | |
| for bundle_dirname in os.listdir('study'): |
jimallman
/ local-devtree-proxy.pac
Last active
May 30, 2017 00:00
Test of Proxy Auto-Configuration (PAC) file as a replacement for messing with /etc/hosts
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| function FindProxyForURL( url, host ) { | |
| var debugging = false; | |
| var debugPAC; | |
| if (debugging) { | |
| debugPAC = "host: "+ host +"\n"; | |
| debugPAC += "url: "+ url +"\n"; | |
| debugPAC += "dnsDomainIs(host, 'devtree.opentreeoflife.org'): "+ dnsDomainIs(host, "devtree.opentreeoflife.org") +"\n"; | |
| debugPAC += "dnsDomainIs( host, '.devtree.opentreeoflife.org' ): "+ dnsDomainIs( host, '.devtree.opentreeoflife.org' ) +"\n"; | |
| debugPAC += "shExpMatch(host, 'devtree.opentreeoflife.org'): "+ shExpMatch(host, "devtree.opentreeoflife.org") +"\n"; | |
| } |
jimallman
/ config-test.py
Created
July 16, 2015 15:35
Quick test of local config file (for web-app configuration, etc)
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| # A quick validator for web-app config files | |
| import os | |
| from ConfigParser import SafeConfigParser | |
| conf = SafeConfigParser({}) | |
| if not os.path.isfile("./config"): | |
| print("Expecting a file 'config' in the current directory") | |
| exit() | |
| conf.read("./config") | |
| try: |
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| curl 'http://api.opentreeoflife.org/treemachine/v1/getDraftTreeMRCAForNodes' -H 'Origin: http://tree.opentreeoflife.org' -H 'Accept-Encoding: gzip,deflate,sdch' -H 'Accept-Language: en-US,en;q=0.8' -H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/35.0.1916.153 Safari/537.36' -H 'Content-Type: application/json; charset=UTF-8' -H 'Accept: application/json, text/javascript, */*; q=0.01' -H 'Referer: http://tree.opentreeoflife.org/curator/study/edit/pg_420/?tab=trees&tree=tree522' -H 'Connection: keep-alive' --data-binary '{"ottIds":[1085741,613883,463177,568571,28336,515158,370815,507121,699624,952596,901831,531218,73933,390841,44860,1041027,799167,683046,463185,872124,44875,622872,29742,682886,1020126,989086,276608,512910,332937,619340,438662,786441,438656,1015202,966327,549518,989084,284297,483804,244695,989088,483803,484896,815707,291638,733986,467838,991312,1097399,834690,412128,989089,1065611,897862,1039512,261312,178684,1065605,98071,427905,119211 |
jimallman
/ Quick check of final .jar
Created
April 17, 2014 01:37
Output from pushing taxomachine (after pushing waaay back to old version)
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| $ ls -alF /home/opentree/repo/taxomachine/target/taxomachine-0.0.1-SNAPSHOT.jar | |
| -rw-r--r-- 1 opentree opentree 162163 Apr 17 01:35 /home/opentree/repo/taxomachine/target/taxomachine-0.0.1-SNAPSHOT.jar | |
| $ ls -alF /home/opentree/.m2/repository/org/opentree/taxomachine/0.0.1-SNAPSHOT/taxomachine-0.0.1-SNAPSHOT.jar | |
| -rw-r--r-- 1 opentree opentree 162163 Apr 17 01:35 /home/opentree/.m2/repository/org/opentree/taxomachine/0.0.1-SNAPSHOT/taxomachine-0.0.1-SNAPSHOT.jar |
jimallman
/ gist:10946897
Created
April 17, 2014 01:27
Output from push (taxomachine, after forcing to previous version)
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| WARNING: Missing GitHub client ID! Curation UI will be disabled. | |
| WARNING: Missing GitHub client ID! Tree-view feedback will be disabled. | |
| host=ec2-54-203-194-13.us-west-2.compute.amazonaws.com, admin=admin, pem=/Users/jima/.ssh/opentree/opentree.pem, controller=jima, command=taxomachine | |
| Syncing | |
| JAVA_HOME is /usr/lib/jvm/java-7-openjdk-amd64 | |
| Using branch master of repo jade | |
| Already up-to-date. | |
| Repository jade is unchanged since last time | |
| Using branch master of repo ot-base | |
| Already up-to-date. |
jimallman
/ gist:10946715
Created
April 17, 2014 01:22
Output from push to ot9 (taxomachine only, up to date)
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| WARNING: Missing GitHub client ID! Curation UI will be disabled. | |
| WARNING: Missing GitHub client ID! Tree-view feedback will be disabled. | |
| host=ec2-54-203-194-13.us-west-2.compute.amazonaws.com, admin=admin, pem=/Users/jima/.ssh/opentree/opentree.pem, controller=jima, command=taxomachine | |
| Syncing | |
| JAVA_HOME is /usr/lib/jvm/java-7-openjdk-amd64 | |
| Using branch master of repo jade | |
| Your branch is behind 'origin/master' by 2 commits, and can be fast-forwarded. | |
| Updating 601fb15..1c55c91 | |
| Fast-forward | |
| CONTRIBUTORS | 23 ++ |
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| ~/repo/phylesystem_test$ git status | |
| # On branch jimallman_study_10 | |
| # Changes to be committed: | |
| # | |
| # modified: study/9/9.json | |
| # | |
| # Unmerged paths: | |
| # (use "git add/rm <file>..." as appropriate to mark resolution) | |
| # | |
| # both modified: study/10/10.json |
jimallman
/ d3.phylogram.js
Created
November 27, 2013 01:00
— forked from kueda/d3.phylogram.js
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| /* | |
| d3.phylogram.js | |
| Wrapper around a d3-based phylogram (tree where branch lengths are scaled) | |
| Also includes a radial dendrogram visualization (branch lengths not scaled) | |
| along with some helper methods for building angled-branch trees. | |
| d3.phylogram.build(selector, nodes, options) | |
| Creates a phylogram. | |
| Arguments: | |
| selector: selector of an element that will contain the SVG |
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