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cfriedline / gist:1ffb358fe3f03a85ef1b
Last active August 29, 2015 14:06
ncbi epost out of order
ids = ["148908191", "297793721", "48525513", "507118461"]
search_results = Entrez.read(Entrez.epost("protein", id=','.join(ids)))
webenv = search_results["WebEnv"]
query_key = search_results["QueryKey"]
print Entrez.read(Entrez.elink(webenv=webenv,
query_key=query_key,
dbfrom="protein",
db="taxonomy"))
print "-------"
@cfriedline
cfriedline / gist:1086653f09110260fa25
Created August 28, 2014 05:17
revbayes compile fail
[ 99%] Building CXX object ui/CMakeFiles/rb-ui.dir/Users/chris/src/revbayes/src/ui/RbClient.cpp.o
In file included from /Users/chris/src/revbayes/src/ui/RbClient.cpp:1:
In file included from /Users/chris/src/revbayes/projects/cmake/../../src/ui/RbClient.h:8:
In file included from /Users/chris/src/revbayes/projects/cmake/../../src/libs/lineedit/EditorMachineObserver.h:11:
In file included from /Users/chris/src/revbayes/projects/cmake/../../src/libs/lineedit/EditorState.h:8:
/Users/chris/src/revbayes/projects/cmake/../../src/libs/lineedit/lineeditUtils.h:35:20: warning: implicit conversion
from 'const size_type' (aka 'const unsigned long') to 'int' changes value from 18446744073709551615 to -1
[-Wconstant-conversion]
int rPos = std::string::npos, _rPos, tmpInt;
~~~~ ^~~~~~~~~~~~~~~~~
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@cfriedline
cfriedline / gist:3b55323a5cc695eadede
Last active August 29, 2015 14:04
Workflow for importing a foreign library to Papers3

#Workflow for importing a foreign library to Papers3

the idea is to write down workflow ideas and their features/flaws using the AppleScript API in papers 3.

##Starting material

  1. exported bib or xml from Sente
  2. a directory of PDFs in the Sente/Contents/Attachments directory
@cfriedline
cfriedline / gist:0b2f5ab92aec3f5bf0dc
Last active August 30, 2020 01:54
WIP: Migrating from Sente 6 to Papers 3 via Endnote XML export

#This is a work in progress: YMMV (I'm working on an AppleScript supplement, so stay tuned...)

Migrating from Sente 6 to Papers3 via Endnote XML export

This process will export all of the references from Sente to an EndNote XML library suitable for import into Papers3. With a little shell magic, it will also set up the PDFs

Export

{
"metadata": {
"name": "",
"signature": "sha256:bc90adee1b70109c60e4cf9accb82fd4c44c3b7d2319687d80501a95605340bb"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"metadata": {
"name": "",
"signature": "sha256:0d945e3af4321846bc634bd26d0b5510f02df4d8b749db49ace3f7b88a913e57"
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [