simonthompson99

#-- stacked bar plot of proportions with totals above
# d is listing of single row per participants with eth_cat and quarter columns
# totals is d %>% group_by(quarter) %>% summarise(total = n())
ggplot(d, aes(fill = eth_cat, x = quarter)) +
    geom_bar(position = "fill") +
    scale_fill_brewer(palette = "RdYlBu") +
    labs(title = "Participant ethnicity per quarter of 100,000 Genomes Project",
         x = "Quarter",
         y = "Proportion",
         fill = "Ethnicity",

simonthompson99

1. Stem of the link is the jira instance ticket will be created in i.e. https://jiraservicedesk.extge.co.uk or https://jira.extge.co.uk;
2. Then /secure/CreateIssueDetails!init.jspa? if you want them to add info, or if you just want the ticket created remove !init (will still need them to click on 'Retry Operation'. Can get around this by adding in token (Dimitris from Valiantys to advise on how to get this)
3. Then list of key=value pairs separated by &. Easiest way to get these is by creating a ticket and then looking at what comes back from API (i.e. visit <url stem>/rest/api/2/issue/<issue-key>. Often a bit of trial and error, replace spaces with %20, use ID numbers for things like project (pid) or issuetype.

Examples: https://jiraservicedesk.extge.co.uk/secure/CreateIssueDetails!init.jspa?pid=10102&issuetype=10608&customfield_10799=test&summary=DQ%20Report%20Rule%20Failure%20Override

`https://jira.extge.co.uk/secure/CreateIssueDetails!init.jspa?reporter=sthompson&issuetype=3&assignee=

simonthompson99

/*

Fresh install:
brew install postgresql
brew services start postgresql

simonthompson is the superuser, no password has been created for them.

If wiping:

simonthompson99

# Combine pdfs in afolder into a single file
pdftk *.pdf cat output combined.pdf
# Extract single page r2 (reverse 2) gives penultimate page
pdftk in.pdf cat r2 output penultimatepage.pdf
# Split multipage doc into single pages
pdftk in.pdf burst
# remove first page from multiple pdfs
for file in *.pdf ; do pdftk "$file" cat 1 output "pg-1-${file%.pdf}.pdf" ; done
# get number of pages in pdf
pdftk in.pdf dump_data | grep NumberOfPages

simonthompson99

To format a date into a string - format(<date>, <format_string>)

To read in dates in a format - as.Date(<date_string>, format = <format_string>)

Symbol	Meaning	Example
%d	day as a number (0-31)	Jan-31
%a	abbreviated weekday	Mon
%A	unabbreviated weekday	Monday
%m	month (00-12)	00-12

simonthompson99

def send_slack_msg(m, api_token, channel):
    """
    Send a message to a slack channel, requires a valid API token
    """
    import requests
    data = {
        'token': api_token,
        'channel':channel, 
        'as_user': True,
        'text':m

simonthompson99

import hashlib
def md5(fname):
    """
    returns the md5 for a filepath
    """
    BLOCKSIZE = 65536
    hasher = hashlib.md5()
    with open(fname, 'rb') as afile:
        buf = afile.read(BLOCKSIZE)
        while len(buf) > 0:

simonthompson99

run_query <- function(conn, f) {
    # run the contents of sql file - f- on a given db connection - conn
    require(DBI)
    q <- trimws(readLines(f))
    # remove lines starting with --
    q <- gsub("^--.*$", "", q)
    d <- dbGetQuery(conn, paste(q, collapse = " "))
    cat(paste0(f, ' - ', nrow(d), 'Rx', ncol(d), 'C\n'))
    return(d)
}

simonthompson99

-- update a table using a standard query
with t as (
select <the primary key of the table> as rowid, <value to use to update> as update_value
from <table>
left join ....
where ....
)
update <table to update>
set <field to update> = t.update_value
from t

simonthompson99

def send_file_to_slack(fp, channel, fn = None):
    """
    Send a file to a slack channel
    - fp - path to file
    - channel - channel to send to
    - fn - the filename
    """
    import requests
    import os