| 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 |
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 |
| # 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 |
| /* | |
| Fresh install: | |
| brew install postgresql | |
| brew services start postgresql | |
| simonthompson is the superuser, no password has been created for them. | |
| If wiping: |
https://jiraservicedesk.extge.co.uk or https://jira.extge.co.uk;/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)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
| #-- 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", |
.tar.gz from the package archiveR CMD INSTALL .tar.gz or to get the dependencies installed run install.packages(".tar.gz", repos = NULL, type = "source")
| #-- convert df to tibble | |
| tbl <- tbl_df(df) | |
| #-- aggregate by multiple groups | |
| d <- df %>% filter(<filter_conditional>) %>% | |
| group_by(<grouping_variable1>, ...) %>% | |
| summarise(<out_var> = <out_var_function_call>,...) | |
| #-- get crosstabs table and replace low counts | |
| tab_ldp <- d %>% |
| #-- get latest rds file from filelisting with datestamps | |
| get_latest_rds <- function(d, kw){ | |
| ls <- list.files(d, pattern = "*.rds", full.names = T) | |
| f <- sort(ls[grepl(kw, ls)], decreasing = T)[1] | |
| d <- readRDS(f) | |
| cat(paste("Fetched", f, "--", nrow(d), "rows", ncol(d), "columns\n")) | |
| return(d) | |
| } |
| -- on query | |
| pg_dump -h 10.1.24.39 -p 5433 --schema <schema-name> <db_name> > ~/scratch/<dump_file>.sql | |
| -- local | |
| cd ~/scratch | |
| scp sthompson@10.1.24.38:~/scratch/<dump_file>.sql . | |
| sed -i .bak 's/OWNER TO cdt_user;/OWNER TO simon;/g' <dump_file>.sql | |
| psql -d <target_db> -h localhost -p 5432 -U simon < <dump_file>.sql |