I'm trying to read or redirect the test console output. I'm doing an AssertAreEqualIgnoringOrder and I need to parse some of the values within the failures. The failures output looks like this:
Expected elements to be equal but possibly in a different order.
Ensure the list of idols matches with the db
Equal Elements : ["98932", "670945", "6747749", "6770804", "7110604", "13280109", "13280121", "13280149", "14448042", "14448336", "15726213", "17009409", "17245584", "93123", "2212314", "10129661", "13280123", "13280125", "13280135", "13280144", "17245263", "18784003", "1112597", "2885514", "8505390", "13279857", "15032800", "17009391", "17009396", "17009398", "17880635", "18340462", "3606775", "13280116", "13280133", "13280137", "14448341", "15050039", "16711731", "17008920", "17009377", "17009381", "17009402", "17245606", "17901335", "865871", "6029748", "17009372", "17009386", "17009406", "17245604", "19113286", "19865372"]
Excess Elements : ["14419207"]
Missing Elements : ["17241620"]
How can I read this directly or redirect it to a file? If I can just parse the output, I can work it afterwards with some RegEx, that will not be a problem.
Another solution would be to parse the Gallio report file, but I'm sure there is a faster way.
Can you help me, please?
Thanks,
Andrei
Related
I'm switching over to using the Auto-IVC component as opposed to the IndepVar component. I'd like to be able to get a list of the promoted output names of the Auto-IVC component, so I can then use them to go and pull the appropriate value out of a configuration file and set the values that way. This will get rid of some boilerplate.
p.model._auto_ivc.list_outputs()
returns an empty list. It seems that p.model__dict__ has this information encoded in it, but I don't know exactly what is going on there so I am wondering if there is an easier way to do it.
To avoid confusion from future readers, I assume you meant that you wanted the promoted input names for the variables connected to the auto_ivc outputs.
We don't have a built-in function to do this, but you could do it with a bit of code like this:
seen = set()
for n in p.model._inputs:
src = p.model.get_source(n)
if src.startswith('_auto_ivc.') and src not in seen:
print(src, p.model._var_allprocs_abs2prom['input'][n])
seen.add(src)
assuming 'p' is the name of your Problem instance.
The code above just prints each auto_ivc output name followed by the promoted input it's connected to.
Here's an example of the output when run on one of our simple test cases:
_auto_ivc.v0 par.x
I'm trying to practice writing workflows in snakemake.
The contents of my Snakefile:
configfile: "config.yaml"
rule get_col:
input:
expand("data/{file}.csv",file=config["datname"])
output:
expand("output/{file}_col{param}.csv",file=config["datname"],param=config["cols"])
params:
col=config["cols"]
script:
"scripts/getCols.R"
The contents of config.yaml:
cols:
[2,4]
datname:
"GSE3790_expression_data"
My R script:
getCols=function(input,output,col) {
dat=read.csv(input)
dat=dat[,col]
write.csv(dat,output,row.names=F)
}
getCols(snakemake#input[[1]],snakemake#output[[1]],snakemake#params[['col']])
It seems like both columns are being called at once. What I'm trying to accomplish is one column being called from the list per output file.
Since the second output never gets a chance to be created (both columns are used to create first output), snakemake throws an error:
Waiting at most 5 seconds for missing files.
MissingOutputException in line 3 of /Users/rebecca/Desktop/snakemake-tutorial/practice/Snakefile:
Job completed successfully, but some output files are missing.
On a slightly unrelated note, I thought I could write the input as:
'"data/{file}.csv"'
But that returns:
WildcardError in line 4 of /Users/rebecca/Desktop/snakemake-tutorial/practice/Snakefile:
Wildcards in input files cannot be determined from output files:
'file'
Any help would be much appreciated!
Looks like you want to run your Rscript twice per file, once for every value of col. In this case, the rule needs to be called twice as well.
The use of expand is also a bit too much here, in my opinion. expand fills your wildcards with all possible values and returns a list of the resulting files. So the output for this rule would be all possible combinations between files and cols, which the simple script can not create in one run.
This is also the reason why file can not be inferred from the output - it gets expanded there.
Instead, try writing your rule easier for just one file and column and expand on the resulting output, in a rule which needs this output as an input. If you generated the final output of your workflow, put it as input in a rule all to tell the workflow what the ultimate goal is.
rule all:
input:
expand("output/{file}_col{param}.csv",
file=config["datname"], param=config["cols"])
rule get_col:
input:
"data/{file}.csv"
output:
"output/{file}_col{param}.csv"
params:
col=lambda wc: wc.param
script:
"scripts/getCols.R"
Snakemake will infer from rule all (or any other rule to further use the output) what needs to be done and will call the rule get_col accordingly.
zsh version 5.2
I'm attempting an array assignment using filename generation like so:
files=(/some/path/*/dir/myfile)
Indeed this is the way the zshoptions manual recommends to achieve what I want.
When no matches exist I want the array to be empty. Instead it's producing
no matches found: /some/path/*/dir/file
and the script terminates.
I've tried setting NULL_GLOB, CSH_NULL_GLOB and ensured NOMATCH is not set.
When matches do exist it works as expected.
Any help is appreciated.
Thank you in advance,
Wayne
Well of course I found the solution after posting my question.
For this to work EXTENDED_GLOB needs to be set as well as NULL_GLOB. Or a glob qualifier can be used so that NULL_GLOB only effects this particular expansion.
This is how to set NULL_GLOB for a single operation:
files=(/some/path/*/dir/myfile(N))
Hope that can help someone else who encounters this.
Wayne
Okay guys, I have, what I'm sure, is an entry-level problem. Still, I cannot explain it. Here's my code and its error:
> sample1 = readHTMLTable(http://www.pro-football-reference.com/boxscores/201609150buf.htm, which = 16)
Error: unexpected '/' in "sample1 = readHTMLTable(http:/"
It's having a problem with the second front-slash? Not only does every URL have two front-slashes, but I've poured through countless examples of this function, both on this site and others, and they've all formatted this code in this way. So, what am I doing wrong?
Additionally, I've tried it without the back-slashes:
> sample1 = readHTMLTable(www.pro-football-reference.com/boxscores/201609150buf.htm, which = 16)
Error: unexpected symbol in "sample1 = readHTMLTable(www.pro-football-reference.com/boxscores/201609150buf.htm"
Here, I'm not even sure which symbol it's talking about.
Please explain.
The issue is that you need to place your url in quotes (""). The following does return the table from your specified url:
sample1 = readHTMLTable("www.pro-football-reference.com/boxscores/201609150buf.htm")
As you probably know, the "which=" parameter is used to select which of the tables in that page you would like to retrieve. However my own attempts show that only 1 and 2 work. Could you tell me which table you are attempted to read into R? If this method doesn't end up working you can also attempt to read in the entirety of the webpage and parse out the table in question.
Hope this helps get things started!
So this is my .pro file content (AMZI PROLOG) :
room(kitchen).
room(office).
room(hall).
room('dining room').
room(cellar).
door(office, hall).
door(kitchen, office).
door(hall, 'dining room').
door(kitchen, cellar).
door('dining room', kitchen).
location(desk,office).
location(apple,kitchen).
location(flashlight,desk).
location('washing machine',cellar).
location(nani,'washing machine').
location(broccoli,kitchen).
location(crackers,kitchen).
location(computer,office).
location(envelope,desk).
location(stamp,envelope).
location(key,envelope).
edible(apple).
edible(crackers).
tastes_yucky(broccoli).
here(kitchen).
is_located_in(T1,T2):-location(X,T2),is_located_in(T1,X).
What I want to achieve is that if I use, for example, is_located_in(X,office), then the result will be :
X=desk,
X=flashlight,
X=computer,
X=envelope,
X=stamp,
X=key,
no
(in no particular order).
That way, the result will include things that basically located in / on the object in the office, instead of things that located directly in the office.
This is the source : http://www.amzi.com/AdventureInProlog/a8recurs.php
There is stated that the code are fine, but when I test it, it just returned :
no
Please help. Thanks.
Try this (in this order):
is_located_in(T1,T2):-location(T1,T2).
is_located_in(T1,T2):-location(X,T2),is_located_in(T1,X).