Apologies if this is a straightforward question, I couldn't find anything in the docs.
currently my workflow looks something like this. I'm taking a number of input files created as part of this workflow, and summarizing them.
Is there a way to avoid this manual regex step to parse the wildcards in the filenames?
I thought about an "expand" of cross_ids and config["chromosomes"], but unsure to guarantee conistent order.
rule report:
output:
table="output/mendel_errors.txt"
input:
files=expand("output/{chrom}/{cross}.in", chrom=config["chromosomes"], cross=cross_ids)
params:
req="h_vmem=4G",
run:
df = pd.DataFrame(index=range(len(input.files), columns=["stat", "chrom", "cross"])
for i, fn in enumerate(input.files):
# open fn / make calculations etc // stat =
# manual regex of filename to get chrom cross // chrom, cross =
df.loc[i] = stat, chrom, choss
This seems a bit awkward when this information must be in the environment somewhere.
(via Johannes Köster on the google group)
To answer your question:
Expand uses functools.product from the standard library. Hence, you could write
from functools import product
product(config["chromosomes"], cross_ids)
Related
I have a problem with terraform configuration which I really don't know how to resolve. I have written module for policy assigments, module as parameters taking object with 5 attributes. The question is if it is possible to split into folder structure tfvars file. I mean eg.
I have main folder subscriptions -> folder_subscription_name -> some number of files tfvars with configuration for each of the policy assigment
Example of each of the file
testmap = {
var1 = "test1"
var2 = "test2"
var3 = "test3"
var4 = "test4"
var5 = "test5"
}
In the module I would like to iterate over all of the maps combine into list of maps. Is it good approach? How to achive that or maybe I should use something other to do it like terragrunt ?
Please give me some tips what is the best way to achive that, basically the goal is that I don't want to have one insanely big tvars file with list of 100 maps but splitted into 100 configuration file for each of the assignment.
Based on the comment on the original question:
The question is preety simple how to keep input variables for each of
resource in seperate file instead of keeping all of them in one very
big file
I would say you aim at having different .tfvars files. For example, you could have a dev.tfvars and a prod.tfvars file.
To plan your deployment, you can pass those file with:
terraform plan --var-file=dev.tfvars -out planoutput
To apply those changes
terraform apply planoutput
I am trying to use SpaCy for entity context recognition in the world of ontologies. I'm a novice at using SpaCy and just playing around for starters.
I am using the ENVO Ontology as my 'patterns' list for creating a dictionary for entity recognition. In simple terms the data is an ID (CURIE) and the name of the entity it corresponds to along with its category.
Screenshot of my sample data:
The following is the workflow of my initial code:
Creating patterns and terms
# Set terms and patterns
terms = {}
patterns = []
for curie, name, category in envoTerms.to_records(index=False):
if name is not None:
terms[name.lower()] = {'id': curie, 'category': category}
patterns.append(nlp(name))
Setup a custom pipeline
#Language.component('envo_extractor')
def envo_extractor(doc):
matches = matcher(doc)
spans = [Span(doc, start, end, label = 'ENVO') for matchId, start, end in matches]
doc.ents = spans
for i, span in enumerate(spans):
span._.set("has_envo_ids", True)
for token in span:
token._.set("is_envo_term", True)
token._.set("envo_id", terms[span.text.lower()]["id"])
token._.set("category", terms[span.text.lower()]["category"])
return doc
# Setter function for doc level
def has_envo_ids(self, tokens):
return any([t._.get("is_envo_term") for t in tokens])
##EDIT: #################################################################
def resolve_substrings(matcher, doc, i, matches):
# Get the current match and create tuple of entity label, start and end.
# Append entity to the doc's entity. (Don't overwrite doc.ents!)
match_id, start, end = matches[i]
entity = Span(doc, start, end, label="ENVO")
doc.ents += (entity,)
print(entity.text)
#########################################################################
Implement the custom pipeline
nlp = spacy.load("en_core_web_sm")
matcher = PhraseMatcher(nlp.vocab)
#### EDIT: Added 'on_match' rule ################################
matcher.add("ENVO", None, *patterns, on_match=resolve_substrings)
nlp.add_pipe('envo_extractor', after='ner')
and the pipeline looks like this
[('tok2vec', <spacy.pipeline.tok2vec.Tok2Vec at 0x7fac00c03bd0>),
('tagger', <spacy.pipeline.tagger.Tagger at 0x7fac0303fcc0>),
('parser', <spacy.pipeline.dep_parser.DependencyParser at 0x7fac02fe7460>),
('ner', <spacy.pipeline.ner.EntityRecognizer at 0x7fac02f234c0>),
('envo_extractor', <function __main__.envo_extractor(doc)>),
('attribute_ruler',
<spacy.pipeline.attributeruler.AttributeRuler at 0x7fac0304a940>),
('lemmatizer',
<spacy.lang.en.lemmatizer.EnglishLemmatizer at 0x7fac03068c40>)]
Set extensions
# Set extensions to tokens, spans and docs
Token.set_extension('is_envo_term', default=False, force=True)
Token.set_extension("envo_id", default=False, force=True)
Token.set_extension("category", default=False, force=True)
Doc.set_extension("has_envo_ids", getter=has_envo_ids, force=True)
Doc.set_extension("envo_ids", default=[], force=True)
Span.set_extension("has_envo_ids", getter=has_envo_ids, force=True)
Now when I run the text 'tissue culture', it throws me an error:
nlp('tissue culture')
ValueError: [E1010] Unable to set entity information for token 0 which is included in more than one span in entities, blocked, missing or outside.
I know why the error occurred. It is because there are 2 entries for the 'tissue culture' phrase in the ENVO database as shown below:
Ideally I'd expect the appropriate CURIE to be tagged depending on the phrase that was present in the text. How do I address this error?
My SpaCy Info:
============================== Info about spaCy ==============================
spaCy version 3.0.5
Location *irrelevant*
Platform macOS-10.15.7-x86_64-i386-64bit
Python version 3.9.2
Pipelines en_core_web_sm (3.0.0)
It might be a little late nowadays but, complementing Sofie VL's answer a little bit, and to anyone who might be still interested in it, what I (another spaCy newbie, lol) have done to get rid of overlapping spans, goes as follows:
import spacy
from spacy.util import filter_spans
# [Code to obtain 'entity']...
# 'entity' should be a list, i.e.:
# entity = ["Carolina", "North Carolina"]
pat_orig = len(entity)
filtered = filter_spans(ents) # THIS DOES THE TRICK
pat_filt =len(filtered)
doc.ents = filtered
print("\nCONVERSION REPORT:")
print("Original number of patterns:", pat_orig)
print("Number of patterns after overlapping removal:", pat_filt)
Important to mention that I am using the most recent version of spaCy at this date, v3.1.1. Additionally, it will work only if you actually do not mind about overlapping spans being removed, but if you do, then you might want to give this thread a look. More info regarding 'filter_spans' here.
Best regards.
Since spacy v3, you can use doc.spans to store entities that may be overlapping. This functionality is not supported by doc.ents.
So you have two options:
Implement an on_match callback that will filter out the results of the matcher before you use the result to set doc.ents. From a quick glance at your code (and the later edits), I don't think resolve_substrings is actually resolving conflicts? Ideally, the on_match function should check whether there are conflicts with existing ents, and decide which of them to keep.
Use doc.spans instead of doc.ents if that works for your use-case.
I am new to Flink and have gone through site(s)/examples/blogs to get started. I am struggling with the correct use of operators. Basically I have 2 questions
Question 1: Does Flink support declarative exception handling, I need to handle parse/validate/... errors?
Can I use org.apache.flink.runtime.operators.sort.ExceptionHandler or similar
to handle errors?
or Rich/FlatMap function my best option?
If Rich/FlatMap the only option then is there a way to get handle to Stream inside Rich/FlatMap function so Sink(s) could be attached for error processing?
Question 2: Can I conditionally attach different Sink(s)?
Based on certain field(s) in keyed split streams I need to select different sink(s), do I split the stream again or use a Rich/FlatMap to handle that?
I am using Flink 1.3.2. Here is the relevant portion of my job
.....
.....
DataStream<String> eventTextStream = env.addSource(messageSource)
KeyedStream<EventPojo, Tuple> eventPojoStream = eventTextStream
// parse, transform or enrich
.flatMap(new MyParseTransformEnrichFunction())
.assignTimestampsAndWatermarks(new EventAscendingTimestampExtractor())
.keyBy("eventId");
// split stream based on eventType as different reduce and windowing functions need to be applied
SplitStream<EventPojo> splitStream = eventPojoStream
.split(new EventStreamSplitFunction());
// need to apply reduce function
DataStream<EventPojo> event1TypeStream = splitStream.select("event1Type");
// need to apply reduce function
DataStream<EventPojo> event2TypeStream = splitStream.select("event2Type");
// need to apply time based windowing function
DataStream<EventPojo> event3TypeStream = splitStream.select("event3Type");
....
....
env.execute("Event Processing");
Am I using the correct operators here?
Update 1:
Tried using the ProcessFunction as suggested by #alpinegizmo but that didn't work as it depends upon a keyed stream which I don't have until I parse/validate input. I get "InvalidProgramException: Field expression must be equal to '*' or '_' for non-composite types. ".
It's such a common use case where your first parse/validate input and won't have keyed stream yet, so how do you solve it?
Thanks for your patience and help.
There's one key building block that you've overlooked. Take a look at side outputs.
This mechanism provides a typesafe way to produce any number of additional output streams. This can be a clean way to report errors, among other uses. In Flink 1.3 side outputs can only be used with ProcessFunction, but 1.4 will add side outputs to ProcessWindowFunction.
I’m pretty new to python (using python 3) and spacy (and programming too). Please bear with me.
I have three questions where two are more or less the same I just can’t get it to work.
I took the “syntax specific search with spacy” (example) and tried to make different things work.
My program currently reads txt and the normal extraction
if w.lower_ != 'music':
return False
works.
My first question is: How can I get spacy to extract two words?
For example: “classical music”
With the previous mentioned snippet I can make it extract either classical or music. But if I only search for one of the words I also get results I don’t want like.
Classical – period / era
Or when I look for only music
Music – baroque, modern
The second question is: How can I get the dependencies to work?
The example dependency with:
elif w.dep_ != 'nsubj': # Is it the subject of a verb?
return False
works fine. But everything else I tried does not really work.
For example, I want to extract sentences with the word “birthday” and the dependency ‘DATE’. (so the dependency is an entity)
I got
if d.ent_type_ != ‘DATE’:
return False
To work.
So now it would look like:
def extract_information(w,d):
if w.lower_ != ‘birthday’:
return False
elif d.ent_type_ != ‘DATE’:
return False
else:
return True
Does something like this even work?
If it works the third question would be how I can filter sentences for example with a DATE. So If the sentence contains a certain word and a DATE exclude it.
Last thing maybe, I read somewhere that the dependencies are based on the “Stanford typed dependencies manual”. Is there a list which of those dependencies work with spacy?
Thank you for your patience and help :)
Before I get into offering some simple suggestions to your questions, have you tried using displaCy's visualiser on some of your sentences?
Using an example sentence 'John's birthday was yesterday', you'll find that within the parsed sentence, birthday and yesterday are not necessarily direct dependencies of one another. So searching based on the birthday word having a dependency of a DATE type entity, might not be yield the best of results.
Onto the first question:
A brute force method would be to look for matching subsequent words after you have parsed the sentence.
doc = nlp(u'Mary enjoys classical music.')
for (i,token) in enumerate(doc):
if (token.lower_ == 'classical') and (i != len(doc)-1):
if doc[i+1].lower_ == 'music':
print 'Target Acquired!'
If you're unsure of what enumerate does, look it up. It's the pythonic way of using python.
To questions 2 and 3, one simple (but not elegant) way of solving this is to just identify in a parsed sentence if the word 'birthday' exists and if it contains an entity of type 'DATE'.
doc = nlp(u'John\'s birthday was yesterday.')
for token in doc:
if token.lower_ == 'birthday':
for entities in doc.ents:
if entities.label_ == 'DATE':
print 'Found ya!'
As for the list of dependencies, I presume you're referring to the Part-Of-Speech tags. Check out the documentation on this page.
Good luck! Hope that helped.
I know other people have asked similar questions in past but I am still stuck on how to solve the problem and was hoping someone could offer some help. Using PsychoPy, I would like to present different images, specifically 16 emotional trials, 16 neutral trials and 16 face trials. I would like to pseudo randomize the loop such that there would not be more than 2 consecutive emotional trials. I created the experiment in Builder but compiled a script after reading through previous posts on pseudo randomization.
I have read the previous posts that suggest creating randomized excel files and using those, but considering how many trials I have, I think that would be too many and was hoping for some help with coding. I have tried to implement and tweak some of the code that has been posted for my experiment, but to no avail.
Does anyone have any advice for my situation?
Thank you,
Rae
Here's an approach that will always converge very quickly, given that you have 16 of each type and only reject runs of more than two emotion trials. #brittUWaterloo's suggestion to generate trials offline is very good--this what I do myself typically. (I like to have a small number of random orders, do them forward for some subjects and backwards for others, and prescreen them to make sure there are no weird or unintended juxtapositions.) But the algorithm below is certainly safe enough to do within an experiment if you prefer.
This first example assumes that you can represent a given trial using a string, such as 'e' for an emotion trial, 'n' neutral, 'f' face. This would work with 'emo', 'neut', 'face' as well, not just single letters, just change eee to emoemoemo in the code:
import random
trials = ['e'] * 16 + ['n'] * 16 + ['f'] * 16
while 'eee' in ''.join(trials):
random.shuffle(trials)
print trials
Here's a more general way of doing it, where the trial codes are not restricted to be strings (although they are strings here for illustration):
import random
def run_of_3(trials, obj):
# detect if there's a run of at least 3 objects 'obj'
for i in range(2, len(trials)):
if trials[i-2: i+1] == [obj] * 3:
return True
return False
tr = ['e'] * 16 + ['n'] * 16 + ['f'] * 16
while run_of_3(tr, 'e'):
random.shuffle(tr)
print tr
Edit: To create a PsychoPy-style conditions file from the trial list, just write the values into a file like this:
with open('emo_neu_face.csv', 'wb') as f:
f.write('stim\n') # this is a 'header' row
f.write('\n'.join(tr)) # these are the values
Then you can use that as a conditions file in a Builder loop in the regular way. You could also open this in Excel, and so on.
This is not quite right, but hopefully will give you some ideas. I think you could occassionally get caught in an infinite cycle in the elif statement if the last three items ended up the same, but you could add some sort of a counter there. In any case this shows a strategy you could adapt. Rather than put this in the experimental code, I would generate the trial sequence separately at the command line, and then save a successful output as a list in the experimental code to show to all participants, and know things wouldn't crash during an actual run.
import random as r
#making some dummy data
abc = ['f']*10 + ['e']*10 + ['d']*10
def f (l1,l2):
#just looking at the output to see how it works; can delete
print "l1 = " + str(l1)
print l2
if not l2:
#checks if second list is empty, if so, we are done
out = list(l1)
elif (l1[-1] == l1[-2] and l1[-1] == l2[0]):
#shuffling changes list in place, have to copy it to use it
r.shuffle(l2)
t = list(l2)
f (l1,t)
else:
print "i am here"
l1.append(l2.pop(0))
f(l1,l2)
return l1
You would then run it with something like newlist = f(abc[0:2],abc[2:-1])