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I think this is a simple task, but I'm a biologist who only knows a teeny bit of code and after several days of trying to figure this out, I'm out of ideas.
Using terminal on a Mac. I have a CSV file that I want to split into separate files by row (162 rows) and I want to name the file by the content of the first and second column (genus_species). Then I need all 162 genus_species to be saved as HTML files.
I have only attempted the "splitting" part with Ruby (recommendation from StackExchange/overflow). Below are some of my attempts. They are frankensteins of helpful-ish forums, and after each I made a little comment on why it did not work.
Example HTML
<!DOCTYPE html>
<html><head>
<meta charset="UTF-8">
<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script></head>
<body>
<h1><em><!-- Species name --></em> - <!-- Common name --></h1>
<h2>Status</h2>
<p></p>
<h2>Info</h2>
<p></p>
<h2>Time of year this bee is seen</h2>
<p></p>
<h2>Identification</h2>
<p></p>
<h3>Similar Species</h3>
<p></p>
<h2>Flowers</h2>
<p></p>
<h2>Sociality</h2>
<p></p>
<h2>Nest</h2>
<p></p>
<div id="refs" class="references">
--<br>More information:<br> <!-- Bug Guide --></div>
</body></html>
More Info Based on Comments
Here are some lines copied from the text file:
Genus,species,Common name,Status,Info,Time of year this bee is seen,Identification,Similar Species,Flowers,Sociality,Nest,Bug Guide,Discover Life,Other,
Agapostemon,melliventris,Honey-tailed Striped-Sweat bee,Secure G5,Excavates into deep burrows in ground nests,March-December,Agapostemon males have black and yellow stripes on the abdomen. Females have a yellow band on the lower margin of the clypeus.,All other Agapostemon species,Wide variety of plants,Solitary,"Deep, underground excavation",https://bugguide.net/node/view/70932,https://www.discoverlife.org/20/q?search=Agapostemon+melliventris,https://explorer.natureserve.org/Taxon/ELEMENT_GLOBAL.2.928401/Agapostemon_melliventris,
Agapostemon,sericeus,Silky Striped Sweat Bee,Secure G5,"Not choosy about lawn, as long as flowers are present",April-October,Agapostemon males have black and yellow stripes on the abdomen. A. sericeus males have a tooth on its hind femur. Female has metallic green abdomen.,All other Agapostemon species,Wide variety of plants,Solitary,Ground-nester in loamy soils,https://bugguide.net/node/view/83023,https://www.discoverlife.org/mp/20q?search=Agapostemon+sericeus,https://www.sharpeatmanguides.com/sweat-bees,
Agapostemon,splendens,Brown-winged Striped-Sweat Bee,Secure G5,This is the most common Agapostemon found in the southeast region,April-October,Agapostemon males have black and yellow stripes on the abdomen. A. splendens have brown wings. The female abdomen is often somewhat bluish.,All other Agapostemon species,"Jacquemontia reclinata, wide variety of plants",Solitary,Ground-nester in sandy soils,https://bugguide.net/node/view/74478,https://www.discoverlife.org/mp/20q?search=Agapostemon+splendens,,
Updated code I've tried based on comments.
This worked and I think it's heading in the direction I want, but it's hard to tell in the terminal window:
f = File.new("bee_key_fact_sheet .csv")
f.each_line { |line| puts line }
Currently playing with some kind of File.write line to add here and then close?
Attempt #1
file = File.open("bee_key_fact_sheet.csv")
awk
'(NR==1){header=$0;next}
(NR%l==2) {
close(file);
file=sprintf("%s.%0.5d.csv",FILENAME,++c)
sub(/csv[.]/,"",file)
print header > file
}
{f.write}'
File.close
#AWK not recognized, asks to "display all possibilities (y/n)" I tried returning "y" and "yes" and both times it says my answer is not recognized
Attempt #2
file_data = File.read("bee_key_fact_sheet.csv").split
#This works but splits by each comma
Attempt #3
file_data = File.foreach("bee_key_fact_sheet.csv") { |line| puts line}.split
#This returned something slightly less messy than splitting by each comma but got this error message "undefined method `split' for nil:NilClass"
Attempt #4
bee_key_fact_sheet.csv.foreach('so1.csv', :headers => true, :col_sep => ",", :skip_blanks => true) do |row|
id, name = row[0], row[1]
unless (id =~ /#/)
names = name.split
end
#This returned nothing
Your example of CSV input (bee_key_fact_sheet.csv):
Genus,species,Common name,Status,Info,Time of year this bee is seen,Identification,Similar Species,Flowers,Sociality,Nest,Bug Guide,Discover Life,Other,
Agapostemon,melliventris,Honey-tailed Striped-Sweat bee,Secure G5,Excavates into deep burrows in ground nests,March-December,Agapostemon males have black and yellow stripes on the abdomen. Females have a yellow band on the lower margin of the clypeus.,All other Agapostemon species,Wide variety of plants,Solitary,"Deep, underground excavation",https://bugguide.net/node/view/70932,https://www.discoverlife.org/20/q?search=Agapostemon+melliventris,https://explorer.natureserve.org/Taxon/ELEMENT_GLOBAL.2.928401/Agapostemon_melliventris,
Agapostemon,sericeus,Silky Striped Sweat Bee,Secure G5,"Not choosy about lawn, as long as flowers are present",April-October,Agapostemon males have black and yellow stripes on the abdomen. A. sericeus males have a tooth on its hind femur. Female has metallic green abdomen.,All other Agapostemon species,Wide variety of plants,Solitary,Ground-nester in loamy soils,https://bugguide.net/node/view/83023,https://www.discoverlife.org/mp/20q?search=Agapostemon+sericeus,https://www.sharpeatmanguides.com/sweat-bees,
Agapostemon,splendens,Brown-winged Striped-Sweat Bee,Secure G5,This is the most common Agapostemon found in the southeast region,April-October,Agapostemon males have black and yellow stripes on the abdomen. A. splendens have brown wings. The female abdomen is often somewhat bluish.,All other Agapostemon species,"Jacquemontia reclinata, wide variety of plants",Solitary,Ground-nester in sandy soils,https://bugguide.net/node/view/74478,https://www.discoverlife.org/mp/20q?search=Agapostemon+splendens,,
In this CSV, all the lines (including the header) end with a comma, so the last column probably doesn't mean anything and is to be discarded.
Also, you have commas inside the data (fields with double-quotes), so you'll need a real CSV parser to read the content of the file. BTW, you're right in choosing Ruby for this task because it includes a CSV parser in its core library.
Here's one way of reading your CSV (Edit: fixed CSV#Row conversion for older Rubys):
require 'csv'
filepath = 'bee_key_fact_sheet.csv'
CSV.foreach(filepath, headers: true) do |row|
genus, species = row[0], row[1]
#data = row[0...-1] # NOTE: not sure about the Ruby version compatibility
data = row.to_hash.values[0...-1]
filename = "#{genus}_#{species}.txt".tr("\0/",'')
filecontent = " * #{data.join("\n * ")}"
puts "\n#{filename}:\n#{filecontent}"
end
About tr("\0/",''): The characters that are allowed in a filename depend on the filesystem. All the filesystems (that I know of) ban at least the NULL-byte and the slash characters, so I strip them (but you may want to strip a few more).
Question: What exactly is the expected HTML output? A table row?
Update: HTML generation
When generating content programmatically, it's fundamental to escape your data for the right format/language/context. In Ruby you can escape HTML with CGI.escapeHTML
Your example of HTML output:
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
</head>
<body>
<h1><em><!-- Species name --></em> - <!-- Common name --></h1>
<h2>Status</h2>
<p></p>
<h2>Info</h2>
<p></p>
<h2>Time of year this bee is seen</h2>
<p></p>
<h2>Identification</h2>
<p></p>
<h3>Similar Species</h3>
<p></p>
<h2>Flowers</h2>
<p></p>
<h2>Sociality</h2>
<p></p>
<h2>Nest</h2>
<p></p>
<div id="refs" class="references">
--
<br>More information:
<br> <!-- Bug Guide -->
</div>
</body>
</html>
I'll make a few changes to the HTML:
Add a title to the page.
Remove MathJax which seams unnecessary.
Convert the <h3> tag to <h2> because you use it only for "Similar Species". Changing it also permits the use of a loop while generating the HTML.
You have 2 links in the CSV that you don't use in the HTML: "Discover Life" and "Other", don't you want to display them ? I added the code for that ;-)
OK, first, you create a function that, given a CSV row, generates the corresponding HTML. Here I use ERB templating but you can do it directly with string literals (Edit: fixed ERB#result arguments for Ruby < 2.4.0):
require 'cgi'
require 'erb'
def renderHTML row
htmlsafe = row.each_with_object({}) { |(k,v),h| h[k] = CGI.escapeHTML v if v }
template = <<-'EOF'
<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title><%= "#{htmlsafe['Genus']} #{htmlsafe['species']}" %></title>
</head>
<body>
<h1><em><%= "#{htmlsafe['Genus']} #{htmlsafe['species']}" %></em> - <%= htmlsafe['Common name'] %></h1>
<% for key in ['Status','Info','Time of year this bee is seen','Identification','Similar Species','Flowers','Sociality','Nest'] %>
<h2><%= key %></h2>
<p><%= htmlsafe[key] %></p>
<% end %>
<div id="refs" class="references">
--
<br>More information:
<% for key in ['Bug Guide', 'Discover Life', 'Other'].select{ |k| htmlsafe[k] } %>
<br><%= key %>
<% end %>
</div>
</body>
</html>
EOF
#ERB.new(template, trim_mode: "<>").result(binding) # NOTE: only for Ruby >= 2.4.0
ERB.new(template, nil, "<>").result(binding)
end
Then you can call the previous function while reading each row of your CSV file:
require 'csv'
filepath = 'bee_key_fact_sheet.csv'
CSV.foreach(filepath, headers: true) do |row|
filename = "#{row['Genus']}_#{row['species']}.html".tr("\0/",'')
html = renderHTML row
puts "\n# #{filename}\n#{html}"
#File.write(filename, html)
end
Note: I commented out the File.write line that will create the HTML files.
Can you try this? It should be reading lines of file
f = File.new("name_of_file")
f.each_line { |line| puts line }
You can later save them as new file, more on that here:
How to create a file in Ruby
how to replace text content of html tag in file and save them to another(some), file ?
Ex. there is a file index.html
<!DOCTYPE html>
<html>
<head>
</head>
<body>
<p itemprop="someprop">SOME BIG TEXT</p>
</body>
</html>
I need to replace the text "SOME BIG TEXT" in the "p" tag to "ANOTHER BIG TEXT"
from bs4 import BeautifulSoup
with open("index.html","r") as file:
fcontent=file.read()
sp=BeautifulSoup(fcontent,'lxml')
t='new_text_for_replacement'
print(sp.replace(sp.find(itemprop="someprop").text,t))
What am I doing wrong ?
Thank you
Use open() on the output file to write to it.
with open('index.html', 'r') as file:
fcontent = file.read()
sp = BeautifulSoup(fcontent, 'html.parser')
t = 'new_text_for_replacement'
# replace the paragraph using `replace_with` method
sp.find(itemprop='someprop').replace_with(t)
# open another file for writing
with open('output.html', 'w') as fp:
# write the current soup content
fp.write(sp.prettify())
If you want to replace just the inner content of the paragraph instead of the paragraph element itself, you can set the .string property.
sp.find(itemprop='someprop').string = t
The problem relies upon on the way you are searching for the criteria try changing the following code:
print(sp.replace(sp.find(itemprop="someprop").text,t))
to this:
print(sp.replace(sp.find({"itemprop":"someprop"}).text,t))
hopefully, this helps
(PS: based of your questionI'm assuming that you only have one thing to replace)