Complete newbie, I know you probably can't use the variables like that in there but I have 20 minutes to deliver this so HELP
read -r -p "Month?: " month
read -r -p "Year?: " year
URL= "https://gz.blockchair.com/ethereum/blocks/"
wget -w 2 --limit-rate=20k "${URL}blockchair_ethereum_blocks_$year$month*.tsv.gz"
exit
There are two issues with your code.
First, you should remove the whitespace that follows the equal symbol when you declare your URL variable. So the line becomes
URL="https://gz.blockchair.com/ethereum/blocks/"
Then, you are building your URL using a wildcard, which is not allowed in this case. So you cannot do something like month*.tsv.gz as you are doing right know. If you need to perform requests to several URLs, you need to run wget for each one of them.
It's possible to do what you're trying to do with wget, however, this particular site's robots.txt has a rule to disallow crawling of all files (https://gz.blockchair.com/robots.txt):
User-agent: *
Disallow: /
That means the site's admins don't want you to do this. wget respects robots.txt by default, but it's possible to turn that off with -e robots=off.
For this reason, I won't post a specific, copy/pasteable solution.
Here is a generic example for selecting (and downloading) files using a glob pattern, from a typical html index page:
url=https://www.example.com/path/to/index
wget \
--wait 2 --random-wait --limit=20k \
--recursive --no-parent --level 1 \
--no-directories \
-A "file[0-9][0-9]" \
"$url"
This would download all files named file, with a two digit suffix (file52 etc), that are linked on the page at $url, and whose parent path is also $url (--no-parent).
This is a recursive download, recursing one level of links (--level 1). wget allows us to use patterns to accept or reject filenames when recursing (-A and -R for globs, also --accept-regex, --reject-regex).
Certain sites block may block the wget user agent string, it can be spoofed with --user-agent.
Note that certain sites may ban your IP (and/or add it to a blacklist) for scraping, especially doing it repeatedly, or not respecting robots.txt.
In case of downloading blocks for every day in a month, you may just change in original script the * symbol to a argument, let's say day and previously assign a variable days to a list of days.
Then iterate like for day in days… and do your wget stuff.
Related
Trying to do the following on contos7 works as I expect:
pod_in_question=$(curl -u uname:password -k very.cluster.com/api/v1/namespaces/default/pods/ | grep -i '"name": "myapp-' | cut -d '"' -f 4)
echo "$pod_in_question"
curl -u uname:password -k -X DELETE "very.cluster.com/api/v1/namespaces/default/pods/${pod_in_question}"
However, trying the same thing on MacOS (10.12.1) yields:
curl: (3) [globbing] bad range in column 92
When I try to curl the last line with a -g option it substitutes with a malformed name such as: myapp-\\x1b[m\\x1b[Kl1eti\
The echo statement would always execute just fine and show something like myapp-v7454 which I later want to put into the last curl statement. So where are these other characters coming from?
A robust solution - Basic cURL CLI debugging.
This answer is revised after it's been identified that the issue for the OP relates to curl applying color output.
There's a proposed answer which explains clearly what the embedded special characters meant, and instructions to override the grep behaviour to not output color. Certainly this is a good practise for grep use in piping. There are however a number of best practises that can help diagnose this or a similar issue with cURL and ultimately lead to the most robust solution.
Re-creating the problem
Assuming it's a JSON Content-Type, we use echo {'"name": "myapp-7414"'} to simulate the output from cURL
We filter the text and set a variable with it that we use in a cURL command
We force grep to output color, since it doesn't normally by default when outputting to a tty.
Recreation:
myvar=$(echo {'"name": "myapp-7414"'} | grep --color=always -i '"name": "myapp-' | cut -d '"' -f 4)
curl "https://www.google.com/${myvar}"
Output:
curl: (3) [globbing] bad range in column 32
First up:
'{}' are special characters to cURL, period.
The best practise for URL syntax in cURL:
If Variable Expansion is required:
Apply the -g switch to disable potential globbing done by cURL
Otherwise:
Use $variable as part of a "quoted" url string, instead of ${variable}
Second: In addition to -g, we add --libcurl /tmp/libcurl so we can get some insight into what cURL is seeing.
Recreation with -g and --libcurl:
curl -g --libcurl /tmp/libcurl "https://www.google.com/${myvar}"
Output:
<p>Your client has issued a malformed or illegal request <ins>That’s all we know.
Perfect, at least now everything is getting to the server and back! Let's see what cURL sent out to the server:
cat /tmp/libcurl
Surely enough we find this line: (note the bold part).
curl_easy_setopt(hnd, CURLOPT_URL, "https://www.google.com/myapp-\033[m7414");
So we know that:
The shell is doing something strange with our variable.
cURL knows not to try glob once we send the -g switch. That way - If there is an error with the shell variable, we can actually see what it is. We shouldn't be debugging a globbing error if we're not trying to use URL Ranges.
The special characters are colors. They represent the --color=always that we added to simulate the OPs environment.
At this point. Since it looks like we're working with JSON data, why not just use a widely available, high performance JSON parsing tool. That has a number of benefits, including:
Not relying on any environment that could affect string filtering
Can request the data we want (aka. "name")
The app name "myapp" can change and we won't have to re-write the code to retrieve it.
It's cleaner and accounts for things I haven't considered yet.
If we used jq for example (while we're at it, we don't need the -g switch because we don't need '{}' for the variable because we're already double " the URL):
myvar=$(echo {'"name": "myapp-7414"'} | jq -r .name)
curl --libcurl /tmp/libcurl "https://www.google.com/$myvar"
Now we get:
<p>The requested URL /myapp-7414 was not found on this server. That’s all we know.
Great. It's all working now. It should be obvious that the test URL here being www.google.com is obviously not going to know was myapp-7414 was.
So we've gone from :
Globbing bad range, to:
Malformed URL, to:
URL not found on server.
We could also as suggested elsewhere change the grep output and override it to --color=never (As I have noted: If grep has to be used, the --color=never is a great way to use it as a best practise when piping strings, period.). However, given the portability issues already experienced because of string filtering, and the fact that we are already handed structured data on a plate that can be parsed reliably, the more robust solution would be to do just that, if possible.
The substitution you showed at the last part looks like one of your calls injected ANSI escape sequences. It's possible that grep isn't detecting non-TTY output and is colorizing.
On a terminal that supports ANSI escape sequences, your particular codes might not be visible. The codes ^E[m^E[K set the screen mode and clear the current line. That's why you thought the echo command proved your data was correct.
You can examine the raw data with:
echo "$pod_in_question" | hexdump -C
And you should see there are other characters in there which did not appear in your terminal before. When you put these "invisible" codes into the URL, curl tries to encode them and then fails when it encounters a control character (ESC).
The solution is to add the argument --color=never to your grep call, which will disable colorization.
Have a pile of 50 .rar files on a web server and I want to download them all.
And, the names of the files have nothing in common other than .rar.
I wanted to try aria2 to download all of them altogether, but I think I need to write a script to fetch the addresses of all the .rar files.
I have no idea how to start writing the scrip. Any hint will be appreciated.
You can try to play with wget with -A parameter in your shell script:
wget -r "https://foo/" -P /tmp -A "*.rar"
Here is an explanation of what -A does
Specify comma-separated lists of file name suffixes or patterns to accept or reject (see Types of Files). Note that if any of the wildcard characters, ‘’, ‘?’, ‘[’ or ‘]’, appear in an element of acclist or rejlist, it will be treated as a pattern, rather than a suffix. In this case, you have to enclose the pattern into quotes to prevent your shell from expanding it, like in ‘-A ".mp3"’ or ‘-A '*.mp3'’.
I am reading a file (with URL's) line by line:
#!/bin/bash
while read line
do
url=$line
wget $url
wget $url_{001..005}.jpg
done < $1
For first, I want to download primary url as you see wget $url. After that I want to add to the url sequence of numbers (_001.jpg, _002.jpg, _003.jpg, _004.jpg, _005.jpg):
wget $url_{001..005}.jpg
...but for some reason it's not working.
Sorry, missed out one thing: the url's are like http://xy.com/052914.jpg. Is there any easy way to add _001 before the extension? http://xy.com/052914_001.jpg. Or I have to remove ".jpg" from the file containing URL's then simply add later to the variable?
Another way escaping the underscore char:
wget $url\_{001..005}.jpg
Try encapsulating your variable name:
wget ${url}_{001..005}.jpg
Bash is trying to expand the variable $url_ in your command.
As for your jpg within the URL followup, see substring expansion in the bash manual.
wget ${url:0: -4}_{001..005}.jpg
The :0: -4 means, expand to the variable from position zero (the first character), minus the last 4 characters.
Or from this answer:
wget ${url%.jpg}_{001..005}.jpg
%.jpg removes .jpg specifically and will work on older versions of bash.
I'm trying to fetch the JSON output by an internal API and add 100 to a parameter value between cURL requests. I need to loop through because it restricts the maximum number of results per request to 100. I was told to "increment and you should be able to get what you need".
Anyway, here's what I wrote:
#!/bin/bash
COUNTER=100
until [ COUNTER -gt 30000 ]; do
curl -vs "http://example.com/locations/city?limit=100&offset=$COUNTER" >> cities.json
let COUNTER=COUNTER+100
done
The problem is that I get a bunch of weird messages in the terminal and the file I'm trying to redirect the output too still contains it's original 100 objects. I feel like I'm probably missing something terrifically obvious. Any thoughts? I did use a somewhat old tutorial on the until loop, so maybe it's a syntax issue?
Thank you in advance!
EDIT: I'm not opposed to a completely alternate method, but I had hoped this would be somewhat straightforward. I figured my lack of experience was the main limiter.
You might find you can do this faster, and pretty easily with GNU Parallel:
parallel -k curl -vs "http://example.com/locations/city?limit=100\&offset={}" ::: $(seq 100 100 30000) > cities.json
If you want to overwrite the file's content only once, for your entire loop...
#!/bin/bash
# ^-- NOT /bin/sh, as this uses bash-only syntax
for (( counter=100; counter<=30000; counter+=100 )); do
curl -vs "http://example.com/locations/city?limit=100&offset=$counter"
done >cities.json
This is actually more efficient than putting >>cities.json on each curl command, as it only opens the output file once, and has the side effect (which you appear to want) of clearing the file's former contents when the loop is started.
this is my very first post on Stackoverflow, and I should probably point out that I am EXTREMELY new to a lot of programming. I'm currently a postgraduate student doing projects involving a lot of coding in various programs, everything from LaTeX to bash, MATLAB etc etc.
If you could explicitly explain your answers that would be much appreciated as I'm trying to learn as I go. I apologise if there is an answer else where that does what I'm trying to do, but I have spent a couple of days looking now.
So to the problem I'm trying to solve: I'm currently using a selection of bioinformatics tools to analyse a range of genomes, and I'm trying to somewhat automate the process.
I have a few sequences with names that look like this for instance (all contained in folders of their own currently as paired files):
SOL2511_S5_L001_R1_001.fastq
SOL2511_S5_L001_R2_001.fastq
SOL2510_S4_L001_R1_001.fastq
SOL2510_S4_L001_R2_001.fastq
...and so on...
I basically wish to automate the process by turning these in to variables and passing these variables to each of the programs I use in turn. So for example my idea thus far was to assign them as wildcards, using the R1 and R2 (which appears in all the file names, as they represent each strand of DNA) as follows:
#!/bin/bash
seq1=*R1_001*
seq2=*R2_001*
On a rudimentary level this works, as it returns the correct files, so now I pass these variables to my first function which trims the DNA sequences down by a specified amount, like so:
# seqtk is the program suite, trimfq is a function within it,
# and the options -b -e specify how many bases to trim from the beginning and end of
# the DNA sequence respectively.
seqtk trimfq -b 10 -e 20 $seq1 >
seqtk trimfq -b 10 -e 20 $seq2 >
So now my problem is I wish to be able to append something like "_trim" to the output file which appears after the >, but I can't find anything that seems like it will work online.
Alternatively, I've been hunting for a script that will take the name of the folder that the files are in, and create a variable for the folder name which I can then give to the functions in question so that all the output files are named correctly for use later on.
Many thanks in advance for any help, and I apologise that this isn't really much of a minimum working example to go on, as I'm only just getting going on all this stuff!
Joe
EDIT
So I modified #ghoti 's for loop (does the job wonderfully I might add, rep for you :D ) and now I append trim_, as the loop as it was before ended up giving me a .fastq.trim which will cause errors later.
Is there any way I can append _trim to the end of the filename, but before the extension?
Explicit is usually better than implied, when matching filenames. Your wildcards may match more than you expect, especially if you have versions of the files with "_trim" appended to the end!
I would be more precise with the wildcards, and use for loops to process the files instead of relying on seqtk to handle multiple files. That way, you can do your own processing on the filenames.
Here's an example:
#!/bin/bash
# Define an array of sequences
sequences=(R1_001 R2_001)
# Step through the array...
for seq in ${sequences[#]}; do
# Step through the files in this sequence...
for file in SOL*_${seq}.fastq; do
seqtk trimfq -b 10 -e 20 "$file" > "${file}.trim"
done
done
I don't know how your folders are set up, so I haven't addressed that in this script. But the basic idea is that if you want the script to be able to manipulate individual filenames, you need something like a for loop to handle the that manipulation on a per-filename basis.
Does this help?
UPDATE:
To put _trim before the extension, replace the seqtk line with the following:
seqtk trimfq -b 10 -e 20 "$file" > "${file%.fastq}_trim.fastq"
This uses something documented in the Bash man page under Parameter Expansion if you want to read up on it. Basically, the ${file%.fastq} takes the $file variable and strips off a suffix. Then we add your extra text, along with the suffix.
You could also strip an extension using basename(1), but there's no need to call something external when you can use something built in to the shell.
Instead of setting variables with the filenames, you could pipe the output of ls to the command you want to run with these filenames, like this:
ls *R{1,2}_001* | xargs -I# sh -c 'seqtk trimfq -b 10 -e 20 "$1" > "${1}_trim"' -- #
xargs -I# will grab the output of the previous command and store it in # to be used by seqtk