Reading the file lines as locs in Rascal - rascal

In the file IO module there is a function that reads the lines from the file.
list[str] fileLines = readFileLines(fileLoc);
The function neatly returns the strings. Each of these strings are also denotable as a loc with the fileLoc(O, L, <BL, BC> , <EL,EC>) format. How can I load the lines from the file as loc resources?

Short answer: The library function readFiles takes a source location as argument and reads the contents of the file. If that source location contains position information then it will only read the part of the file corresponding to that position information.
Somewhat longer answer:
Here is an illustration:
module Example
void main() {
str text = "a\nbc\ndef\n";
loc tmpLoc = |home:///tmp.txt|;
writeFile(tmpLoc, text); // write example text to file
// Read lines back and print them
println("Using readFileLines:");
for(s <- readFileLines(tmpLoc)) println(s);
// Add position information to tmpLoc that corresponds to each of the lines,
// read it back and print it:
println("Using source location with position info:");
println(readFile(tmpLoc[offset=0][length=1]));
println(readFile(tmpLoc[offset=2][length=2]));
println(readFile(tmpLoc[offset=5][length=3]));
}
the expected output is:
Using readFileLines:
a
bc
def
Using source location with position info:
a
bc
def
Final remarks:
Usually position information is generated automatically
by tools (for example a parser); programmers mostly use that information, they don't have to create it (but they can).
Parsers usually generate full line and column information, here we only use offset and length.

Related

Biopython : how to extract only relevant atom and save a pdb file (not locally)?

Using Biopython. I have a list of atoms. rep_atoms = [CA, CB, CD3] (Carbon atoms).
I want to save only these from any given PDB file. I don't want to save it locally; I want it to save in the memory (Lots of iteration).
I have arrived at the code below, but it saves the file locally and is very slow.
So, my goal is from each atom in PDB, if it is present in rep_atoms. Make a new_pdb store only that information so that when I call it later in my code, it should be a PDB file without getting saved in my computer in a local folder.
How do I append each atom? Printing all atoms is very fast. I want to append it, but it wouldn't be a PDB structure file. What should I do?
from Bio.PDB import .... PDBIO, Select ....
class rep_atom_Select(Select):
def accept_atom(self, atom):
if atom.get_name() in rep_atoms:
return 1
else:
return 0
def rep_atoms_pdb(input_pdb):
io = PDBIO()
io.set_structure(input_pdb)
for model in input_pdb:
for chain in model:
for residue in chain:
for atom in residue:
if atom.get_name() in rep_atoms:
print(atom)
# dnr_only = io.save("dnr_only.pdb", rep_atom_Select())
Save after the loop, once, instead of thousands of times inside the loop.
def rep_atoms_pdb(input_pdb):
my_atoms = list()
for model in input_pdb:
for chain in model:
for residue in chain:
for atom in residue:
if atom.get_name() in rep_atoms: # or if rep_atom_Select().accept_atom(atom):
my_atoms.append(atom) # or something like this
# The function returns the list of extracted atoms
return my_atoms
Your definition of rep_atom_Select() does not seem to be directly compatible with this design, nor am I sure receiving the atoms as a list is actually what you want, but this should at least give you a nudge in the right direction.
Brief reading of the Bio.PDB.PDBIO documentation suggests that you might simply want to return the actual PDBIO object. I think something like this:
class rep_atom_Select(Select):
def accept_atom(self, atom):
if atom.get_name() in rep_atoms:
return 1
else:
return 0
def rep_atoms_pdb(input_pdb):
io = rep_atom_Select()
io.set_structure(input_pdb)
return io
This is based on a very cursory reading of the documentation, but at least demonstrates how you would use your overridden class to select only some of the atoms in the input_pdb structure.

Modifying strings with source_span package in dartlang?

I want to transform some parts of my source files with an own transformer in dart.
I have a dart file as input and i want to edit this file.
I know that I can get the contents of the file with:
var content = transform.primaryInput.readAsString(encoding: UTF8);
from inside transformers.
I know also how to find the offset in my source where I want to apply some changes.
Is there some kind of "Cursor"-Style editing Package for strings in Dart?
I want to do some kind of (Pseudo-Code!):
String sourceString = transform.primaryInput.readAsString(encoding: UTF8);
//SourceFile comes from source_span package, could be wrapped by cursor implementation
SourceFile source = new SourceFile(sourceString);
var cursor = new Cursor(sourceFile);
//.jumpTo(int lineNumber, [int columnNumber])
cursor.jumpTo(30);
//deletes the next two chars
cursor.delete(2);
//adds new text after cursor
cursor.write("Hello World!");
//accept sourceSpans for deletion
cursor.delete(sourceSpanObject)
Or is there a better way to change contents of source files in transfomers in dart?

How to remove non-ascii char from MQ messages with ESQL

CONCLUSION:
For some reason the flow wouldn't let me convert the incoming message to a BLOB by changing the Message Domain property of the Input Node so I added a Reset Content Descriptor node before the Compute Node with the code from the accepted answer. On the line that parses the XML and creates the XMLNSC Child for the message I was getting a 'CHARACTER:Invalid wire format received' error so I took that line out and added another Reset Content Descriptor node after the Compute Node instead. Now it parses and replaces the Unicode characters with spaces. So now it doesn't crash.
Here is the code for the added Compute Node:
CREATE FUNCTION Main() RETURNS BOOLEAN
BEGIN
DECLARE NonPrintable BLOB X'0001020304050607080B0C0E0F101112131415161718191A1B1C1D1E1F7F808182838485868788898A8B8C8D8E8F909192939495969798999A9B9C9D9E9FA0A1A2A3A4A5A6A7A8A9AAABACADAEAFB0B1B2B3B4B5B6B7B8B9BABBBCBDBEBFC0C1C2C3C4C5C6C7C8C9CACBCCCDCECFD0D1D2D3D4D5D6D7D8D9DADBDCDDDEDFE0E1E2E3E4E5E6E7E8E9EAEBECEDEEEFF1F2F3F4F5F6F7F8F9FAFBFCFDFEFF';
DECLARE Printable BLOB X'20202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020202020';
DECLARE Fixed BLOB TRANSLATE(InputRoot.BLOB.BLOB, NonPrintable, Printable);
SET OutputRoot = InputRoot;
SET OutputRoot.BLOB.BLOB = Fixed;
RETURN TRUE;
END;
UPDATE:
The message is being parsed as XML using XMLNSC. Thought that would cause a problem, but it does not appear to be.
Now I'm using PHP. I've created a node to plug into the legacy flow. Here's the relevant code:
class fixIncompetence {
function evaluate ($output_assembly,$input_assembly) {
$output_assembly->MRM = $input_assembly->MRM;
$output_assembly->MQMD = $input_assembly->MQMD;
$tmp = htmlentities($input_assembly->MRM->VALUE_TO_FIX, ENT_HTML5|ENT_SUBSTITUTE,'UTF-8');
if (!empty($tmp)) {
$output_assembly->MRM->VALUE_TO_FIX = $tmp;
}
// Ensure there are no null MRM fields. MessageBroker is strict.
foreach ($output_assembly->MRM as $key => $val) {
if (empty($val)) {
$output_assembly->MRM->$key = '';
}
}
}
}
Right now I'm getting a vague error about read only messages, but before that it wasn't working either.
Original Question:
For some reason I am unable to impress upon the senders of our MQ
messages that smart quotes, endashes, emdashes, and such crash our XML
parser.
I managed to make a working solution with SQL queries, but it wasted
too many resources. Here's the last thing I tried, but it didn't work
either:
CREATE FUNCTION CLEAN(IN STR CHAR) RETURNS CHAR BEGIN
SET STR = REPLACE('–',STR,'–');
SET STR = REPLACE('—',STR,'—');
SET STR = REPLACE('·',STR,'·');
SET STR = REPLACE('“',STR,'“');
SET STR = REPLACE('”',STR,'”');
SET STR = REPLACE('‘',STR,'&lsqo;');
SET STR = REPLACE('’',STR,'’');
SET STR = REPLACE('•',STR,'•');
SET STR = REPLACE('°',STR,'°');
RETURN STR;
END;
As you can see I'm not very good at this. I have tried reading about
various ESQL string functions without much success.
So in ESQL you can use the TRANSLATE function.
The following is a snippet I use to clean up a BLOB containing non-ASCII low hex values so that it then be cast into a usable character string.
You should be able to modify it to change your undesired characters into something more benign. Basically each hex value in NonPrintable gets translated into its positional equivalent in Printable, in this case always a full-stop i.e. x'2E' in ASCII. You'll need to make your BLOB's long enough to cover the desired range of hex values.
DECLARE NonPrintable BLOB X'000102030405060708090A0B0C0D0E0F101112131415161718191A1B1C1D1E1F202122232425262728292A2B2C2D2E2F303132333435363738393A3B3C3D3E3F';
DECLARE Printable BLOB X'2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E2E';
SET WorkBlob = TRANSLATE(WorkBlob, NonPrintable, Printable);
BTW if messages with invalid characters only come in every now and then I'd probably specify BLOB on the input node and then use something similar to the following to invoke the XMLNSC parser.
CREATE LASTCHILD OF OutputRoot DOMAIN 'XMLNSC'
PARSE(InputRoot.BLOB.BLOB CCSID InputRoot.Properties.CodedCharSetId ENCODING InputRoot.Properties.Encoding);
With the exception terminal wired up you can then correct the BLOB's of any messages containing parser breaking invalid characters before attempting to reparse.
Finally my best wishes as I've had a number of battles over the years with being forced to correct invalid message content in the "Integration Layer" after all that's what it's meant to do.

Groovy- searching and excretion xml code from log file

I have so many texts in log file but sometimes i got responses as a xml code and I have to cut this xml code and move to other files.
For example:
sThread1....dsadasdsadsadasdasdasdas.......dasdasdasdadasdasdasdadadsada
important xml code to cut and move to other file: <response><important> 1 </import...></response>
important xml code to other file: <response><important> 2 </important...></response>
sThread2....dsadasdsadsadasdasdasdas.......dasdasdasdadasdasdasdadadsada
Hindrance: xml code starting from difference numbers of sign (not always start in the same number of sign)
Please help me with finding method how to find xml code in text
Right now i tested substring() method but xml code not always start from this same sign :(
EDIT:
I found what I wanted, function which I searched was indexOf().
I needed a number of letter where String "Response is : " ending: so I used:
int positionOfXmlInLine = lineTxt.indexOf("<response")
And after this I can cut string to the end of the line :
def cuttedText = lineTxt.substring(positionOfXmlInLine);
So I have right now only a XML text/code from log file.
Next is a parsing XML value like BDKosher wrote under it.
Hoply that will help someone You guys
You might be able to leverage XmlSlurper for this, assuming your XML is valid enough. The code below will take each line of the log, wrap it in a root element, and parse it. Once parsed, it extracts and prints out the value of the <important> element's value attribute, but instead you could do whatever you need to do with the data:
def input = '''
sThread1..sdadassda..sdadasdsada....sdadasdas...
important code to cut and move to other file: **<response><important value="1"></important></response>**
important code to other file: ****<response><important value="3"></important></response>****
sThread2..dsadasd.s.da.das.d.as.das.d.as.da.sd.a.
'''
def parser = new XmlSlurper()
input.eachLine { line, lineNo ->
def output = parser.parseText("<wrapper>$line</wrapper>")
if (!output.response.isEmpty()) {
println "Line $lineNo is of importance ${output.response.important.#value.text()}"
}
}
This prints out:
Line 2 is of importance 1
Line 3 is of importance 3

Preprocessing Scala parser Reader input

I have a file containing a text representation of an object. I have written a combinator parser grammar that parses the text and returns the object. In the text, "#" is a comment delimiter: everything from that character to the end of the line is ignored. Blank lines are also ignored. I want to process text one line at a time, so that I can handle very large files.
I don't want to clutter up my parser grammar with generic comment and blank line logic. I'd like to remove these as a preprocessing step. Converting the file to an iterator over line I can do something like this:
Source.fromFile("file.txt").getLines.map(_.replaceAll("#.*", "").trim).filter(!_.isEmpty)
How can I pass the output of an expression like that into a combinator parser? I can't figure out how to create a Reader object out of a filtered expression like this. The Java FileReader interface doesn't work that way.
Is there a way to do this, or should I put my comment and blank line logic in the parser grammar? If the latter, is there some util.parsing package that already does this for me?
The simplest way to do this is to use the fromLines method on PagedSeq:
import scala.collection.immutable.PagedSeq
import scala.io.Source
import scala.util.parsing.input.PagedSeqReader
val lines = Source.fromFile("file.txt").getLines.map(
_.replaceAll("#.*", "").trim
).filterNot(_.isEmpty)
val reader = new PagedSeqReader(PagedSeq.fromLines(lines))
And now you've got a scala.util.parsing.input.Reader that you can plug into your parser. This is essentially what happens when you parse a java.io.Reader, anyway—it immediately gets wrapped in a PagedSeqReader.
Not the prettiest code you'll ever write, but you could go through a new Source as follows:
val SEP = System.getProperty("line.separator")
def lineMap(fileName : String, trans : String=>String) : Source = {
Source.fromIterable(
Source.fromFile(fileName).getLines.flatMap(
line => trans(line) + SEP
).toIterable
)
}
Explanation: flatMap will produce an iterator on characters, which you can turn into an Iterable, which you can use to build a new Source. You need the extra SEP because getLines removes it by default (using \n may not work as Source will not properly separate the lines).
If you want to apply filtering too, i.e. remove some of the lines, you could for instance try:
// whenever `trans` returns `None`, the line is dropped.
def lineMapFilter(fileName : String, trans : String=>Option[String]) : Source = {
Source.fromIterable(
Source.fromFile(fileName).getLines.flatMap(
line => trans(line).map(_ + SEP).getOrElse("")
).toIterable
)
}
As an example:
lineMapFilter("in.txt", line => if(line.isEmpty) None else Some(line.reverse))
...will remove empty lines and reverse non-empty ones.

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