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  • Python - urllib2 & cookielib

    - by Adrian
    I am trying to open the following website and retrieve the initial cookie and use it for the second url-open BUT if you run the following code it outputs 2 different cookies. How do I use the initial cookie for the second url-open? import cookielib, urllib2 cj = cookielib.CookieJar() opener = urllib2.build_opener(urllib2.HTTPCookieProcessor(cj)) home = opener.open('https://www.idcourts.us/repository/start.do') print cj search = opener.open('https://www.idcourts.us/repository/partySearch.do') print cj Output shows 2 different cookies every time as you can see: <cookielib.CookieJar[<Cookie JSESSIONID=0DEEE8331DE7D0DFDC22E860E065085F for www.idcourts.us/repository>]> <cookielib.CookieJar[<Cookie JSESSIONID=E01C2BE8323632A32DA467F8A9B22A51 for www.idcourts.us/repository>]>

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  • BioPython: extracting sequence IDs from a Blast output file

    - by Jon
    Hi, I have a BLAST output file in XML format. It is 22 query sequences with 50 hits reported from each sequence. And I want to extract all the 50x22 hits. This is the code I currently have, but it only extracts the 50 hits from the first query. from Bio.Blast import NCBIXM blast_records = NCBIXML.parse(result_handle) blast_record = blast_records.next() save_file = open("/Users/jonbra/Desktop/my_fasta_seq.fasta", 'w') for alignment in blast_record.alignments: for hsp in alignment.hsps: save_file.write('>%s\n' % (alignment.title,)) save_file.close() Somebody have any suggestions as to extract all the hits? I guess I have to use something else than alignments. Hope this was clear. Thanks! Jon

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  • Program received signal from GDB: EXC_BAD_ACCESS

    - by user577185
    Well, I'm starting development on the Mac OS X this code that you'll see is in a book that I bought, really basic like Chapter 3. And I can't run it. PLEASE HELP ME: C301.m : #import <Foundation/Foundation.h> int main (int argc, const char * argv[]) { if (argc == 1) { NSLog (@"You need to provide a file name"); return -1; } FILE *wordFile = fopen("tmp/words.txt", "r"); char word[100]; while (fgets(word, 100, wordFile)) { word[strlen(word) - 1] = '\0'; NSLog(@"%s is %d characters long", word, strlen(word)); } fclose(wordFile); return 0; } //main The file is in its place. Thank you so much!

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  • Grails Unit Tests: Why does this statement fail?

    - by leeand00
    I've developed in Java in the past, and now I'm trying to learn Grails/Groovy using this slightly dated tutorial. import grails.test.* class DateTagLibTests extends TagLibUnitTestCase { def dateTagLib protected void setUp() { super.setUp() dateTagLib = new DateTagLib() } protected void tearDown() { super.tearDown() } void testThisYear() { String expected = Calendar.getInstance().get(Calendar.YEAR) // NOTE: This statement fails assertEquals("the years dont match and I dont know why.", expected, dateTagLib.thisYear()) } } DateTagLibTests.groovy (Note: this TagLibUnitTestCase is for Grails 1.2.1 and not the version used in the tutorial) For some reason the above test fails with: expected:<2010 but was:<2010 I've tried replacing the test above with the following alternate version of the test, and the test passes just fine: void testThisYear() { String expected = Calendar.getInstance().get(Calendar.YEAR) String actual = dateTagLib.thisYear() // NOTE: The following two assertions work: assertEquals("the years don\'t match", expected, actual) assertTrue("the years don\'t match", expected.equals(actual)) } These two versions of the test are basically the same thing right? Unless there's something new in Grails 1.2.1 or Groovy that I'm not understanding. They should be of the same type because the values are both the value returned by Calendar.getInstance().get(Calendar.YEAR)

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  • ExternalInterface.addCallback doesn't work on firefox??

    - by dome
    i'm trying to call a method inside a flash movie from js, every time the mouse leaves the "div". It works on Internet Explorer, but not in firefox. any ideas? here is the html script: <script type="text/javascript"> window.onload = function(e){ init(); } function init(){ document.getElementById('div').onmouseout = function(e) { method(); } } function method(){ flashid.anothermethod(); } </script> and the flash script: import flash.external.ExternalInterface; function outdiv(){ //do something; } ExternalInterface.addCallback('anothermethod', outdiv); Any ideas what's wrong?

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  • Creating a web-service client directly from the source

    - by ben
    Hi, I am trying to generate the WS client jar directly from the @Webservice class(es). Let's take this example : package com.example.maven.jaxws.helloservice; import javax.jws.WebService; @WebService public class Hello { public String sayHello(String param) { ; return "Hello " + param; } } I can generate a war file and use glassfish to serve this webservice, and from there I can use the glassfish WSDL URL to generate the client sources. What I am trying to do is to skip the glassfish part. From my maven project defining the webservice, I would like to use the jaxws-maven-plugin to create the client classes but I cannot find any way to specify the actual URL of the webservice. It should be possible right? @see also http://stackoverflow.com/questions/2097789/creating-a-web-service-client-with-a-known-but-inaccessible-wsdl

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  • Using Tkinter in python to edit the title bar

    - by Dan
    I am trying to add a custom title to a window but I am having troubles with it. I know my code isn't right but when I run it, it creates 2 windows instead, one with just the title tk and another bigger window with "Simple Prog". How do I make it so that the tk window has the title "Simple Prog" instead of having a new additional window. I dont think I'm suppose to have the Tk() part because when i have that in my complete code, there's an error from tkinter import Tk, Button, Frame, Entry, END class ABC(Frame): def __init__(self,parent=None): Frame.__init__(self,parent) self.parent = parent self.pack() ABC.make_widgets(self) def make_widgets(self): self.root = Tk() self.root.title("Simple Prog")

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  • Error With Foundation.h

    - by Nathan Campos
    Hello, I learning Objective-C in Linux(Ubuntu), but when i tryed to compile my application that needs the Foundation headers i got an error saying that the file cannot be found, but i have installed the GNUstep development package(gnustep-devel). Here is my code: // Fraction.h #import <Foundation/NSObject.h> @interface Fraction: NSObject { int numerator; int denominator; } - (void) print; - (void) setNumerator: (int) n; - (void) setDenominator: (int) d; - (void) numerator; - (void) denominator; @end And here is the console log: ubuntu@eeepc:~$ gcc main.m -o frac -lobjc In file included from main.m:3: Fraction.h:2:26: error: objc/NSObject.h: No such file or directory In file included from main.m:3: Fraction.h:4: error: cannot find interface declaration for ‘NSObject’, superclass of ‘Fraction’ ubuntu@eeepc:~$ What i need to do?

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  • Server database -> client database update based on version

    - by user296191
    Hi, What is the recommended method of collecting items in a server database, versioning the database then deploying only the version differences to a client ? Should it by a field in the table (ie. Version: 3.3.9876) against each record ? Should it be DateTime (server based) in each record ? And whats the best way to just deploy the changes to a client with an older version of the database ? Is it a DUMP to a file with a Bulk import of some description ? Open to comments.. Suggestions. Database can be anything (firebird, mysql, sqlserver, sqlite)... Any info greatly appreciated.

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  • Significant figures in the decimal module

    - by Jason Baker
    So I've decided to try to solve my physics homework by writing some python scripts to solve problems for me. One problem that I'm running into is that significant figures don't always seem to come out properly. For example this handles significant figures properly: from decimal import Decimal >>> Decimal('1.0') + Decimal('2.0') Decimal("3.0") But this doesn't: >>> Decimal('1.00') / Decimal('3.00') Decimal("0.3333333333333333333333333333") So two questions: Am I right that this isn't the expected amount of significant digits, or do I need to brush up on significant digit math? Is there any way to do this without having to set the decimal precision manually? Granted, I'm sure I can use numpy to do this, but I just want to know if there's a way to do this with the decimal module out of curiosity.

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  • Encoding in python with lxml - complex solution

    - by Vojtech R.
    Hi, I need to download and parse webpage with lxml and build UTF-8 xml output. I thing schema in pseudocode is more illustrative: from lxml import etree webfile = urllib2.urlopen(url) root = etree.parse(webfile.read(), parser=etree.HTMLParser(recover=True)) txt = my_process_text(etree.tostring(root.xpath('/html/body'), encoding=utf8)) output = etree.Element("out") output.text = txt outputfile.write(etree.tostring(output, encoding=utf8)) So webfile can be in any encoding (lxml should handle this). Outputfile have to be in utf-8. I'm not sure where to use encoding/coding. Is this schema ok? (I cant find good tutorial about lxml and encoding, but I can find many problems with this...) I need robust approved solution so I ask you seniors. Many thanks

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  • Python: Why is IDLE so slow?

    - by Adam Matan
    Hi, IDLE is my favorite Python editor. It offers very nice and intuitive Python shell which is extremely useful for unit-testing and debugging, and a neat debugger. However, code executed under IDLE is insanely slow. By insanely I mean 3 orders of magnitude slow: bash time echo "for i in range(10000): print 'x'," | python Takes 0.052s, IDLE import datetime start=datetime.datetime.now() for i in range(10000): print 'x', end=datetime.datetime.now() print end-start Takes: >>> 0:01:44.853951 Which is roughly 2,000 times slower. Any thoughts, or ideas how to improve this? I guess it has something to do with the debugger in the background, but I'm not really sure. Adam

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  • Safest way to copy a file

    - by aron
    Hello, I need to merg two PDF files. However sometimes a file might be locked up I wrote this code, but I'm wondering if it's not the smartest solution: private static int FILE_LOCKED_WAIT_PERIOD = 1000; while (true) { // If the file is in use, IOException will be thrown. // If file is not permitted to be opened because of Permission // Restrictions, UnauthorizedAccessException will be thrown. // For all other, Use normal Exception. try { inputDocument1 = PdfReader.Open(fileToMerge, PdfDocumentOpenMode.Import); break; } catch (IOException) { Thread.Sleep(FILE_LOCKED_WAIT_PERIOD); } catch (UnauthorizedAccessException) { Thread.Sleep(FILE_LOCKED_WAIT_PERIOD); } catch (Exception) { Thread.Sleep(FILE_LOCKED_WAIT_PERIOD); } }

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  • Idiomatic way to do list/dict in Cython?

    - by ramanujan
    My problem: I've found that processing large data sets with raw C++ using the STL map and vector can often be considerably faster (and with lower memory footprint) than using Cython. I figure that part of this speed penalty is due to using Python lists and dicts, and that there might be some tricks to use less encumbered data structures in Cython. For example, this page (http://wiki.cython.org/tutorials/numpy) shows how to make numpy arrays very fast in Cython by predefining the size and types of the ND array. Question: Is there any way to do something similar with lists/dicts, e.g. by stating roughly how many elements or (key,value) pairs you expect to have in them? That is, is there an idiomatic way to convert lists/dicts to (fast) data structures in Cython? If not I guess I'll just have to write it in C++ and wrap in a Cython import.

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  • I'm trying to build a to-do-list application in Objective C but coming up short.

    - by lampShade
    I'm getting this error: -[NSCFArray insertObject:atIndex:]: attempt to insert nil Here is the .m file: /* IBOutlet NSTextField *textField; IBOutlet NSTabView *tableView; IBOutlet NSButton *button; NSMutableArray *myArray; */ #import "AppController.h" @implementation AppController -(IBAction)addNewItem:(id)sender { myArray = [[NSMutableArray alloc]init]; tableView = [[NSTableView alloc] init]; [tableView setDataSource:self]; [textField stringValue]; NSString *string = [[NSString alloc] init]; string = [textField stringValue]; [myArray addObject:string]; NSLog(@"%d",[myArray count]); NSLog(@"%@",string); } - (int)numberOfRowsInTableView:(NSTableView *)aTableView { return [myArray count]; } - (id)tableView:(NSTableView *)aTableView objectValueForTableColumn:(NSTableColumn *)aTableColumn row:(int)rowIndex { //NSString *data = [myArray objectAtIndex:rowIndex]; return [myArray objectAtIndex:rowIndex]; } @end

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  • Rake don't know how to build task?

    - by Schroedinger
    Using a rake task to import data into a database: file as follows namespace :db do desc "load imported data from csv" task :load_csv_data => :environment do require 'fastercsv' require 'chronic' FasterCSV.foreach("input.csv", :headers => true) do |row| Trade.create( :name => row[0], :type => row[4], :price => row[6].to_f, :volume => row[7].to_i, :bidprice => row[10].to_f, :bidsize => row[11].to_i, :askprice => row[14].to_f, :asksize => row[15].to_i ) end end end When attempting to use this, with the right CSV files and the other elements in place, it will say Don't know how to build task 'db:import_csv_data' I know this structure works because I've tested it, I'm just trying to get it to convert to the new values on the fly. Suggestions?

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  • Python re.sub MULTILINE caret match

    - by cdleary
    The Python docs say: re.MULTILINE: When specified, the pattern character '^' matches at the beginning of the string and at the beginning of each line (immediately following each newline)... By default, '^' matches only at the beginning of the string... So what's going on when I get the following unexpected result? >>> import re >>> s = """// The quick brown fox. ... // Jumped over the lazy dog.""" >>> re.sub('^//', '', s, re.MULTILINE) ' The quick brown fox.\n// Jumped over the lazy dog.'

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  • Best Practices of fault toleration and reliability for scheduled tasks or services

    - by user177883
    I have been working on many applications which run as windows service or scheduled tasks. Now, i want to make sure that these applications will be fault tolerant and reliable. For example; i have a service that runs every hour. if the service crashes while its operating or running, i d like the application to run again for the same period, to avoid data loss. moreover, i d like the program to report the error with details. My goal is to avoid data loss and not falling behind for running the program. I have built a class library that a user can import into a project. Library is supposed to keep information of running instance of the program, ie. program reads and writes information of running interval, running status etc. This data is stored in a database. I was curious, if there are some best practices to make the scheduled tasks/ windows services fault tolerant and reliable.

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  • pubsub link with Project Rome

    - by itsadok
    I want to use Project Rome to create an RSS feed, using the code from the tutorial as base. I would like to add a pubsubhubbub discovery link, but there doesn't seem to be a general way to do so. I can use a Link object if I create an atom feed (which I don't want to limit myself to), or I can just add foreign markup, like this: // import org.jdom.Element Element element = new Element("link"); element.setAttribute("rel", "hub"); element.setAttribute("href", "https://myhub.example.com/endpoint"); feed.setForeignMarkup(Arrays.asList(element)); But it feels ugly. Is this really the best way to do this?

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  • NSStream sockets missing data

    - by Chris T.
    I am trying to pull some sample data from FreeDB as a proof of concept, but I am having a tough time retrieving all of the data off the incoming stream (I am only getting the last bits for the final query listed here (if handshakeCode = 3) I think this may be something with the threading on the main runloop, but I am not sure. Odd thing is when the buffer size is larger than 1-2 bytes (which works as expected), I seem to be losing access to the data programmatically (the totalOutput variable on the first set of data is incomplete). I set up a packet capture, and it looks like those 1024 bytes are coming across the wire, but the app just isn't working with it. It looks like the next event is coming through and basically taking over. I tried using an NSLock to no avail as well. If I drop the buffer size down to 1 or 2, things seem to be reading just fine. This is probably obvious to someone who does this all the time, but this is my first foray into this with something I am familiar with, technology wise in other languages / platforms. The following code will show you what is happening. Run with the buffer set to 1024, and you will see a short final string, but once you set it to 1, you will see the amount of data I was expecting (I was even expecting it to be split, so that's not a big worry) #import <Foundation/Foundation.h> #import <Cocoa/Cocoa.h> //STACK OVERFLOW CODE: @interface stackoverflow : NSObject <NSStreamDelegate> { NSInputStream *iStream; NSOutputStream *oStream; int handshakeCode; NSString *selectedDiscId; NSString *selectedGenre; } -(void)getMatchesFromFreeDB; -(void)sendToOutputStream:(NSString*)command; @end @implementation stackoverflow -(void)getMatchesFromFreeDB { NSHost *host = [NSHost hostWithName:@"freedb.freedb.org"]; [NSStream getStreamsToHost:host port:8880 inputStream:&iStream outputStream:&oStream]; [iStream retain]; [oStream retain]; [iStream setDelegate:self]; [oStream setDelegate:self]; [iStream scheduleInRunLoop:[NSRunLoop currentRunLoop] forMode:NSDefaultRunLoopMode]; [oStream scheduleInRunLoop:[NSRunLoop currentRunLoop] forMode:NSDefaultRunLoopMode]; [iStream open]; [oStream open]; handshakeCode = 0; //not done any processing } -(void)stream:(NSStream *)aStream handleEvent:(NSStreamEvent)eventCode { switch(eventCode) { case NSStreamEventOpenCompleted: { NSLog(@"Stream open completed"); break; } case NSStreamEventHasBytesAvailable: { NSLog(@"Stream has bytes available"); if (aStream == iStream) { NSMutableString *totalOutput = [NSMutableString stringWithString:@""]; //read data uint8_t buffer[1024]; int len; while ([iStream hasBytesAvailable]) { len = [iStream read:buffer maxLength:sizeof(buffer)]; if (len 0) { NSString *output = [[NSString alloc] initWithBytes:buffer length:len encoding:NSUTF8StringEncoding]; //this could have also been put into an NSData object if (nil != output) { //append to the total output [totalOutput appendString:output]; } } } NSLog(@"OUTPUT , %i:\n\n%@", [totalOutput lengthOfBytesUsingEncoding:NSUTF8StringEncoding], totalOutput); NSArray *outputComponents = [totalOutput componentsSeparatedByString:@" "]; //Attempt to get handshake code, since we haven't done it yet: if (handshakeCode == 1) { //we are just getting the sign-on banner: //let's move on: handshakeCode = 2; } else if (handshakeCode == 2) { handshakeCode = [[outputComponents objectAtIndex:0] intValue]; if (handshakeCode == 200) { NSLog(@"---Handshake OK %i", handshakeCode); NSMutableString *query = [NSMutableString stringWithString:@"cddb query f3114b11 17 225 19915 36489 54850 69425 87025 103948 123242 136075 152817 178335 192850 211677 235104 262090 284882 308658 4430\n"]; handshakeCode = 3; [self sendToOutputStream:query]; } } else if (handshakeCode == 3) { //now, we are reading out the matches: if ([[outputComponents objectAtIndex:0] intValue] == 200) //found exact match: { NSLog(@"Found exact match"); selectedGenre = [outputComponents objectAtIndex:1] ; selectedDiscId = [outputComponents objectAtIndex:2]; if (selectedGenre && selectedDiscId) { //send off the request to get the entry: NSString *query = [NSString stringWithFormat:@"cddb read %@ %@\n", selectedGenre, selectedDiscId]; [self sendToOutputStream:query]; handshakeCode = 4; } } } } break; } case NSStreamEventEndEncountered: { NSLog(@"Stream event end encountered"); break; } case NSStreamEventErrorOccurred: { NSLog(@"Stream error occurred"); break; } case NSStreamEventHasSpaceAvailable: { NSLog(@"Stream has space available"); if (aStream == oStream) { if (handshakeCode == 0) { handshakeCode = 1; [self sendToOutputStream:@"cddb hello stackoverflow localhost.localdomain test .01BETA\n"]; } } break; } } } -(void)sendToOutputStream:(NSString*)command { const uint8_t *rawCommand = (const uint8_t *)[command UTF8String]; [oStream write:rawCommand maxLength:strlen(rawCommand)]; NSLog(@"Sent command: %@",command); } @end int main (int argc, const char * argv[]) { NSAutoreleasePool * pool = [[NSAutoreleasePool alloc] init]; stackoverflow *test = [[stackoverflow alloc] init]; [test getMatchesFromFreeDB]; NSRunLoop *runLoop = [NSRunLoop currentRunLoop]; [runLoop run]; [pool drain]; return 0; } Any help is much appreciated! Thanks

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  • Python SQLite: database is locked

    - by user322683
    I'm trying this code: import sqlite connection = sqlite.connect('cache.db') cur = connection.cursor() cur.execute('''create table item (id integer primary key, itemno text unique, scancode text, descr text, price real)''') connection.commit() cur.close() I'm catching this exception: Traceback (most recent call last): File "cache_storage.py", line 7, in <module> scancode text, descr text, price real)''') File "/usr/lib/python2.6/dist-packages/sqlite/main.py", line 237, in execute self.con._begin() File "/usr/lib/python2.6/dist-packages/sqlite/main.py", line 503, in _begin self.db.execute("BEGIN") _sqlite.OperationalError: database is locked Permissions for cache.db are ok. Any ideas?

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  • Difference between C# and java big endian bytes using miscutil

    - by Eric Hauser
    I'm using the miscutil library to communicate between and Java and C# application using a socket. I am trying to figure out the difference between the following code (this is Groovy, but the Java result is the same): import java.io.* def baos = new ByteArrayOutputStream(); def stream = new DataOutputStream(baos); stream.writeInt(5000) baos.toByteArray().each { println it } /* outputs - 0, 0, 19, -120 */ and C#: using (var ms = new MemoryStream()) using (EndianBinaryWriter writer = new EndianBinaryWriter(EndianBitConverter.Big, ms, Encoding.UTF8)) { writer.Write(5000); ms.Position = 0; foreach (byte bb in ms.ToArray()) { Console.WriteLine(bb); } } /* outputs - 0, 0, 19, 136 */ As you can see, the last byte is -120 in the Java version and 136 in C#.

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  • Xcode & passing command line arguments

    - by Brisco
    I just started working with C & Xcode and I've run into a little difficulty. All I want to do is read a file from the command line and see the output in the terminal. I think my problem lies with the path to the file that I want to read in. I'm using a Mac and the file is on my desktop, so the path should be Users/myName/Desktop/words.txt. Is this correct? This is my code: #import <Foundation/Foundation.h> int main (int argc, const char* argv[]){ if(argc == 1){ NSLog(@" you must pass at least one arguement"); return 1; } NSLog(@"russ"); FILE* wordFile = fopen(argv[1] , "r"); char word[100]; while (fgets(word,100,wordFile)) { NSLog(@" %s is %d chars long", word,strlen(word)); } fclose(wordFile); return 0; }//main

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  • Connecting to Python XML RPC from the Mac

    - by MAC
    Hi, I wrote an XML RPC server in python and a simple Test Client for it in python. The Server runs on a linux box. I tested it by running the python client on the same linux machine and it works. I then tried to run the python client on a Mac and i get the following error socket.error: (61, 'Connection Refused') I can ping and ssh into the linux machine from the Mac. So i dont think its a configuration or firewall error. Does anyone have any idea what could be going wrong? The code for the client is as below: import xmlrpclib s = xmlrpclib.ServerProxy('http://143.252.249.141:8000') print s.GetUsers() print s.system.listMethods()

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  • Importing already existing git repo with multiple branches and tags into gerrit

    - by Daniel
    I'm trying to import an already existing git repository with multiple branches and tags into gerrit. I'm following the official guide at https://gerrit-review.googlesource.com/Documentation/install-quick.html#_already_existing_project. However, when issuing the push command all the branches and tags, except "master" which I'm currently in, are "prohibited by Gerrit". The output is something like this: user@host:~/my-project$ git push ssh://user@localhost:29418/demo-project *:* [....] * [new branch] master -> master ! [remote rejected] origin/Branch1 -> origin/Branch1 (prohibited by Gerrit) ! [remote rejected] origin/Branch2 -> origin/Branch2 (prohibited by Gerrit) [....] ! [remote rejected] Tag1 -> Tag1 (prohibited by Gerrit) ! [remote rejected] Tag2 -> Tag2 (prohibited by Gerrit) [....] I'm administrator so it shouldn't be an access rights issue.

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