#26592 closed defect (fixed)
py3: combinat/designs: byteslike object is required, not 'str'
Reported by:  slabbe  Owned by:  

Priority:  major  Milestone:  sage8.8 
Component:  python3  Keywords:  thursdaysbdx 
Cc:  dgordon, slabbe, slelievre, vklein, zerline  Merged in:  
Authors:  Samuel Lelièvre  Reviewers:  Frédéric Chapoton 
Report Upstream:  N/A  Work issues:  
Branch:  1f3afa8 (Commits)  Commit:  
Dependencies:  Stopgaps: 
Description (last modified by )
sage: print(version()) SageMath version 8.5.beta1, Release Date: 20181027 sage: print(sys.version) 3.6.6 (default, Oct 27 2018, 01:34:38) [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang700.1.81)] sage: C = designs.best_known_covering_design_from_LJCR(7, 3, 2)  TypeError Traceback (most recent call last) <ipythoninput1a3d9f9e592f1> in <module>() > 1 C = designs.best_known_covering_design_from_LJCR(Integer(7), Integer(3), Integer(2)) /opt/s/sage/local/lib/python3.6/sitepackages/sage/combinat/designs/covering_design.py in best_known_covering_design_www(v, k, t, verbose) 505 f.close() 506 > 507 if 'covering not in database' in s: #not found 508 str = "no (%d,%d,%d) covering design in database\n"%(v,k,t) 509 raise ValueError(str) TypeError: a byteslike object is required, not 'str'
Change History (39)
comment:1 Changed 7 months ago by
comment:2 Changed 7 months ago by
This needs some Python 3 love now though.
Here's what I get with a Python3based Sage:
sage: print(version()) SageMath version 8.5.beta1, Release Date: 20181027 sage: print(sys.version) 3.6.6 (default, Oct 27 2018, 01:34:38) [GCC 4.2.1 Compatible Apple LLVM 7.0.2 (clang700.1.81)] sage: C = designs.best_known_covering_design_from_LJCR(7, 3, 2)  TypeError Traceback (most recent call last) <ipythoninput1a3d9f9e592f1> in <module>() > 1 C = designs.best_known_covering_design_from_LJCR(Integer(7), Integer(3), Integer(2)) /opt/s/sage/local/lib/python3.6/sitepackages/sage/combinat/designs/covering_design.py in best_known_covering_design_www(v, k, t, verbose) 505 f.close() 506 > 507 if 'covering not in database' in s: #not found 508 str = "no (%d,%d,%d) covering design in database\n"%(v,k,t) 509 raise ValueError(str) TypeError: a byteslike object is required, not 'str'
comment:3 Changed 7 months ago by
Feel free to repurpose the present ticket for that.
comment:4 Changed 6 months ago by
 Component changed from doctest coverage to python3
 Description modified (diff)
 Summary changed from internet doctest failing in combinat/designs [SSL: UNKNOWN_PROTOCOL] to py3: combinat/designs: byteslike object is required, not 'str'
Ok, I updated the goal of this ticket as suggested.
comment:5 Changed 5 months ago by
 Milestone changed from sage8.5 to sage8.7
comment:6 Changed 3 months ago by
As suggested in https://trac.sagemath.org/ticket/26502#comment:8, the url address apparently changed to:
So we need to redo the changes that were made in #26502 in order to fix this issue.
comment:7 Changed 3 months ago by
The problem with dmgordon.org is that the server certificate chain is incomplete:
sage: from six.moves.urllib.request import urlopen sage: url = "https://dmgordon.org/cover/" sage: f = urlopen(url)  URLError Traceback (most recent call last) <ipythoninput6152a0d5393b6> in <module>() > 1 f = urlopen(url) ... /home/vklein/odk/sage/local/lib/python2.7/urllib2.pyc in do_open(self, http_class, req, **http_conn_args) 1196 except socket.error, err: # XXX what error? 1197 h.close() > 1198 raise URLError(err) 1199 else: 1200 try: URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:726)>
Should we find a way to ignore ssl verification or to contact dmgordon.org owner ?
comment:8 Changed 3 months ago by
 Cc slelievre added
I just emailed Dan Gordon to report the various issues we are trying to tackle here:
 http vs https
get_cover.php
seems gone from http://ljcr.dmgordon.org/cover/ (show_cover.php
returns some htmlformatted string)
comment:9 Changed 3 months ago by
Thank you Samuel.
For the http vs https part, note that urlopen("http://dmgordon.org/cover/get_cover.php")
return the famous HTTP Error 404: Not Found
.
comment:10 Changed 3 months ago by
 Keywords thursdaysbdx added
comment:11 Changed 3 months ago by
My attempt so far is using:

src/sage/combinat/designs/covering_design.py
diff git a/src/sage/combinat/designs/covering_design.py b/src/sage/combinat/designs/covering_design.py index 87dda39064..23beebc2e8 100644
a b def best_known_covering_design_www(v, k, t, verbose=False): 497 497 498 498 param = ("?v=%s&k=%s&t=%s"%(v,k,t)) 499 499 500 url = "http s://math.ccrwest.org/cover/get_cover.php"+param500 url = "http://ljcr.dmgordon.org/cover/show_cover.php" + param 501 501 if verbose: 502 502 print("Looking up the bounds at %s" % url) 503 503 f = urlopen(url)
which returns html instead of plain text, but I guess we could easily dehtmlify it.
comment:12 Changed 3 months ago by
It's feasible but calling get_cover.php
will be far cleaner.
Another concern for me is that without https, given that the current code call sage_eval
on the result, this code look like an open door to inject any (sage) code you want on a sage user's computer.
comment:13 Changed 2 months ago by
 Cc dgordon slabbe vklein added
The following changes should suffice once get_cover.php
is repaired.
(I think it currently gives an extra initial \n\n<html>\n<body>\n
we don't expect.)

src/sage/combinat/designs/covering_design.py
diff git a/src/sage/combinat/designs/covering_design.py b/src/sage/combinat/designs/covering_design.py index 87dda39064..ef7512b704 100644
a b design from this database, we include extra information: 21 21 REFERENCES: 22 22 23 23 .. [1] La Jolla Covering Repository, 24 http s://math.ccrwest.org/cover.html24 http://ljcr.dmgordon.org/cover.html 25 25 26 26 .. [2] Coverings, 27 27 Daniel Gordon and Douglas Stinson, 28 https:// math.ccrwest.org/gordon/hcd.pdf28 https://drive.google.com/file/d/0B6s9_JNV1EjtUFd4MkhBc0hSdVU/view 29 29 from the Handbook of Combinatorial Designs 30 30 31 31 AUTHORS: … … class CoveringDesign(SageObject): (this hunk was shorter than expected) 452 452 453 453 def best_known_covering_design_www(v, k, t, verbose=False): 454 454 r""" 455 Gives the best known `(v,k,t)` covering design, using the database 456 available at `<https://math.ccrwest.org/cover.html>`_ 455 Return the best known `(v, k, t)` covering design from an online database. 456 457 This uses the La Jolla Covering Repository, a database 458 available at `<http://ljcr.dmgordon.org/cover.html>`_ 457 459 458 460 INPUT: … … def best_known_covering_design_www(v, k, t, verbose=False): 488 490 """ 489 491 # import compatible with py2 and py3 490 492 from six.moves.urllib.request import urlopen 491 493 from sage.cpython.string import bytes_to_str 492 494 from sage.misc.sage_eval import sage_eval 493 495 494 496 v = int(v) … … def best_known_covering_design_www(v, k, t, verbose=False): 497 499 498 500 param = ("?v=%s&k=%s&t=%s"%(v,k,t)) 499 501 500 url = "http s://math.ccrwest.org/cover/get_cover.php"+param502 url = "http://ljcr.dmgordon.org/cover/get_cover.php" + param 501 503 if verbose: 502 504 print("Looking up the bounds at %s" % url) 503 f = urlopen(url) 504 s = f.read() 505 f.close() 505 with urlopen(url) as f: 506 s = bytes_to_str(f.read()) 506 507 507 508 if 'covering not in database' in s: #not found 508 509 str = "no (%d,%d,%d) covering design in database\n"%(v,k,t)
I'll propose a branch if Dan Gordon confirms this about get_cover.php
.
comment:14 Changed 2 months ago by
Dan Gordon was able to get rid of the extra initial \n\n<html>\n<body>\n
.
We're almost there, but one thing puzzles me about sage t
.
With the following code in src/sage/combinat/designs/covering_design.py
def best_known_covering_design_www(v, k, t, verbose=False): r""" Return the best known `(v, k, t)` covering design from an online database. This uses the La Jolla Covering Repository, a database available at `<http://ljcr.dmgordon.org/cover.html>`_ INPUT:  ``v``  integer, the size of the point set for the design  ``k``  integer, the number of points per block  ``t``  integer, the size of sets covered by the blocks  ``verbose``  bool (default: ``False``), print verbose message OUTPUT: A :class:`CoveringDesign` object representing the ``(v, k, t)``covering design with smallest number of blocks available in the database. EXAMPLES:: sage: from sage.combinat.designs.covering_design import ( ....: best_known_covering_design_www) # optional  internet sage: C = best_known_covering_design_www(7, 3, 2) # optional  internet sage: print(C) # optional  internet C(7,3,2) = 7 Method: lex covering Submitted on: 19961201 00:00:00 0 1 2 0 3 4 0 5 6 1 3 5 1 4 6 2 3 6 2 4 5 A ValueError is raised if the ``(v, k, t)`` parameters are not found in the database. """ # import compatible with py2 and py3 from six.moves.urllib.request import urlopen from sage.cpython.string import bytes_to_str from sage.misc.sage_eval import sage_eval v = int(v) k = int(k) t = int(t) param = "?v=%s&k=%s&t=%s" % (v, k, t) url = "http://ljcr.dmgordon.org/cover/get_cover.php" + param if verbose: print("Looking up the bounds at %s" % url) with urlopen(url) as f: s = bytes_to_str(f.read()) if 'covering not in database' in s: # not found str = "no (%d, %d, %d) covering design in database\n" % (v, k, t) raise ValueError(str) return sage_eval(s)
the function now works manually, i.e. I can do
sage: from sage.combinat.designs.covering_design import ( ....: best_known_covering_design_www) sage: C = best_known_covering_design_www(7, 3, 2) sage: print(C) C(7, 3, 2) = 7 Method: lex covering Submitted on: 19961201 00:00:00 0 1 2 0 3 4 0 5 6 1 3 5 1 4 6 2 3 6 2 4 5
but, for some reason I cannot figure out, sage t
gives a NameError
saying
name 'best_known_covering_design_www' is not defined
:
$ sage t optional=internet src/sage/combinat/designs/covering_design.py Running doctests with ID 20190308212922a6581694. Git branch: t26592coveringdesignswww Using optional=internet Doctesting 1 file. sage t warnlong 81.7 src/sage/combinat/designs/covering_design.py ********************************************************************** File "src/sage/combinat/designs/covering_design.py", line 514, in sage.combinat.designs.covering_design.best_known_covering_design_www Failed example: C = best_known_covering_design_www(7, 3, 2) # optional  internet Exception raised: Traceback (most recent call last): File "/opt/s/sage/local/lib/python3.6/sitepackages/sage/doctest/forker.py", line 671, in _run self.compile_and_execute(example, compiler, test.globs) File "/opt/s/sage/local/lib/python3.6/sitepackages/sage/doctest/forker.py", line 1095, in compile_and_execute exec(compiled, globs) File "<doctest sage.combinat.designs.covering_design.best_known_covering_design_www[0]>", line 1, in <module> C = best_known_covering_design_www(Integer(7), Integer(3), Integer(2)) # optional  internet NameError: name 'best_known_covering_design_www' is not defined ********************************************************************** File "src/sage/combinat/designs/covering_design.py", line 515, in sage.combinat.designs.covering_design.best_known_covering_design_www Failed example: print(C) # optional  internet Exception raised: Traceback (most recent call last): File "/opt/s/sage/local/lib/python3.6/sitepackages/sage/doctest/forker.py", line 671, in _run self.compile_and_execute(example, compiler, test.globs) File "/opt/s/sage/local/lib/python3.6/sitepackages/sage/doctest/forker.py", line 1095, in compile_and_execute exec(compiled, globs) File "<doctest sage.combinat.designs.covering_design.best_known_covering_design_www[1]>", line 1, in <module> print(C) # optional  internet NameError: name 'C' is not defined ********************************************************************** 1 item had failures: 2 of 3 in sage.combinat.designs.covering_design.best_known_covering_design_www [2 tests, 2 failures, 0.01 s]  sage t warnlong 81.7 src/sage/combinat/designs/covering_design.py # 2 doctests failed  Total time for all tests: 0.1 seconds cpu time: 0.0 seconds cumulative wall time: 0.0 seconds
Can somebody enlighten me?
comment:15 Changed 2 months ago by
 do not break the import line
 OR tag the first line of the import
 OR use optional=sage,internet ?
comment:16 Changed 2 months ago by
@slelievre with your patch and python 2 i obtain the following:
sage: best_known_covering_design_www(7, 3, 2)  AttributeError Traceback (most recent call last) <ipythoninput2a930c6c24a1d> in <module>() > 1 best_known_covering_design_www(Integer(7), Integer(3), Integer(2)) <ipythoninput1598f13fbcc94> in best_known_covering_design_www(v, k, t, verbose) 55 if verbose: 56 print("Looking up the bounds at %s" % url) > 57 with urlopen(url) as f: 58 s = bytes_to_str(f.read()) 59 AttributeError: addinfourl instance has no attribute '__exit__'
comment:17 Changed 2 months ago by
 Branch set to u/vklein/26592
comment:18 Changed 2 months ago by
 Commit set to 27eeb10c43f0a090de107ebd5f427ad26de3bf53
The py2 and py3 tests pass with branch u/vklein/26592.
I will now look for a way to avoid calling sage_eval
on a internet given result.
It really looks like an highway for code injection to me.
New commits:
27eeb10  Trac #26592: apply and fix slelievre's patch ...

comment:19 Changed 2 months ago by
Constructing "manually" the CoveringDesign
is not that easy because his __init__
function has eleven named parameters with default values, that mean there is a lot of potential string format that get_cover.php
could return.
Do we know if get_cover.php always return a string in the form "CoveringDesign?(<all init parameters positionally>)" ?
comment:20 Changed 2 months ago by
 Cc zerline added
comment:21 Changed 2 months ago by
 Status changed from new to needs_info
comment:22 Changed 2 months ago by
 Milestone changed from sage8.7 to sage8.8
Ticket retargeted after milestone closed (if you don't believe this ticket is appropriate for the Sage 8.8 release please retarget manually)
comment:23 Changed 5 weeks ago by
 Branch changed from u/vklein/26592 to u/slelievre/26592
comment:24 Changed 5 weeks ago by
 Commit changed from 27eeb10c43f0a090de107ebd5f427ad26de3bf53 to e863721bac6eca92b83d17a220692c127dffc88d
 Status changed from needs_info to needs_review
New branch based on Sage 8.8.beta2.
A first commit does pep8 reformatting + updating urls.
The second commit has the actual bytes_to_str
fix in
best_known_covering_design_www
and a minor
improvement to is_covering
.
Please review.
New commits:
a1437e5  26592: Fix urls and do a round of pep8 in covering_designs.py

e863721  26592: Fix py3 bytes_to_str + minor speedup

comment:25 Changed 5 weeks ago by
There is no point in these being inline imports:
from six.moves.urllib.request import urlopen  + from sage.cpython.string import bytes_to_str
Those modules are always loaded by Sage so they might as well go at the modulelevel.
comment:26 Changed 5 weeks ago by
 Commit changed from e863721bac6eca92b83d17a220692c127dffc88d to a69f4ecdf33625f037bbad1375c6b3f24a5b5f12
Branch pushed to git repo; I updated commit sha1. New commits:
a69f4ec  26592: Move imports to beginning of file

comment:27 Changed 5 weeks ago by
Like this?
comment:28 followup: ↓ 29 Changed 3 weeks ago by
This line:
https://drive.google.com/file/d/0B6s9_JNV1EjtUFd4MkhBc0hSdVU/view
is not something that we should link to.
Otherwise, looks good. In the future, please avoid doing large scale pep8 cleanup at the same time as serious changes.
comment:29 in reply to: ↑ 28 ; followup: ↓ 31 Changed 3 weeks ago by
Replying to chapoton:
This line:
https://drive.google.com/file/d/0B6s9_JNV1EjtUFd4MkhBc0hSdVU/viewis not something that we should link to.
Other options I can see are the following:
 Dan Gordon's publications page: https://www.dmgordon.org/Publications/
 the CRC Press page for the book: https://www.crcpress.com/HandbookofCombinatorialDesignsSecondEdition/ColbournDinitz/p/book/9781584885061
 one of the editors' page for the book: http://www.cems.uvm.edu/~jdinitz/hcd.html
Otherwise, looks good. In the future, please avoid doing large scale pep8 cleanup at the same time as serious changes.
Sorry about that, I got slightly carried away. I tried to use a different commit for each type of changes, but probably could have done a better job of that, or used different tickets altogether. Thanks for reviewing anyway and for the advice for the future.
comment:30 Changed 3 weeks ago by
Or we could link to the copy archived at the Internet Archive's Wayback Machine:
comment:31 in reply to: ↑ 29 Changed 3 weeks ago by
Replying to slelievre:
Replying to chapoton:
This line:
https://drive.google.com/file/d/0B6s9_JNV1EjtUFd4MkhBc0hSdVU/viewis not something that we should link to.
Other options I can see are the following:
 Dan Gordon's publications page: https://www.dmgordon.org/Publications/
Yes, this one is better. One should also give the title (Coverings, chapter 1 of whatever)
comment:32 Changed 3 weeks ago by
Having my papers on google drive was the last part of my website that I hadn't updated. I've moved them now, so that paper can now be linked to at https://www.dmgordon.org/papers/hcd.pdf.
comment:33 Changed 3 weeks ago by
 Commit changed from a69f4ecdf33625f037bbad1375c6b3f24a5b5f12 to 1f3afa8ed60c5ab665a2d7ed3421323fe21dd6c1
Branch pushed to git repo; I updated commit sha1. New commits:
1f3afa8  Update GordonStinson bibliographic reference

comment:34 Changed 3 weeks ago by
Updated now, please review.
comment:35 Changed 3 weeks ago by
 Reviewers set to Frédéric Chapoton
 Status changed from needs_review to positive_review
ok, thx
comment:36 Changed 2 weeks ago by
 Branch changed from u/slelievre/26592 to 1f3afa8ed60c5ab665a2d7ed3421323fe21dd6c1
 Resolution set to fixed
 Status changed from positive_review to closed
comment:37 Changed 8 days ago by
 Commit 1f3afa8ed60c5ab665a2d7ed3421323fe21dd6c1 deleted
With 8.8.beta5, I get:
sage: C = designs.best_known_covering_design_from_LJCR(7, 3, 2)  AttributeError Traceback (most recent call last) <ipythoninput1a3d9f9e592f1> in <module>() > 1 C = designs.best_known_covering_design_from_LJCR(Integer(7), Integer(3), Integer(2)) /home/slabbe/GitBox/sage/local/lib/python2.7/sitepackages/sage/combinat/designs/covering_design.pyc in best_known_covering_design_www(v, k, t, verbose) 525 if verbose: 526 print("Looking up the bounds at %s" % url) > 527 with urlopen(url) as f: 528 s = bytes_to_str(f.read()) 529 if 'covering not in database' in s: # not found AttributeError: addinfourl instance has no attribute '__exit__'
Were you obtaining the same issue with this branch?
comment:38 Changed 8 days ago by
I think so with urelopen(url) as...
syntax has been introduced with commit e863721
.
It should be avoided (see comment:16)
comment:39 Changed 8 days ago by
Open a new ticket to fix that #27821
The whole https://math.ccrwest.org was down for a few days. It's back up now.