Unable to run Waldo in Ubuntu 12.04.5

[icaoberg]

I am trying to build the database as well as deploy Waldo. I am trying to do it in

icaoberg@lanec1web3a:~/waldo/src/waldo$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.5 LTS
Release:    12.04
Codename:   precise

In the past I succeeded in doing the same process in an Ubuntu 14.04.1 VM. Now I get the following error.

icaoberg@lanec1web3a:~/waldo/src/waldo$ ./install.sh 
Traceback (most recent call last):
  File "./bin/update-waldo", line 13, in <module>
    import waldo.locate.load
  File "/usr/local/lib/python2.7/dist-packages/waldo-0.1-py2.7.egg/waldo/locate/__init__.py", line 6, in <module>
    from .retrieve import \
  File "/usr/local/lib/python2.7/dist-packages/waldo-0.1-py2.7.egg/waldo/locate/retrieve.py", line 9, in <module>
    from waldo.locate.models import Entry
  File "/usr/local/lib/python2.7/dist-packages/waldo-0.1-py2.7.egg/waldo/locate/models.py", line 29, in <module>
    class Isoform(Base):
  File "/usr/local/lib/python2.7/dist-packages/waldo-0.1-py2.7.egg/waldo/locate/models.py", line 31, in Isoform
    id = Column(Integer(11), primary_key=True)
TypeError: object.__new__() takes no parameters

Any feedback will be appreciated.

[magsol]

Are you using the latest version of waldo from the repository? That particular file where the error is originating hasn't been modified in over two years.

[magsol]

Actually, I'm curious if the Integer(11) constructor was recently removed from sqlalchemy. That particular invocation doesn't appear in the mgi, go, goslim, or uniprot models, all of which are invoked before locate, which is where the failure is occurring.

Luis, you would know the state of affairs in sqlalchemy better than I would--I could submit a PR simply doing a "s / Integer(11) / Integer / g", but I'm curious if that's even the right problem.

Ivan, what version of sqlalchemy are you using?

[icaoberg]

In the production machine

In [4]: sqlalchemy.__version__
Out[4]: '0.9.7'

in the virtual machine

[icaoberg]

Given @magsol comment I ran the same code in the production system using virtualenv with sqlalchemy version 0.8.4 and it is working so far

And I was using the latest version of the code that included the merge https://github.com/luispedro/waldo/commit/2c364ffb9fa1202109eccdef240214766a4984f0

[magsol]

I believe locate is built after uniprot so we'll know soon.

iPhone'd

On Sep 4, 2014, at 14:38, "Ivan E. Cao-Berg" notifications@github.com wrote:

Given @magsol comment I ran the same code in the production system using virtualenv with sqlalchemy version 0.8.4 and it is working so far

— Reply to this email directly or view it on GitHub.

[icaoberg]

@magsol the issue was resolved by using sqlalchemy version 0.8.4 instead of the latest.

It builds the database

It loads the webserver (for my user I have no tried doing it system wide)

And a search returns results

[magsol]

Clearly a versioning issue. How do you want to handle it? Should we fix the version incompatibility, or file it away for later and stick with 0.8.4?

[icaoberg]

Whatever works for you. If I can have it running with 0.8.4 it is fine with me since the only service I have in the production server using sqlalchemy is waldo. I only care that the working version matches the version you will put out for the paper.

[magsol]

Works for me; let's stick with 0.8.4 then.

iPhone'd

On Sep 4, 2014, at 17:26, "Ivan E. Cao-Berg" notifications@github.com wrote:

Whatever works for you. If I can have it running with 0.8.4 it is fine with me since the only service I have in the production server using sqlalchemy is waldo. I only care that the working version matches the version you will put out for the paper.

— Reply to this email directly or view it on GitHub.

[icaoberg]

Sticking with sqlalchemy version 0.8.4