qiita_test_install #805

antgonza · 2015-01-20T14:32:08Z

Initial commit for discussion during meeting.

squirrelo · 2015-01-20T20:21:36Z

scripts/qiita_test_install

+    option_parser, opts, args = parse_command_line_parameters(**script_info)
+
+    if opts.haiku:
+        print "Qiita provides insight\nmicrobial in nature\nto ecology"


6-7-5, should be 5-7-5 🗼

A haiku doesn't actually have an enforced syllabic structure, but the
abused English form does. It is 5-7-5 though for that form though
On Jan 20, 2015 9:21 PM, "Joshua Shorenstein" notifications@github.com
wrote:

In scripts/qiita_test_install
#805 (diff):

test.assertTrue(exists(fp), "%s set to an invalid file path: %s" %

(variable, fp))

modes = {R_OK: "readable",

W_OK: "writable",

X_OK: "executable"}

test if file readable

test.assertTrue(access(fp, access_var),

"%s is not %s: %s" % (variable, modes[access_var], fp))

+def main():

option_parser, opts, args = parse_command_line_parameters(**script_info)

if opts.haiku:

print "Qiita provides insight\nmicrobial in nature\nto ecology"

6-7-6, should be 5-7-5 [image: 🗼]

—
Reply to this email directly or view it on GitHub
https://github.com/biocore/qiita/pull/805/files#r23252284.

oh noes, the secret feature!

On (Jan-20-15|21:28), Daniel McDonald wrote:

test.assertTrue(exists(fp), "%s set to an invalid file path: %s" %

(variable, fp))

modes = {R_OK: "readable",

W_OK: "writable",

X_OK: "executable"}

test if file readable

test.assertTrue(access(fp, access_var),

"%s is not %s: %s" % (variable, modes[access_var], fp))

+def main():

option_parser, opts, args = parse_command_line_parameters(**script_info)

if opts.haiku:

print "Qiita provides insight\nmicrobial in nature\nto ecology"

A haiku doesn't actually have an enforced syllabic structure, but the
abused English form does. It is 5-7-5 though for that form though
On Jan 20, 2015 9:21 PM, "Joshua Shorenstein" notifications@github.com
wrote:

In scripts/qiita_test_install
#805 (diff):

test.assertTrue(exists(fp), "%s set to an invalid file path: %s" %

(variable, fp))

modes = {R_OK: "readable",

W_OK: "writable",

X_OK: "executable"}

test if file readable

test.assertTrue(access(fp, access_var),

"%s is not %s: %s" % (variable, modes[access_var], fp))

+def main():

option_parser, opts, args = parse_command_line_parameters(**script_info)

if opts.haiku:

print "Qiita provides insight\nmicrobial in nature\nto ecology"

6-7-6, should be 5-7-5 [image: 🗼]

—
Reply to this email directly or view it on GitHub
https://github.com/biocore/qiita/pull/805/files#r23252284.

Reply to this email directly or view it on GitHub:
https://github.com/biocore/qiita/pull/805/files#r23278780

ElDeveloper · 2015-01-20T22:25:10Z

Would be nice to

Whether or not this is a test environment.
Check if we can send e-mail with the current config file.
Path of the configuration file being used.
Postgres is running.
Redis is running.
IPython clusters are running and submittable.
Whether or not there are EBI credentials.
Whether or not there are VAMPS credentials.

coveralls · 2015-01-22T14:50:46Z

Coverage remained the same at 78.48% when pulling f9df8db on antgonza:testing-qiita-install into 3c79e6b on biocore:master.

coveralls · 2015-01-22T15:23:34Z

Coverage remained the same at 78.48% when pulling 64d8eee on antgonza:testing-qiita-install into 3c79e6b on biocore:master.

antgonza · 2015-01-22T15:23:56Z

This is ready for review.

squirrelo · 2015-01-22T19:22:03Z

.travis.yml

  # we need to run the test suite from setup.py for coveralls to grab the info
  # - coverage run setup.py test
  # - coverage report -m
+  - qiita_test_install


Should this be moved up to second thing called in the script? That way we have all the info before tests are run, so we can fix things as they error if needed.

Could be, no preference.

Probably better, since if anything fails we won't have that information for diagnosis.

squirrelo · 2015-01-22T19:37:41Z

Traceback (most recent call last):
File "./scripts/qiita_test_install", line 396, in
main()
File "./scripts/qiita_test_install", line 360, in main
_, _, ar = submit_nouser(sum, 1, 2)
ValueError: need more than 2 values to unpack

antgonza · 2015-01-22T19:42:24Z

How do I reproduce that?

squirrelo · 2015-01-22T19:42:46Z

I just ran it and that happened.

antgonza · 2015-01-22T19:44:34Z

Which version of moi are you using?

squirrelo · 2015-01-22T19:52:05Z

Lets use the script :)

System information
==================

         Platform:  darwin
   Python version:  2.7.6 (default, Sep  9 2014, 15:04:36)  [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)]
Python executable:  /Users/jshorens/.virtualenvs/qiita/bin/python

Dependency versions
===================

     click library version: 3.3
    future library version: 0.14.3
     numpy library version: 1.9.1
    pandas library version: 0.15.2
   tornado library version: 3.1.1
     redis library version: 2.10.3
    bcrypt library version: 1.0.2
 pyparsing library version: 2.0.3
  networkX library version: 1.9.1
   WTForms library version: 2.0.1
     qiime library version: 1.9.0-rc1, for more info use print_qiime_config.py
      mock library version: 1.0.1
       MOI library version: 0.1.0
      MOI config file path: /Users/jshorens/moi_config.txt
   IPython library version: 2.3.1
  psycopg2 library version: 2.5.4 (dt dec pq3 ext)
Qiita core library version: 0.0.1-dev
  Qiita db library version: 0.0.1-dev
 Qiita pet library version: 0.0.1-dev
Qiita ware library version: 0.0.1-dev
Traceback (most recent call last):
  File "./scripts/qiita_test_install", line 396, in <module>
    main()
  File "./scripts/qiita_test_install", line 360, in main
    _, _, ar = submit_nouser(sum, 1, 2)
ValueError: need more than 2 values to unpack

squirrelo · 2015-01-22T20:06:20Z

scripts/qiita_test_install

+        print "%*s:\t%s" % (max_len, v[0], v[1])
+
+    qiita_config = ConfigurationManager()
+    try:


This needs an exists test after the try-except to make sure the file actually exists at the path given

squirrelo · 2015-01-22T20:07:25Z

scripts/qiita_test_install

+        else:
+            ipython_running = False
+    except e:
+        print e


This needs something better here than just a print of the error, for user information sake. This is what I am getting with the paste in the main discussion thread.

Agree, that was left by mistake.

…g-qiita-install

coveralls · 2015-01-25T06:35:12Z

Coverage remained the same at 78.55% when pulling 6cef34d on antgonza:testing-qiita-install into 01225be on biocore:master.

antgonza · 2015-01-30T18:43:42Z

@squirrelo @ElDeveloper any other comments? Is this ready for merge?

squirrelo · 2015-01-30T19:01:30Z

scripts/qiita_test_install

+            ipython_running = True
+        else:
+            ipython_running = False
+    except e:


Line 365 is still thorwing a traceback and not showing the rest on my computer. Perhaps this should be

except Exception as e:

or just

except:

since we don't actually need e.

Good point, done!

coveralls · 2015-02-01T06:10:53Z

Coverage increased (+0.01%) to 78.56% when pulling 9c0c45c on antgonza:testing-qiita-install into 01225be on biocore:master.

qiita_test_install

ElDeveloper · 2015-02-03T19:48:21Z

scripts/qiita_test_install

+missing_deps_errors = []
+missing_deps_warnings = []
+
+try:


I know exec is usually frowned upon, but what about replacing these few lines with something like this:

for dependency in ['wtforms', 'networkx']: try: exec 'from {0} import __version__ as {0}_lib_version'.format(dependency) except ImportError: missing_deps_warnings.append((e, 'Some message')) exec "{0}_lib_version = 'Not Installed'"

what about using importlib?

That would have also worked, though note that this PR is now merged, so
we may want to open a separate issue about this.

On (Feb-03-15|13:06), Daniel McDonald wrote:

'Qiita Installation Guide: '

'https://github.com/biocore/qiita/blob/master/INSTALL.md')

+extra_info = (core_dependency_missing_msg + '. It is also possible that you '

'have an old version of this package, if so, please update to '

'the latest.')

+dependency_missing_msg = (

'"%s" is missing but this is not a core requirement, for more '

'information see the Qiita Installation Guide: '

'https://github.com/biocore/qiita/blob/master/INSTALL.md')

+missing_deps_errors = []
+missing_deps_warnings = []
+
+try:

what about using importlib?

Reply to this email directly or view it on GitHub:
https://github.com/biocore/qiita/pull/805/files#r24039719

ElDeveloper · 2015-02-03T19:50:29Z

Oh ... ok ;l

antgonza added 2 commits January 20, 2015 07:31

initial push for discussion

569a576

some fixes and updates

b372581

squirrelo reviewed Jan 20, 2015
View reviewed changes

antgonza added 13 commits January 21, 2015 13:56

should be ready for review

60eeec1

fixing error in variable name

35234d8

fixing errors

65e702f

to figure out why we can not find click

0bdc87f

assuring click version

0944c9c

click 1

a6c4a79

fixing click pip install

f5fea06

rm click from conda

09d3322

click 2

2210687

click 3

ddadbb6

click 4

14d5b14

click 5

a515ca8

click 6

f9df8db

finally!

64d8eee

antgonza changed the title ~~WIP: initial push for discussion~~ qiita_test_install Jan 22, 2015

squirrelo reviewed Jan 22, 2015
View reviewed changes

antgonza added 3 commits January 24, 2015 10:57

Merge branch 'master' of https://github.com/biocore/qiita into testin…

2dcaf62

…g-qiita-install

addressing @squirrelo comments

4e49d45

fixing flake8

6cef34d

squirrelo reviewed Jan 30, 2015
View reviewed changes

adding @squirrelo comment

9c0c45c

josenavas added a commit that referenced this pull request Feb 3, 2015

Merge pull request #805 from antgonza/testing-qiita-install

c8d3767

qiita_test_install

josenavas merged commit c8d3767 into qiita-spots:master Feb 3, 2015

ElDeveloper reviewed Feb 3, 2015
View reviewed changes

This was referenced Feb 10, 2015

script to check for dependencies and to start all services #14

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print_qiita_config.py #193

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qiita_test_install #805

qiita_test_install #805

antgonza commented Jan 20, 2015

squirrelo Jan 20, 2015

wasade Jan 21, 2015

test if file readable

ElDeveloper Jan 21, 2015

test if file readable

test if file readable

ElDeveloper commented Jan 20, 2015

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coveralls commented Jan 22, 2015

antgonza commented Jan 22, 2015

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antgonza Jan 22, 2015

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ElDeveloper commented Feb 3, 2015

qiita_test_install #805

qiita_test_install #805

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test if file readable

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ElDeveloper commented Feb 3, 2015