Dev

CHANGELOG.rst

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+=========
+CHANGELOG
+=========
+
+Version 0.1.0
+-------------
+* Created module to sync samples from a MiSeq SampleSheet
+* Created module (autosync.py) to poll and detect finished runs

miseqpipeline/miseq_sync.py

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+
+
+def sync(src, ngsdata):
+    pass

redmine.travis.yml

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+# Redmine runs tests on own continuous integration server.
+# http://www.redmine.org/projects/redmine/wiki/Continuous_integration
+# You can also run tests on your environment.
+language: ruby
+rvm:
+  - 1.9.3
+  - 2.0
+  - 2.1
+  - 2.2
+  - jruby
+env:
+  - "SUITE=units       DB=postgresql"
+  - "SUITE=functionals DB=postgresql"
+  - "SUITE=integration DB=postgresql"
+  - "SUITE=ui          DB=postgresql"
+  - "SUITE=units       DB=mysql-5.5"
+  - "SUITE=functionals DB=mysql-5.5"
+  - "SUITE=integration DB=mysql-5.5"
+  - "SUITE=ui          DB=mysql-5.5"
+  - "SUITE=units       DB=mysql-5.6"
+  - "SUITE=functionals DB=mysql-5.6"
+  - "SUITE=integration DB=mysql-5.6"
+  - "SUITE=ui          DB=mysql-5.6"
+  - "SUITE=units       DB=mysql-5.7-dmr"
+  - "SUITE=functionals DB=mysql-5.7-dmr"
+  - "SUITE=integration DB=mysql-5.7-dmr"
+  - "SUITE=ui          DB=mysql-5.7-dmr"
+  - "SUITE=units       DB=mariadb-5.5"
+  - "SUITE=functionals DB=mariadb-5.5"
+  - "SUITE=integration DB=mariadb-5.5"
+  - "SUITE=ui          DB=mariadb-5.5"
+  - "SUITE=units       DB=mariadb-10.0"
+  - "SUITE=functionals DB=mariadb-10.0"
+  - "SUITE=integration DB=mariadb-10.0"
+  - "SUITE=ui          DB=mariadb-10.0"
+  - "SUITE=units       DB=sqlite3"
+  - "SUITE=functionals DB=sqlite3"
+  - "SUITE=integration DB=sqlite3"
+  - "SUITE=ui          DB=sqlite3"
+matrix:
+  allow_failures:
+    # SCM tests fail randomly due to IO.popen().
+    # http://www.redmine.org/issues/19091
+    # https://github.com/jruby/jruby/issues/779
+    - rvm: jruby
+    # http://www.redmine.org/issues/17460
+    # http://www.redmine.org/issues/19344
+    - env: "SUITE=units       DB=mysql-5.6"
+    - env: "SUITE=units       DB=mysql-5.7-dmr"
+    - env: "SUITE=units       DB=mariadb-5.5"
+    - env: "SUITE=units       DB=mariadb-10.0"
+before_install:
+  - "sudo apt-get update -qq"
+  - "sudo apt-get --no-install-recommends install bzr cvs git mercurial subversion"
+  - if [[ $DB =~ (mariadb|mysql-5\.[67]) ]] ;
+    then
+      sudo service mysql stop ;
+      sudo apt-get install python-software-properties ;
+      if [[ $DB =~ mariadb ]] ;
+      then
+        sudo apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 0xcbcb082a1bb943db ;
+        MARIADB_VER=`echo $DB | sed -e 's/mariadb-//'` ;
+        sudo add-apt-repository ''"deb http://ftp.osuosl.org/pub/mariadb/repo/${MARIADB_VER}/ubuntu precise main"'' ;
+        sudo apt-get update ;
+        sudo DEBIAN_FRONTEND=noninteractive apt-get -q --yes --force-yes -f --option DPkg::Options::=--force-confnew install mariadb-server ;
+        sudo apt-get install libmariadbd-dev ;
+      else
+        echo mysql-apt-config mysql-apt-config/enable-repo select $DB | sudo debconf-set-selections ;
+        wget http://dev.mysql.com/get/mysql-apt-config_0.2.1-1ubuntu12.04_all.deb ;
+        sudo dpkg --install mysql-apt-config_0.2.1-1ubuntu12.04_all.deb ;
+        sudo apt-get update -q ;
+        sudo apt-get install -q -y -o Dpkg::Options::=--force-confnew mysql-server ;
+      fi
+    fi
+script:
+  - export DATABASE_ADAPTER=${DB}
+  - "SCMS=bazaar,cvs,subversion,git,mercurial,filesystem"
+  - "export SCMS"
+  - "git --version"
+  - "bundle install"
+  - "RUN_ON_NOT_OFFICIAL='' RUBY_VER=1.9 BRANCH=trunk bundle exec rake config/database.yml"
+  - "bundle install"
+  - "bundle exec rake ci:setup"
+  - phantomjs --webdriver 4444 &
+  - JRUBY_OPTS=-J-Xmx1024m bundle exec rake test:${SUITE}

redsample.config.default

@@ -0,0 +1,48 @@
+# web url to your redmine instance
+siteurl: http://demo.redmine.org
+# Your api key located under My Account
+apikey: fromyouraccount
+# The id of the project that will contain your samples
+sampleprojectid: RedsampleTest
+# The id of the tracker that will be assigned to your samples
+# has to be the id not the name
+sampletrackerid: 1
+
+#If there isn't an API Key use these instead
+username: averagehat
+password: vdbwrair
+
+runtrackerid: 3
+runprojectid: RedSampleRun
+runnameid: 4
+
+destinationpath: /home/EIDRUdata/NGSData
+runbasepath: /Instruments/MiSeq
+
+samplefields:
+- Needs Review
+- Pathogen
+- SRNum
+- CollectionLocation
+- Collaborator
+- Collection Date
+- Sample Type
+- Accession
+- Genbank Ready
+- PR Name
+- Synced Date
+- Media
+- Received
+- Study
+- InfA Ct
+- InfB Ct
+- RNaseP Ct
+- swInfA Ct
+- swH1 Ct
+- AH3 Ct 
+# Currently ignored
+runfields: 
+- Platform
+- Run Name
+- SampleList
+- SamplesSynced

redsample.config.example

@@ -6,4 +6,35 @@ apikey: fromyouraccount
 sampleprojectid: samples
 # The id of the tracker that will be assigned to your samples
 # has to be the id not the name
-sampletrackerid: 1
+sampletrackerid: 1 
+# for automatically creating the runs:
+runtrackerid: 3
+runprojectid: 4
+
+samplefields:
+- Needs Review
+- Pathogen
+- SRNum
+- CollectionLocation
+- Collaborator
+- Collection Date
+- Sample Type
+- Accession
+- Genbank Ready
+- PR Name
+- Synced Date
+- Media
+- Received
+- Study
+- InfA Ct
+- InfB Ct
+- RNaseP Ct
+- swInfA Ct
+- swH1 Ct
+- AH3 Ct 
+# Currently ignored
+runfields: 
+- Platform
+- Run Name
+- SampleList
+- SamplesSynced

redsample.default

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+# web url to your redmine instance
+siteurl: https://www.example.com
+# Your api key located under My Account
+apikey: fromyouraccount
+# The id of the project that will contain your samples
+sampleprojectid: samples
+# The id of the tracker that will be assigned to your samples
+# has to be the id not the name
+sampletrackerid: 1

redsample/autosync.py

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+from __future__ import print_function
+import time
+from miseqpipeline import miseq_sync
+from functools import partial
+import os
+import sys
+from outline import get_run_name, get_my_new_runs, update_percent_done, config, compose
+'''
+ Get run name from issue
+ import and run miseq_sync
+ skip resample step
+ skip rename step
+ update run issue
+ '''
+
+MAKE_RUN_PATH = partial(os.path.join, config['runbasepath'])
+_sync = partial(miseq_sync.sync, ngsdata=config['destinationpath'])
+copy_samples = compose(_sync, MAKE_RUN_PATH)
+copy_runs_samples = compose(copy_samples, get_run_name)
+
+def poll():
+    ''' Look for new run_issues assigned to "me" as defined in config file.'''
+    #TODO: use a custom field techs won't use instead of progress bar.
+    new_runs = get_my_new_runs()
+    if not new_runs:
+        print("run issues not found at time: {0}".format(time.ctime()))
+        sys.exit(0)
+    else:
+        print("New run issues found at time: {0},  {1}".format(time.ctime(), new_runs))
+        return new_runs
+
+def start():
+    ''' Poll for assigned issues, and miseq_sync them  if found.'''
+    run_issues = poll()
+    assert len(run_issues) == 1, "More than one new run found, something went wrong."
+    mark_as_started = partial(update_percent_done, value=50)
+    map(mark_as_started, run_issues)
+    #pool.map
+    map(copy_runs_samples, run_issues)
+    mark_as_finished = partial(update_percent_done, value=100)
+    map(mark_as_finished, run_issues)
+    return run_issues
+
+def main():
+    start()

redsample/config.py

@@ -1,6 +1,7 @@
 import os.path
 import yaml
 
+DEFAULT_PATH = './redsample.config.default'
 def load_config(configpath):
     '''
     Load yaml config from a path
@@ -13,8 +14,12 @@ def load_config(configpath):
 def load_user_config():
     '''
     Loads config from user home directory
-    
+
     :return: yaml dict
     '''
     p = os.path.join(os.path.expanduser('~/'), '.redsample.config')
     return load_config(p)
+
+def load_default():
+    return load_user_config() or load_config(DEFAULT_PATH)
+