Standard packaging for genologics

.gitignore

@@ -1,3 +1,2 @@
-site_*.py
 *.pyc
 *~

README.md

@@ -22,18 +22,37 @@ instance to the database.
 
 ### Installation
 
-The 'genologics' directory should be made accessible in your Python path,
-by whatever method suits your installation.
+```
+pip install genologics
+```
+
+or for the cutting edge version:
+
+```
+pip install https://github.com/SciLifeLab/genologics/tarball/master
+```
 
 ### Usage
 
-The client script imports the class Lims from the genologics.lims module,
-and instantiates it with the required arguments:
+The URL and credentials should be wrintten in a new file in any
+of those config files (ordered by preference):
+
+```
+$HOME/.genologicsrc, .genologicsrc, genologics.conf, genologics.cfg
+```
+
+or if installed system_wide:
 
-- Base URI of the server, including the port number, but excluding
-  the '/api/v1' segment of the path.
-- User name of the account on the server.
-- Password of the account on the server.
+```
+/etc/genologics.conf
+```
+
+```
+[genologics]
+BASEURI=https://yourlims.example.com:8443
+USERNAME=your_username
+PASSWORD=your_password
+```
 
 ### Example scripts
 
@@ -43,13 +62,9 @@ NOTE: The example files rely on specific entities and configurations
 on the server, and use base URI, user name and password, so to work
 for your server, all these must be reviewed and modified.
 
-### Caveats
-
-The interface has not been used much yet, so it is not properly debugged.
+### Known bugs 
 
-Known issues:
 - Artifact state is part of its URL (as a query parameter).
   It is not entirely clear how to deal with this in the Lims.cache:
   Currently, an artifact that has the current state may be represented
   by a URL that includes the state, and another that does not contain it.
-

examples/attach_delivery_report.py

@@ -0,0 +1,31 @@
+"""Python interface to GenoLogics LIMS via its REST API.
+
+Usage example: Attach customer delivery report to LIMS
+
+
+
+Roman Valls Guimera, Science for Life Laboratory, Stockholm, Sweden.
+"""
+
+import codecs
+from pprint import pprint
+from genologics.lims import *
+
+# Login parameters for connecting to a LIMS instance.
+from genologics.config import BASEURI, USERNAME, PASSWORD
+
+# Create the LIMS interface instance, and check the connection and version.
+lims = Lims(BASEURI, USERNAME, PASSWORD)
+lims.check_version()
+
+project = Project(lims, id="P193")
+
+print 'UDFs:'
+pprint(project.udf.items())
+
+print 'files:'
+for file in project.files:
+    print file.content_location
+
+project.udf['Delivery Report'] = "http://example.com/delivery_note.pdf"
+project.put()

examples/get_application.py

@@ -0,0 +1,26 @@
+"""Python interface to GenoLogics LIMS via its REST API.
+
+Usage example: Attach customer delivery report to LIMS
+
+
+
+Roman Valls Guimera, Science for Life Laboratory, Stockholm, Sweden.
+"""
+
+import codecs
+from pprint import pprint
+from genologics.lims import *
+
+# Login parameters for connecting to a LIMS instance.
+from genologics.config import BASEURI, USERNAME, PASSWORD
+
+# Create the LIMS interface instance, and check the connection and version.
+lims = Lims(BASEURI, USERNAME, PASSWORD)
+lims.check_version()
+
+project = Project(lims, id="P193")
+
+print 'UDFs:'
+pprint(project.udf.items())
+
+print project.udf['Application']

examples/get_artifacts.py

@@ -2,7 +2,7 @@
 
 Usage example: Get artifacts and artifact info.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
@@ -12,8 +12,7 @@
 from genologics.lims import Lims
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)

examples/get_containers.py

@@ -2,7 +2,7 @@
 
 Usage example: Get some containers.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
@@ -12,8 +12,7 @@
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -39,3 +38,17 @@
 
 containertype = container.type
 print containertype, containertype.name, containertype.x_dimension, containertype.y_dimension
+
+
+
+containers = lims.get_containers(type='Illumina Flow Cell',state='Populated')
+for container in containers:
+	print container.name
+	print container.id
+	print container.placements.keys()
+	arts=lims.get_artifacts(containername=container.name)
+	for art in arts:
+		print art.name
+		print art.type
+		print art.udf.items()
+		print art.parent_process.type.name

examples/get_labs.py

@@ -2,7 +2,7 @@
 
 Usage example: Get labs and lab info.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
@@ -11,8 +11,7 @@
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)

examples/get_processes.py

@@ -2,16 +2,15 @@
 
 Usage example: Get some processes.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)

examples/get_projects.py

@@ -2,7 +2,7 @@
 
 Usage example: Get some projects.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
@@ -12,8 +12,7 @@
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)
@@ -29,7 +28,7 @@
 print len(projects), 'projects opened since', day
 
 # Get the project with the specified LIMS id, and print some info.
-project = Project(lims, id='KRA61')
+project = Project(lims, id='P193')
 print project, project.name, project.open_date, project.close_date
 
 print '    UDFs:'
@@ -45,10 +44,6 @@
         value = codecs.encode(value, 'UTF-8')
     print ' ', key, '=', value
 
-print '    notes:'
-for note in project.notes:
-    print note.uri, note.content
-
 print '    files:'
 for file in project.files:
     print file.id

examples/get_samples.py

@@ -2,16 +2,16 @@
 
 Usage examples: Get some samples, and sample info.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)

examples/get_samples2.py

@@ -2,14 +2,14 @@
 
 Usage examples: Get some samples, and sample info.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
 from genologics.lims import *
 
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 lims = Lims(BASEURI, USERNAME, PASSWORD)
 lims.check_version()
 

examples/set_project_queued.py

@@ -2,7 +2,7 @@
 
 Example usage: Set the UDF 'Queued' of a project.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
@@ -12,8 +12,7 @@
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)

examples/set_sample_name.py

@@ -2,16 +2,15 @@
 
 Example usage: Set the name and a UDF of a sample.
 
-NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
+
 
 Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
 """
 
 from genologics.lims import *
 
 # Login parameters for connecting to a LIMS instance.
-# NOTE: Modify according to your setup.
-from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
+from genologics.config import BASEURI, USERNAME, PASSWORD
 
 # Create the LIMS interface instance, and check the connection and version.
 lims = Lims(BASEURI, USERNAME, PASSWORD)

genologics/config.py

@@ -0,0 +1,22 @@
+import os
+import sys
+import warnings
+
+import ConfigParser
+
+config = ConfigParser.SafeConfigParser()
+try:
+	conf_file = config.read([os.path.expanduser('~/.genologicsrc'), '.genologicsrc',
+				'genologics.conf', 'genologics.cfg', '/etc/genologics.conf'])
+
+	# First config file found wins
+	config.readfp(open(conf_file[0]))
+
+	BASEURI = config.get('genologics', 'BASEURI').rstrip()
+	USERNAME = config.get('genologics', 'USERNAME').rstrip()
+	PASSWORD = config.get('genologics', 'PASSWORD').rstrip()
+except:
+	warnings.warn("Please make sure you've created your own Genologics configuration file (i.e: ~/.genologicsrc) as stated in README.md")
+	sys.exit(-1)
+
+