Merge pull request #40 from Galithil/master

Updates to LIMS2DB

LIMS2DB/diff.py

@@ -1,11 +1,10 @@
 
-import LIMS2DB.objectsDB.objectsDB as DB
-
 from genologics.config import BASEURI, USERNAME, PASSWORD
 from genologics.lims import Lims
 from LIMS2DB.utils import setupLog
+from genologics_sql.utils import *
 
-def diff_project_objects(pj_id, couch, logfile):
+def diff_project_objects(pj_id, couch, logfile, new=True):
 
     proj_db = couch['projects']
     samp_db = couch['samples']
@@ -26,11 +25,18 @@ def diff_project_objects(pj_id, couch, logfile):
     old_project.pop('modification_time', None)
     old_project.pop('creation_time', None)
 
-    new_project = DB.ProjectDB(lims, pj_id, samp_db, log)
+    if new:
+        from LIMS2DB.classes import ProjectSQL 
+        session=get_session()
+        host=get_configuration()['url']
+        new_project=ProjectSQL(session, log, pj_id, host, couch)
+    else:
+        import LIMS2DB.objectsDB.objectsDB as DB
+        new_project = DB.ProjectDB(lims, pj_id, samp_db, log)
 
     fediff=diff_objects(old_project, new_project.obj)
 
-    return {pj_id : fediff}
+    return (fediff, old_project, new_project.obj)
 
 
 
@@ -51,11 +57,12 @@ def diff_objects(o1, o2, parent=''):
                     diffs["{} {}".format(parent, key)]=[o1[key], o2[key]]
 
         else:
-            diffs["key {}".format(key)]=[o1[key], "missing"]
+            if o1[key]:
+                diffs["key {} {}".format(parent, key)]=[o1[key], "missing"]
 
     for key in o2:
-        if key not in o1:
-            diffs["key {}".format(key)]=["missing", o2[key]]
+        if key not in o1 and o2[key]:
+            diffs["key {} {}".format(parent, key)]=["missing", o2[key]]
 
 
     return diffs

LIMS2DB/objectsDB/objectsDB.py

@@ -938,6 +938,6 @@ def _get_lib_val_info(self, agrlibQCsteps, libvalstart, latest_caliper_id = None
                 library_validation["average_size_bp"] = average_size_bp
             if latest_caliper_id and (Process(self.lims, id=latest_caliper_id['id'])).date_run >= (Process(self.lims, id=libvalstart['id']).date_run):
                 library_validation["caliper_image"] = get_caliper_img(self.sample_name,
-                                                        latest_caliper_id['id'], self.lims)
+                                                            latest_caliper_id['id'], self.lims)
             library_validations[agrlibQCstep['id']] = delete_Nones(library_validation)
         return delete_Nones(library_validations) 

LIMS2DB/objectsDB/process_categories.py

@@ -34,6 +34,9 @@
     '506': "Pre-Pooling (MiSeq) 4.0",
     '508': "Applications Pre-Pooling",
     '716': 'Library Pooling (HiSeq X) 1.0'}
+PREPSTARTFINLIB = {
+    '255': "Library Pooling (Finished Libraries) 4.0"
+    }
 PREPSTART = {
     '10' : 'Aliquot Libraries for Hybridization (SS XT)',
     '47' : 'mRNA Purification, Fragmentation & cDNA synthesis (TruSeq RNA) 4.0',

LIMS2DB/parallel.py

@@ -183,6 +183,12 @@ def processWSULSQL(args, queue, logqueue):
                 final_doc=lutils.merge(ws.obj, doc)
             else:
                 final_doc=ws.obj
+            #clean possible name duplicates
+            for row in db.view('worksets/name')[ws.obj['name']]:
+                doc=db.get(row.id)
+                if doc['id'] != ws.obj['id']:
+                    proclog.warning("Duplicate name {} for worksets {} and {}".format(doc['name'], doc['id'], final_doc['id']))
+                    db.delete(doc)
             db.save(final_doc)
             proclog.info("updating {0}".format(ws.obj['name']))
             queue.task_done()

scripts/project_summary_upload_LIMS.py

@@ -10,8 +10,10 @@
 from optparse import OptionParser
 from LIMS2DB.utils import formatStack
 from statusdb.db.utils import *
-from genologics_sql.utils import get_session
 from genologics_sql.queries import get_last_modified_projectids
+from genologics_sql.utils import *
+from genologics_sql.tables import Project as DBProject
+from LIMS2DB.classes import ProjectSQL
 
 from pprint import pprint
 
@@ -103,6 +105,8 @@ def main(options):
     proj_db = couch['projects']
     samp_db = couch['samples']
     mainlims = Lims(BASEURI, USERNAME, PASSWORD)
+    lims_db = get_session()
+
     mainlog = logging.getLogger('psullogger')
     mainlog.setLevel(level=logging.INFO)
     mfh = logging.handlers.RotatingFileHandler(options.logfile, maxBytes=209715200, backupCount=5)
@@ -111,13 +115,17 @@ def main(options):
     mainlog.addHandler(mfh)
 
     if options.project_name:
-        proj = mainlims.get_projects(name = options.project_name)
-        if not proj:
-            mainlog.warn('No project named {man_name} in Lims'.format(
-                        man_name = options.project_name))
-        else:
+        if options.old:
+            proj = mainlims.get_projects(name = options.project_name)
+            if not proj:
+                mainlog.warn('No project named {man_name} in Lims'.format(
+                            man_name = options.project_name))
             P = PSUL(proj[0], samp_db, proj_db, options.upload, options.project_name, output_f, mainlog)
             P.handle_project()
+        else:
+            host=get_configuration()['url']
+            pj_id=lims_db.query(DBProject.luid).filter(DBProject.name == options.project_name).scalar()
+            P = ProjectSQL(lims_db, mainlog, pj_id, host, couch)
     else :
         projects=create_projects_list(options, mainlims, mainlog)
         masterProcess(options,projects, mainlims, mainlog)
@@ -189,14 +197,26 @@ def processPSUL(options, queue, logqueue):
                     open(lockfile,'w').close()
                 except:
                     proclog.error("cannot create lockfile {}".format(lockfile))
-                try:
-                    proj=mylims.get_projects(name=projname)[0]
-                    P = PSUL(proj, samp_db, proj_db, options.upload, options.project_name, options.output_f, proclog)
-                    P.handle_project()
-                except :
-                    error=sys.exc_info()
-                    stack=traceback.extract_tb(error[2])
-                    proclog.error("{0}:{1}\n{2}".format(error[0], error[1], formatStack(stack)))
+                if options.old:
+                    try:
+                        proj=mylims.get_projects(name=projname)[0]
+                        P = PSUL(proj, samp_db, proj_db, options.upload, options.project_name, options.output_f, proclog)
+                        P.handle_project()
+                    except :
+                        error=sys.exc_info()
+                        stack=traceback.extract_tb(error[2])
+                        proclog.error("{0}:{1}\n{2}".format(error[0], error[1], formatStack(stack)))
+                else:
+                    try:
+                        db_session=get_session()
+                        pj_id=db.session.query(DBProject.luid).filter(DBProject.name == projname).scalar()
+                        host=get_configuration()['url']
+                        P = ProjectSQL(db_session, proclog, pj_id, host, couch)
+                        P.save()
+                    except :
+                        error=sys.exc_info()
+                        stack=traceback.extract_tb(error[2])
+                        proclog.error("{0}:{1}\n{2}".format(error[0], error[1], formatStack(stack)))
 
                 try:
                     os.remove(lockfile)
@@ -335,6 +355,7 @@ def emit(self, record):
     parser.add_option("-j", "--hours", dest = "hours",type='int', help = ("only handle projects modified in the last X hours"), default=None)
     parser.add_option("-k", "--control", dest = "control", action="store_true", help = ("only perform a dry-run"), default=False)
     parser.add_option("-i", "--input", dest = "input", help = ("path to the input file containing projects to update"), default=None)
+    parser.add_option("--old", dest = "old", help = ("use the old version of psul, via the API"), action="store_true", default=False)
 
     (options, args) = parser.parse_args()
     main(options)