Merge pull request #587 from gwarmstrong/issue586

change labman to labcontrol in .travis.yml
biocore · Sep 11, 2019 · 69cd932 · 69cd932
2 parents 1427ad1 + a704083
commit 69cd932
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Showing 20 changed files with 299 additions and 265 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -97,7 +97,7 @@ install:
 script:
   - python labcontrol/gui/js_tests/js_tester.py all-tests
   - nosetests --exclude-dir=labcontrol/gui/js_tests --with-doctest --with-coverage -v --cover-package=labcontrol
-  - flake8 labman setup.py scripts/*
+  - flake8 labcontrol setup.py scripts/*
   # Run prettier to verify that the JS/CSS ("front end") code doesn't need any
   # stylistic adjustments.
   - make festylecheck

diff --git a/labcontrol/db/composition.py b/labcontrol/db/composition.py
@@ -7,7 +7,6 @@
 # ----------------------------------------------------------------------------
 
 import re
-from enum import Enum
 from . import base
 from . import sql_connection
 from . import process
@@ -1115,7 +1114,6 @@ def get_assay_type_for_sequencing_process(sequencing_process_id):
 
             return assay_type
 
-
     @staticmethod
     def get_components_type(components):
         """Return class name of components of pool

diff --git a/labcontrol/db/configuration_manager.py b/labcontrol/db/configuration_manager.py
@@ -111,10 +111,10 @@ def __init__(self):
             self.conf_fp = expanduser('~/.labcontrol.cfg')
             if not exists(self.conf_fp):
                 raise RuntimeError(
-                    'Please, configure labcontrol using `labcontrol config`. If the '
-                    'config file is not in `~/.labcontrol.cfg`, please set the '
-                    '`LABCONTROL_CONFIG_FP` environment variable to the '
-                    'configuration file')
+                    'Please, configure labcontrol using `labcontrol config`. '
+                    'If the config file is not in `~/.labcontrol.cfg`, please '
+                    'set the `LABCONTROL_CONFIG_FP` environment variable to '
+                    'the configuration file')
 
         # Parse the configuration file
         config = ConfigParser()

diff --git a/labcontrol/db/equipment.py b/labcontrol/db/equipment.py
@@ -44,7 +44,8 @@ def list_equipment(equipment_type=None):
                          if equipment_type is not None else '')
             sql = """SELECT equipment_id, external_id
                      FROM labcontrol.equipment
-                        JOIN labcontrol.equipment_type USING (equipment_type_id)
+                        JOIN labcontrol.equipment_type
+                            USING(equipment_type_id)
                      {}
                      ORDER BY external_id""".format(sql_where)
             TRN.add(sql, [equipment_type])
@@ -101,7 +102,8 @@ def create_type(cls, description):
                     'Equipment type', [('description', description)])
 
             # Proceed to create the new type
-            sql = "INSERT INTO labcontrol.equipment_type (description) VALUES (%s)"
+            sql = "INSERT INTO labcontrol.equipment_type (description)" \
+                  "VALUES (%s)"
             TRN.add(sql, [description])
             TRN.execute()
 

diff --git a/labcontrol/db/plate.py b/labcontrol/db/plate.py
@@ -238,7 +238,8 @@ def list_plates(plate_types=None, only_quantified=False,
                                               creation_timestamp
                               FROM labcontrol.plate
                                 JOIN labcontrol.well USING (plate_id)
-                                JOIN labcontrol.composition USING (container_id)
+                                JOIN labcontrol.composition
+                                    USING (container_id)
                                 JOIN labcontrol.composition_type USING
                                     (composition_type_id)
                                 {}
@@ -433,7 +434,8 @@ def duplicates(self):
                                 array_agg(content ORDER BY well_id)
                      FROM labcontrol.well
                         JOIN labcontrol.composition USING (container_id)
-                        JOIN labcontrol.sample_composition USING (composition_id)
+                        JOIN labcontrol.sample_composition
+                            USING (composition_id)
                      WHERE sample_id IS NOT NULL AND plate_id = %s
                      GROUP BY sample_id
                      HAVING array_length(array_agg(well_id), 1) > 1
@@ -456,7 +458,8 @@ def unknown_samples(self):
             sql = """SELECT well_id
                      FROM labcontrol.well
                         JOIN labcontrol.composition USING (container_id)
-                        JOIN labcontrol.sample_composition USING (composition_id)
+                        JOIN labcontrol.sample_composition
+                            USING (composition_id)
                         JOIN labcontrol.sample_composition_type
                             USING (sample_composition_type_id)
                      WHERE plate_id = %s AND
@@ -517,7 +520,8 @@ def get_wells_by_sample(self, sample_id):
             sql = """SELECT well_id
                      FROM labcontrol.well
                         JOIN labcontrol.composition USING (container_id)
-                        JOIN labcontrol.sample_composition USING (composition_id)
+                        JOIN labcontrol.sample_composition
+                            USING (composition_id)
                      WHERE plate_id = %s AND sample_id = %s
                      ORDER BY well_id"""
             TRN.add(sql, [self.id, sample_id])

diff --git a/labcontrol/db/process.py b/labcontrol/db/process.py
@@ -1016,7 +1016,8 @@ def gdna_plate(self):
                             USING (gdna_composition_id)
                         JOIN labcontrol.composition gc
                             ON gc.composition_id = gdc.composition_id
-                        JOIN labcontrol.well w ON gc.container_id = w.container_id
+                        JOIN labcontrol.well w
+                            ON gc.container_id = w.container_id
                      WHERE lc.upstream_process_id = %s"""
             TRN.add(sql, [self.process_id])
 
@@ -1039,7 +1040,8 @@ def primer_plate(self):
                             USING (primer_composition_id)
                         JOIN labcontrol.composition pc
                             ON pc.composition_id = prc.composition_id
-                        JOIN labcontrol.well w ON pc.container_id = w.container_id
+                        JOIN labcontrol.well w
+                            ON pc.container_id = w.container_id
                      WHERE lc.upstream_process_id = %s"""
             TRN.add(sql, [self.process_id])
             return plate_module.Plate(TRN.execute_fetchlast())
@@ -1231,7 +1233,8 @@ def compressed_plate(self):
                             USING (compressed_gdna_composition_id)
                         JOIN labcontrol.composition cc
                             ON cc.composition_id = cgdnac.composition_id
-                        JOIN labcontrol.well w ON cc.container_id = w.container_id
+                        JOIN labcontrol.well w
+                            ON cc.container_id = w.container_id
                      WHERE nc.upstream_process_id = %s"""
             TRN.add(sql, [self.process_id])
             return plate_module.Plate(TRN.execute_fetchlast())
@@ -1605,7 +1608,8 @@ def normalized_plate(self):
                             USING (normalized_gdna_composition_id)
                         JOIN labcontrol.composition nc
                             ON ngdnac.composition_id = nc.composition_id
-                        JOIN labcontrol.well w ON nc.container_id = w.container_id
+                        JOIN labcontrol.well w
+                            ON nc.container_id = w.container_id
                      WHERE lc.upstream_process_id = %s"""
             TRN.add(sql, [self.process_id])
             return plate_module.Plate(TRN.execute_fetchlast())
@@ -1628,7 +1632,8 @@ def i5_primer_plate(self):
                                 prc.primer_composition_id
                         JOIN labcontrol.composition pc
                             ON prc.composition_id = pc.composition_id
-                        JOIN labcontrol.well w ON pc.container_id = w.container_id
+                        JOIN labcontrol.well w
+                            ON pc.container_id = w.container_id
                      WHERE lc.upstream_process_id = %s"""
             TRN.add(sql, [self.process_id])
             return plate_module.Plate(TRN.execute_fetchlast())
@@ -1651,7 +1656,8 @@ def i7_primer_plate(self):
                                 prc.primer_composition_id
                         JOIN labcontrol.composition pc
                             ON prc.composition_id = pc.composition_id
-                        JOIN labcontrol.well w ON pc.container_id = w.container_id
+                        JOIN labcontrol.well w
+                            ON pc.container_id = w.container_id
                      WHERE lc.upstream_process_id = %s"""
             TRN.add(sql, [self.process_id])
             return plate_module.Plate(TRN.execute_fetchlast())