Merge branch 'master' into mip_family_id_compatibility

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 6.5.0
+current_version = 6.7.0
 commit = True
 tag = True
 tag_name = {new_version}

.github/CODEOWNERS

@@ -5,4 +5,4 @@
 # the repo. Unless a later match takes precedence,
 # @global-owner1 and @global-owner2 will be requested for
 # review when someone opens a pull request.
-*       @jemten @b4ckm4n
+*       @jemten @b4ckm4n @henrikstranneheim

nuxt/package.json

@@ -1,6 +1,6 @@
 {
   "name": "trailblazer",
-  "version": "6.5.0",
+  "version": "6.7.0",
   "description": "Trailblazer web UI",
   "author": "Robin Andeer <robin.andeer@gmail.com>",
   "private": true,

setup.py

@@ -68,7 +68,7 @@ def run_tests(self):
     # Versions should comply with PEP440. For a discussion on
     # single-sourcing the version across setup.py and the project code,
     # see http://packaging.python.org/en/latest/tutorial.html#version
-    version='6.5.0',
+    version='6.7.0',
 
     description=('Track MIP analyses.'),
     long_description=__doc__,

tests/store/test_store_api.py

@@ -24,7 +24,7 @@ def test_track_update(store):
 def test_add_user(store):
     # GIVEN an empty database
     assert store.User.query.first() is None
-    name, email = 'Paul T. Anderson', 'paul.anderson@magnolia.com'
+    name, email = "Paul T. Anderson", "paul.anderson@magnolia.com"
     # WHEN adding a new user
     new_user = store.add_user(name, email)
     # THEN it should be stored in the database
@@ -33,7 +33,7 @@ def test_add_user(store):
 
 def test_user(store):
     # GIVEN a database with a user
-    name, email = 'Paul T. Anderson', 'paul.anderson@magnolia.com'
+    name, email = "Paul T. Anderson", "paul.anderson@magnolia.com"
     store.add_user(name, email)
     assert store.User.query.filter_by(email=email).first().email == email
     # WHEN querying for a user
@@ -42,7 +42,7 @@ def test_user(store):
     assert user_obj.email == email
 
     # WHEN querying for a user that doesn't exist
-    user_obj = store.user('this_is_a_made_up_email@fake_example.com')
+    user_obj = store.user("this_is_a_made_up_email@fake_example.com")
     # THEN it should return as None
     assert user_obj is None
 
@@ -63,20 +63,80 @@ def test_analysis(sample_store):
     assert analysis_obj is None
 
 
-@pytest.mark.parametrize('family, expected_bool', [
-    ('crazygoat', True),     # running
-    ('nicemouse', False),    # completed
-    ('politesnake', False),  # failed
-    ('gentlebird', True),    # pending
-])
-def test_is_running(sample_store, family, expected_bool):
+@pytest.mark.parametrize(
+    "family, expected_bool",
+    [
+        ("crazygoat", True),  # running
+        ("nicemouse", False),  # completed
+        ("politesnake", False),  # failed
+        ("gentlebird", True),  # pending
+    ],
+)
+def test_is_latest_analysis_ongoing(sample_store, family, expected_bool):
     # GIVEN an analysis
     analysis_objs = sample_store.analyses(family=family).first()
     assert analysis_objs is not None
-    # WHEN checking if the family has a running analysis
-    is_running = sample_store.is_running(family)
+    # WHEN checking if the family has an ongoing analysis status
+    is_ongoing = sample_store.is_latest_analysis_ongoing(family)
     # THEN it should return the expected result
-    assert is_running is expected_bool
+    assert is_ongoing is expected_bool
+
+
+@pytest.mark.parametrize(
+    "family, expected_bool",
+    [
+        ("crazygoat", False),  # running
+        ("nicemouse", False),  # completed
+        ("politesnake", True),  # failed
+        ("gentlebird", False),  # pending
+    ],
+)
+def test_is_latest_analysis_failed(sample_store, family, expected_bool):
+    # GIVEN an analysis
+    analysis_objs = sample_store.analyses(family=family).first()
+    assert analysis_objs is not None
+    # WHEN checking if the family has a failed analysis status
+    is_failed = sample_store.is_latest_analysis_failed(family)
+    # THEN it should return the expected result
+    assert is_failed is expected_bool
+
+
+@pytest.mark.parametrize(
+    "family, expected_bool",
+    [
+        ("crazygoat", False),  # running
+        ("nicemouse", True),  # completed
+        ("politesnake", False),  # failed
+        ("gentlebird", False),  # pending
+    ],
+)
+def test_is_latest_analysis_completed(sample_store, family, expected_bool):
+    # GIVEN an analysis
+    analysis_objs = sample_store.analyses(family=family).first()
+    assert analysis_objs is not None
+    # WHEN checking if the family has a failed analysis status
+    is_failed = sample_store.is_latest_analysis_completed(family)
+    # THEN it should return the expected result
+    assert is_failed is expected_bool
+
+
+@pytest.mark.parametrize(
+    "family, expected_status",
+    [
+        ("crazygoat", "running"),
+        ("nicemouse", "completed"),
+        ("politesnake", "failed"),
+        ("gentlebird", "pending"),
+    ],
+)
+def test_get_latest_analysis_status(sample_store, family, expected_status):
+    # GIVEN an analysis
+    analysis_objs = sample_store.analyses(family=family).first()
+    assert analysis_objs is not None
+    # WHEN checking if the family has an analysis status
+    status = sample_store.get_latest_analysis_status(family)
+    # THEN it should return the expected result
+    assert status is expected_status
 
 
 def test_aggregate_jobs(sample_store):
@@ -94,8 +154,8 @@ def test_aggregate_jobs(sample_store):
 
     # ... it should exclude "cancelled" jobs
     assert len(jobs_data) == 1
-    assert jobs_data[0]['name'] == 'samtools_mpileup'
-    assert jobs_data[0]['count'] == 1
+    assert jobs_data[0]["name"] == "samtools_mpileup"
+    assert jobs_data[0]["count"] == 1
 
 
 def test_aggregate_jobs_since_forever_date(sample_store):
@@ -112,8 +172,8 @@ def test_aggregate_jobs_since_forever_date(sample_store):
 
     # THEN it should return a list of dicts per job type with count
     assert len(jobs_data) == 1
-    assert jobs_data[0]['name'] == 'samtools_mpileup'
-    assert jobs_data[0]['count'] == 1
+    assert jobs_data[0]["name"] == "samtools_mpileup"
+    assert jobs_data[0]["count"] == 1
 
 
 def test_aggregate_jobs_since_yesterday(sample_store):

trailblazer/cli/delete.py

@@ -5,43 +5,43 @@
 
 
 @click.command()
-@click.option('-f', '--force', is_flag=True, help='skip sanity checks')
-@click.option('-y', '--yes', is_flag=True, help='skip manual confirmations')
-@click.argument('analysis_id', type=int)
+@click.option("-f", "--force", is_flag=True, help="skip sanity checks")
+@click.option("-y", "--yes", is_flag=True, help="skip manual confirmations")
+@click.argument("analysis_id", type=int)
 @click.pass_context
 def delete(context, force, yes, analysis_id):
     """Mark analysis as deleted in db and remove analysis folder on disk."""
-    analysis_obj = context.obj['store'].analysis(analysis_id)
+    analysis_obj = context.obj["store"].analysis(analysis_id)
     if analysis_obj is None:
-        print(click.style('analysis log not found', fg='red'))
+        print(click.style("analysis log not found", fg="red"))
         context.abort()
 
     print(click.style(f"{analysis_obj.family}: {analysis_obj.status}"))
 
-    if analysis_obj.is_temp:
+    if analysis_obj.has_ongoing_status:
         if yes or click.confirm(f"remove analysis log?"):
             analysis_obj.delete()
-            context.obj['store'].commit()
-            print(click.style(f"analysis deleted: {analysis_obj.family}", fg='blue'))
+            context.obj["store"].commit()
+            print(click.style(f"analysis deleted: {analysis_obj.family}", fg="blue"))
     else:
         if analysis_obj.is_deleted:
-            print(click.style(f"{analysis_obj.family}: already deleted", fg='red'))
+            print(click.style(f"{analysis_obj.family}: already deleted", fg="red"))
             context.abort()
 
         if Path(analysis_obj.out_dir).exists() or force:
-            root_dir = context.obj['store'].families_dir
+            root_dir = context.obj["store"].families_dir
             family_dir = analysis_obj.out_dir
             if not force and (len(family_dir) <= len(root_dir) or root_dir not in family_dir):
-                print(click.style(f"unknown analysis output dir: {analysis_obj.out_dir}", fg='red'))
+                print(click.style(f"unknown analysis output dir: {analysis_obj.out_dir}", fg="red"))
                 print(click.style("use '--force' to override"))
                 context.abort()
 
             if yes or click.confirm(f"remove analysis output: {analysis_obj.out_dir}?"):
                 shutil.rmtree(analysis_obj.out_dir, ignore_errors=True)
                 analysis_obj.is_deleted = True
-                context.obj['store'].commit()
-                print(click.style(f"analysis deleted: {analysis_obj.family}", fg='blue'))
+                context.obj["store"].commit()
+                print(click.style(f"analysis deleted: {analysis_obj.family}", fg="blue"))
         else:
-            print(click.style(f"analysis output doesn't exist: {analysis_obj.out_dir}", fg='red'))
+            print(click.style(f"analysis output doesn't exist: {analysis_obj.out_dir}", fg="red"))
             print(click.style("use '--force' to override"))
             context.abort()

trailblazer/constants.py

@@ -1,2 +1,4 @@
-TEMP_STATUSES = ('pending', 'running')
-DEFAULT_CAPTURE_KIT = 'agilent_sureselect_cre.v1'
+DEFAULT_CAPTURE_KIT = "agilent_sureselect_cre.v1"
+COMPLETED_STATUS = "completed"
+FAILED_STATUS = "failed"
+ONGOING_STATUSES = ("pending", "running")

trailblazer/store/api.py

@@ -6,7 +6,7 @@
 import sqlalchemy as sqa
 
 from trailblazer.mip.config import ConfigHandler
-from trailblazer.constants import TEMP_STATUSES
+from trailblazer.constants import COMPLETED_STATUS, FAILED_STATUS, ONGOING_STATUSES
 from . import models
 
 
@@ -60,7 +60,7 @@ def analyses(
         if isinstance(deleted, bool):
             analysis_query = analysis_query.filter_by(is_deleted=deleted)
         if temp:
-            analysis_query = analysis_query.filter(self.Analysis.status.in_(TEMP_STATUSES))
+            analysis_query = analysis_query.filter(self.Analysis.status.in_(ONGOING_STATUSES))
         if before:
             analysis_query = analysis_query.filter(self.Analysis.started_at < before)
         if is_visible is not None:
@@ -77,10 +77,31 @@ def track_update(self):
         metadata.updated_at = dt.datetime.now()
         self.commit()
 
-    def is_running(self, family: str) -> bool:
-        """Check if an analysis is currently running/pending for a family."""
-        latest_analysis = self.analyses(family=family).first()
-        return latest_analysis and latest_analysis.status in TEMP_STATUSES
+    def is_latest_analysis_ongoing(self, case_id: str) -> bool:
+        """Check if the latest analysis is ongoing for a case_id"""
+        latest_analysis = self.analyses(family=case_id).first()
+        if latest_analysis and latest_analysis.status in ONGOING_STATUSES:
+            return True
+        return False
+
+    def is_latest_analysis_failed(self, case_id: str) -> bool:
+        """Check if the latest analysis is failed for a case_id"""
+        latest_analysis = self.analyses(family=case_id).first()
+        if latest_analysis and latest_analysis.status == FAILED_STATUS:
+            return True
+        return False
+
+    def get_latest_analysis_status(self, case_id: str) -> str:
+        """Get latest analysis status for a case_id"""
+        latest_analysis = self.analyses(family=case_id).first()
+        return latest_analysis.status
+
+    def is_latest_analysis_completed(self, case_id: str) -> bool:
+        """Check if the latest analysis is completed for a case_id"""
+        latest_analysis = self.analyses(family=case_id).first()
+        if latest_analysis and latest_analysis.status == COMPLETED_STATUS:
+            return True
+        return False
 
     def info(self) -> models.Info:
         """Return metadata entry."""

trailblazer/store/models.py

@@ -5,12 +5,12 @@
 from sqlalchemy import Column, ForeignKey, orm, types, UniqueConstraint
 
 from trailblazer.mip import sacct
-from trailblazer.constants import TEMP_STATUSES
+from trailblazer.constants import ONGOING_STATUSES
 
-STATUS_OPTIONS = ('pending', 'running', 'completed', 'failed', 'error', 'canceled')
+STATUS_OPTIONS = ("pending", "running", "completed", "failed", "error", "canceled")
 JOB_STATUS_OPTIONS = [category.lower() for category in sacct.CATEGORIES]
-PRIORITY_OPTIONS = ('low', 'normal', 'high')
-TYPES = ('wes', 'wgs', 'rna')
+PRIORITY_OPTIONS = ("low", "normal", "high")
+TYPES = ("wes", "wgs", "rna")
 
 Model = alchy.make_declarative_base(Base=alchy.ModelBase)
 
@@ -19,7 +19,7 @@ class Info(Model):
 
     """Keep track of meta data."""
 
-    __tablename__ = 'info'
+    __tablename__ = "info"
 
     id = Column(types.Integer, primary_key=True)
     created_at = Column(types.DateTime, default=datetime.datetime.now)
@@ -28,7 +28,7 @@ class Info(Model):
 
 class User(Model):
 
-    __tablename__ = 'user'
+    __tablename__ = "user"
 
     id = Column(types.Integer, primary_key=True)
     google_id = Column(types.String(128), unique=True)
@@ -37,21 +37,22 @@ class User(Model):
     avatar = Column(types.Text)
     created_at = Column(types.DateTime, default=datetime.datetime.now)
 
-    runs = orm.relationship('Analysis', backref='user')
+    runs = orm.relationship("Analysis", backref="user")
 
     @property
     def first_name(self) -> str:
         """First part of name."""
-        return self.name.split(' ')[0]
+        return self.name.split(" ")[0]
 
 
 class Analysis(Model):
 
     """Analysis record."""
 
-    __tablename__ = 'analysis'
-    __table_args__ = (UniqueConstraint('family', 'started_at', 'status',
-                                       name='_uc_family_start_status'),)
+    __tablename__ = "analysis"
+    __table_args__ = (
+        UniqueConstraint("family", "started_at", "status", name="_uc_family_start_status"),
+    )
 
     id = Column(types.Integer, primary_key=True)
     family = Column(types.String(128), nullable=False)
@@ -69,24 +70,24 @@ class Analysis(Model):
     is_visible = Column(types.Boolean, default=True)
     type = Column(types.Enum(*TYPES))
     user_id = Column(ForeignKey(User.id))
-    progress = Column(types.Float, default=0.)
+    progress = Column(types.Float, default=0.0)
 
-    failed_jobs = orm.relationship('Job', backref='analysis')
+    failed_jobs = orm.relationship("Job", backref="analysis")
 
     @property
-    def is_temp(self):
-        """Check if the log is for a temporary status: running/pending."""
-        return self.status in TEMP_STATUSES
+    def has_ongoing_status(self):
+        """Check if the log has an ongoing status: 'running|'pending'"""
+        return self.status in ONGOING_STATUSES
 
 
 class Job(Model):
 
     """Represent a step in the pipeline."""
 
-    __tablename__ = 'job'
+    __tablename__ = "job"
 
     id = Column(types.Integer, primary_key=True)
-    analysis_id = Column(ForeignKey(Analysis.id, ondelete='CASCADE'), nullable=False)
+    analysis_id = Column(ForeignKey(Analysis.id, ondelete="CASCADE"), nullable=False)
     slurm_id = Column(types.Integer)
     name = Column(types.String(64))
     context = Column(types.String(64))