Migrations catchup

neuroscout/config/datasets/ds001132.json

@@ -0,0 +1,38 @@
+{
+  "Sherlock": {
+    "preproc_address": "https://github.com/neuroscout-datasets/Sherlock/",
+    "path": "/datasets/raw/ds001132/",
+    "summary": "Audio/visual presentation of Sherlock episode",
+    "url": "https://openneuro.org/datasets/ds001132/",
+    "tasks": {
+      "sherlockPart1": {
+        "summary": "Audio/visual watching",
+        "converters": [
+        ],
+
+        "extractors": [
+["ComplexTextExtractor", {}],
+    ["PredefinedDictionaryExtractor", {"variables":
+      {"subtlexusfrequency":["FREQcount", "CDcount", "FREQlow", "Cdlow", "SUBTLWF","Lg10WF", "SUBTLCD", "Lg10CD", "Dom_PoS_SUBTLEX", "Freq_dom_PoS_SUBTLEX", "Percentage_dom_PoS", "All_PoS_SUBTLEX", "All_freqs_SUBTLEX", "Zipf-value"]},
+      "missing": "n/a"} ],
+    ["PredefinedDictionaryExtractor", {"variables":
+      {"affect":["V.Mean.Sum", "A.Mean.Sum", "D.Mean.Sum"],
+      "aoa": ["AoA_Kup"],
+      "concreteness": ["Conc.M"]},
+      "missing": "n/a"} ],
+    ["LengthExtractor", {}]
+
+          ],
+        "transformations": [
+ {
+      "function": "dummy",
+      "new_name": "speech",
+      "extractor_name": "ComplexTextExtractor"
+    }
+        ],
+        "ingest_args": {
+        }
+      }
+    }
+  }
+}

neuroscout/models/__init__.py

@@ -1,7 +1,7 @@
 ''' Model hierarchy. '''
 
 from .analysis import (Analysis, Report, NeurovaultCollection,
-                       analysis_predictor)
+                       NeurovaultFileUpload, analysis_predictor)
 from .auth import User, Role, roles_users, user_datastore
 from .group import GroupPredictor, GroupPredictorValue
 from .dataset import Dataset
@@ -31,6 +31,7 @@
     'PredictorCollection',
     'Report',
     'NeurovaultCollection',
+    'NeurovaultFileUpload',
     'Run',
     'analysis_run',
     'Stimulus',

neuroscout/models/analysis.py

@@ -120,10 +120,28 @@ class NeurovaultCollection(db.Model):
     analysis_id = db.Column(db.Text, db.ForeignKey('analysis.hash_id'))
     uploaded_at = db.Column(db.DateTime, default=datetime.datetime.utcnow)
 
+    collection_id = db.Column(db.Integer, unique=True)
+
+    files = db.relationship('NeurovaultFileUpload', backref='collection')
+
+
+class NeurovaultFileUpload(db.Model):
+    """ NV file upload """
+    id = db.Column(db.Integer, primary_key=True)
+    nv_collection_id = db.Column(
+        db.Integer, db.ForeignKey('neurovault_collection.id'),
+        nullable=False)
+
+    path = db.Column(db.Text, nullable=False)
+
     task_id = db.Column(db.Text)
-    collection_id = db.Column(db.Text)
+    level = db.Column(db.Text, nullable=False)
+
+    exception = db.Column(db.Text)
     traceback = db.Column(db.Text)
 
     status = db.Column(db.Text, default='PENDING')
     __table_args__ = (
-        db.CheckConstraint(status.in_(['OK', 'FAILED', 'PENDING'])), )
+        db.CheckConstraint(status.in_(['OK', 'FAILED', 'PENDING'])),
+        db.CheckConstraint(level.in_(['GROUP', 'SUBJECT'])),
+        )

postgres/migrations/migrations/versions/05df5e3a41f3_.py

@@ -0,0 +1,49 @@
+"""empty message
+
+Revision ID: 05df5e3a41f3
+Revises: d4417864ab88
+Create Date: 2019-08-30 16:32:39.066853
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '05df5e3a41f3'
+down_revision = 'd4417864ab88'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('neurovault_file_upload')
+    op.add_column('neurovault_collection', sa.Column('status', sa.Text(), nullable=True))
+    op.add_column('neurovault_collection', sa.Column('task_id', sa.Text(), nullable=True))
+    op.add_column('neurovault_collection', sa.Column('traceback', sa.Text(), nullable=True))
+    op.drop_constraint('neurovault_collection_collection_id_key', 'neurovault_collection', type_='unique')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_unique_constraint('neurovault_collection_collection_id_key', 'neurovault_collection', ['collection_id'])
+    op.drop_column('neurovault_collection', 'traceback')
+    op.drop_column('neurovault_collection', 'task_id')
+    op.drop_column('neurovault_collection', 'status')
+    op.create_table('neurovault_file_upload',
+    sa.Column('id', sa.INTEGER(), autoincrement=True, nullable=False),
+    sa.Column('nv_collection_id', sa.INTEGER(), autoincrement=False, nullable=False),
+    sa.Column('task_id', sa.TEXT(), autoincrement=False, nullable=True),
+    sa.Column('level', sa.TEXT(), autoincrement=False, nullable=False),
+    sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True),
+    sa.Column('exception', sa.TEXT(), autoincrement=False, nullable=True),
+    sa.Column('path', sa.TEXT(), autoincrement=False, nullable=False),
+    sa.Column('traceback', sa.TEXT(), autoincrement=False, nullable=True),
+    sa.CheckConstraint("level = ANY (ARRAY['GROUP'::text, 'SUBJECT'::text])", name='neurovault_file_upload_level_check'),
+    sa.CheckConstraint("status = ANY (ARRAY['OK'::text, 'FAILED'::text, 'PENDING'::text])", name='neurovault_file_upload_status_check1'),
+    sa.ForeignKeyConstraint(['nv_collection_id'], ['neurovault_collection.id'], name='neurovault_file_upload_nv_collection_id_fkey'),
+    sa.PrimaryKeyConstraint('id', name='neurovault_file_upload_pkey')
+    )
+    # ### end Alembic commands ###

postgres/migrations/migrations/versions/398589c37576_.py

@@ -0,0 +1,49 @@
+"""empty message
+
+Revision ID: 398589c37576
+Revises: 05df5e3a41f3
+Create Date: 2019-08-30 16:41:18.575497
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '398589c37576'
+down_revision = '05df5e3a41f3'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('neurovault_file_upload',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('nv_collection_id', sa.Integer(), nullable=False),
+    sa.Column('path', sa.Text(), nullable=False),
+    sa.Column('task_id', sa.Text(), nullable=True),
+    sa.Column('level', sa.Text(), nullable=False),
+    sa.Column('exception', sa.Text(), nullable=True),
+    sa.Column('traceback', sa.Text(), nullable=True),
+    sa.Column('status', sa.Text(), nullable=True),
+    sa.CheckConstraint("level IN ('GROUP', 'SUBJECT')"),
+    sa.CheckConstraint("status IN ('OK', 'FAILED', 'PENDING')"),
+    sa.ForeignKeyConstraint(['nv_collection_id'], ['neurovault_collection.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_unique_constraint(None, 'neurovault_collection', ['collection_id'])
+    op.drop_column('neurovault_collection', 'status')
+    op.drop_column('neurovault_collection', 'traceback')
+    op.drop_column('neurovault_collection', 'task_id')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('neurovault_collection', sa.Column('task_id', sa.TEXT(), autoincrement=False, nullable=True))
+    op.add_column('neurovault_collection', sa.Column('traceback', sa.TEXT(), autoincrement=False, nullable=True))
+    op.add_column('neurovault_collection', sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True))
+    op.drop_constraint(None, 'neurovault_collection', type_='unique')
+    op.drop_table('neurovault_file_upload')
+    # ### end Alembic commands ###

postgres/migrations/migrations/versions/5105cfcc9c86_.py

@@ -0,0 +1,58 @@
+"""empty message
+
+Revision ID: 5105cfcc9c86
+Revises: cc3e935179cb
+Create Date: 2019-08-29 20:24:16.713430
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = '5105cfcc9c86'
+down_revision = 'cc3e935179cb'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('neurovault_file_upload',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('nv_collection_id', sa.Integer(), nullable=False),
+    sa.Column('task_id', sa.Text(), nullable=True),
+    sa.Column('level', sa.Text(), nullable=False),
+    sa.Column('status', sa.Text(), nullable=True),
+    sa.CheckConstraint("status IN ('GROUP', 'SUBJECT')"),
+    sa.CheckConstraint("status IN ('OK', 'FAILED', 'PENDING')"),
+    sa.ForeignKeyConstraint(['nv_collection_id'], ['neurovault_collection.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_unique_constraint(None, 'neurovault_collection', ['collection_id'])
+    op.drop_column('neurovault_collection', 'status')
+    op.drop_column('neurovault_collection', 'traceback')
+    op.drop_column('neurovault_collection', 'task_id')
+    op.alter_column('predictor_collection', 'user_id',
+               existing_type=sa.INTEGER(),
+               nullable=True)
+    op.drop_index('ix_predictor_event_run_id', table_name='predictor_event')
+    op.drop_index('ix_predictor_id_run_id', table_name='predictor_event')
+    op.drop_constraint('predictor_event_onset_run_id_predictor_id_object_id_key', 'predictor_event', type_='unique')
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_unique_constraint('predictor_event_onset_run_id_predictor_id_object_id_key', 'predictor_event', ['onset', 'run_id', 'predictor_id', 'object_id'])
+    op.create_index('ix_predictor_id_run_id', 'predictor_event', ['predictor_id', 'run_id'], unique=False)
+    op.create_index('ix_predictor_event_run_id', 'predictor_event', ['run_id'], unique=False)
+    op.alter_column('predictor_collection', 'user_id',
+               existing_type=sa.INTEGER(),
+               nullable=False)
+    op.add_column('neurovault_collection', sa.Column('task_id', sa.TEXT(), autoincrement=False, nullable=True))
+    op.add_column('neurovault_collection', sa.Column('traceback', sa.TEXT(), autoincrement=False, nullable=True))
+    op.add_column('neurovault_collection', sa.Column('status', sa.TEXT(), autoincrement=False, nullable=True))
+    op.drop_constraint(None, 'neurovault_collection', type_='unique')
+    op.drop_table('neurovault_file_upload')
+    # ### end Alembic commands ###

postgres/migrations/migrations/versions/d4417864ab88_.py

@@ -0,0 +1,32 @@
+"""empty message
+
+Revision ID: d4417864ab88
+Revises: 5105cfcc9c86
+Create Date: 2019-08-29 20:33:30.573981
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = 'd4417864ab88'
+down_revision = '5105cfcc9c86'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column('neurovault_file_upload', sa.Column('exception', sa.Text(), nullable=True))
+    op.add_column('neurovault_file_upload', sa.Column('path', sa.Text(), nullable=False))
+    op.add_column('neurovault_file_upload', sa.Column('traceback', sa.Text(), nullable=True))
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('neurovault_file_upload', 'traceback')
+    op.drop_column('neurovault_file_upload', 'path')
+    op.drop_column('neurovault_file_upload', 'exception')
+    # ### end Alembic commands ###