Merge pull request #59 from Clinical-Genomics/remove_alchy

Remove alchy and use SQLAlchemy instead

CHANGELOG.md

@@ -1,5 +1,9 @@
 # Change log
 
+## [unreleased]
+### Changed
+- Removed alchy dependency
+
 ## 4.10.2 (2023-08-16)
 ### Fixed
 - Timeout when creating report due to slow transcript_stat query

chanjo_report/server/blueprints/index/views.py

@@ -13,7 +13,7 @@
 
 @index_bp.route('/')
 def index():
-    sample_objs = api.query(Sample).limit(20)
-    tx_models = api.query(Transcript).distinct(Transcript.gene_id).limit(20)
+    sample_objs = api.session.query(Sample).limit(20)
+    tx_models = api.session.query(Transcript).distinct(Transcript.gene_id).limit(20)
     return render_template('index/index.html', samples=sample_objs,
                            transcripts=tx_models)

chanjo_report/server/blueprints/report/controllers.py

@@ -5,7 +5,6 @@
 
 from .utils import keymetrics_rows, samplesex_rows, transcripts_rows
 
-
 def report_contents(request):
     """Check args or form provided by user request and prepare contents for report or pdf endpoints
     Args:

chanjo_report/server/blueprints/report/utils.py

@@ -17,7 +17,7 @@ def chromosome_coverage(samples_ids, chrom=None):
     """Return mean coverage over all transcripts of a chromosome for one or more samples"""
 
     query = (
-        api.query(
+        api.session.query(
             TranscriptStat,
             func.avg(TranscriptStat.mean_coverage).label('mean_coverage'),
         )
@@ -32,7 +32,7 @@ def chromosome_coverage(samples_ids, chrom=None):
 
 def transcript_coverage(api, gene_id, *sample_ids):
     """Return coverage metrics per transcript for a given gene."""
-    query = (api.query(TranscriptStat)
+    query = (api.session.query(TranscriptStat)
                 .join(TranscriptStat.transcript)
                 .filter(Transcript.gene_id == gene_id)
                 .order_by(TranscriptStat.transcript_id,
@@ -62,7 +62,7 @@ def map_samples(group_id=None, sample_ids=None):
 
 def samplesex_rows(sample_ids):
     """Generate sex prediction info rows."""
-    sex_query = (api.query(
+    sex_query = (api.session.query(
         TranscriptStat.sample_id,
         Transcript.chromosome,
         func.avg(TranscriptStat.mean_coverage)
@@ -96,7 +96,7 @@ def samplesex_rows(sample_ids):
 def keymetrics_rows(samples_ids, genes=None):
     """Generate key metrics rows."""
     query = (
-        api.query(
+        api.session.query(
             TranscriptStat,
             func.avg(TranscriptStat.mean_coverage).label('mean_coverage'),
             func.avg(TranscriptStat.completeness_10).label('completeness_10'),
@@ -156,8 +156,8 @@ def diagnostic_yield(api, genes=None, samples=None, group=None, level=10):
     str_level = "completeness_{}".format(level)
     completeness_col = getattr(TranscriptStat, str_level)
 
-    all_tx = api.query(Transcript)
-    missed_tx = (api.query(TranscriptStat)
+    all_tx = api.session.query(Transcript)
+    missed_tx = (api.session.query(TranscriptStat)
                     .filter(completeness_col < threshold)
                     .order_by(TranscriptStat.sample_id))
 
@@ -166,7 +166,7 @@ def diagnostic_yield(api, genes=None, samples=None, group=None, level=10):
                               .filter(Transcript.gene_id.in_(genes)))
         all_tx = all_tx.filter(Transcript.gene_id.in_(genes))
 
-    samples_query = api.query(Sample.id)
+    samples_query = api.session.query(Sample.id)
     if samples:
         samples_query = samples_query.filter(Sample.id.in_(samples))
         missed_tx = missed_tx.filter(TranscriptStat.sample_id.in_(samples))

chanjo_report/server/blueprints/report/views.py

@@ -26,7 +26,7 @@ def gene(gene_id):
     """Display coverage information on a gene."""
     sample_ids = request.args.getlist("sample_id")
     sample_dict = map_samples(sample_ids=sample_ids)
-    matching_tx = Transcript.filter_by(gene_id=gene_id).first()
+    matching_tx = api.session.query(Transcript).filter_by(gene_id=gene_id).first()
     if matching_tx is None:
         return abort(404, "gene not found: {}".format(gene_id))
     gene_name = matching_tx.gene_name
@@ -49,12 +49,12 @@ def genes():
     limit = int(request.args.get("limit", 30))
     exonlink = request.args.get("exonlink")
     sample_ids = request.args.getlist("sample_id")
-    samples_q = Sample.filter(Sample.id.in_(sample_ids))
+    samples_q = api.session.query(Sample).filter(Sample.id.in_(sample_ids))
     level = request.args.get("level", 10)
     raw_gene_ids = request.args.get("gene_id") or request.form.get("gene_ids")
     completeness_col = getattr(TranscriptStat, "completeness_{}".format(level))
     query = (
-        api.query(TranscriptStat)
+        api.session.query(TranscriptStat)
         .join(TranscriptStat.transcript)
         .filter(completeness_col < 100)
         .order_by(completeness_col)

chanjo_report/server/extensions.py

@@ -1,34 +1,4 @@
-from alchy import make_declarative_base, QueryModel, ManagerMixin
 from chanjo.store.models import BASE
 from flask_sqlalchemy import SQLAlchemy
-from threading import get_ident
 
-
-class Alchy(SQLAlchemy, ManagerMixin):
-    """Flask extension that integrates alchy with Flask-SQLAlchemy.
-    Originally developed in Flask-Alchy (https://github.com/dgilland/flask-alchy).
-    It has some changes here due to deprecated code in required libs (flask and flask_sqlalchemy)
-    """
-
-    def __init__(
-        self, app=None, use_native_unicode=True, session_options=None, Model=None, metadata=None
-    ):
-        if session_options is None:
-            session_options = {}
-
-        session_options.setdefault("query_cls", QueryModel)
-        session_options.setdefault("scopefunc", get_ident)
-
-        self.Model = Model
-        self.make_declarative_base(Model)
-
-        super(Alchy, self).__init__(app, use_native_unicode, session_options, metadata=metadata)
-
-        self.Query = session_options["query_cls"]
-
-    def __getattr__(self, attr):
-        """Delegate all other attributes to self.session"""
-        return getattr(self.session, attr)
-
-
-api = Alchy(Model=BASE)
+api = SQLAlchemy(model_class=BASE)

requirements.txt

@@ -1,6 +1,5 @@
-alchy
 cairocffi
-chanjo>=4.1.0
+chanjo>=4.7
 cffi
 Flask
 Flask-Assets
@@ -12,7 +11,6 @@ path.py
 pymysql
 pyscss
 six
-sqlservice
 Flask-SQLAlchemy
 tabulate
 toml