added api for predemult report upload

app/iframe_view.py

@@ -6,43 +6,72 @@
 from flask_appbuilder.baseviews import BaseView, expose
 from flask_appbuilder.security.decorators import protect, has_access
 from app import db
-from .models import Project_analysis_info_file
-from .models import Project_seqrun_info_file
-from .models import Project_seqrun_info_data
-from .models import Project_analysis_info_data
-from .metadata_view import ProjectView
+from .models import (
+    Project_analysis_info_file,
+    Project_seqrun_info_file,
+    Project_seqrun_info_data,
+    Project_analysis_info_data,
+    PreDeMultiplexingData)
+
 
 log = logging.getLogger(__name__)
 
 def get_path_for_project_seqrun_info_file(id):
     try:
-        (file_path, project_id) = \
+        record = \
             db.session.\
                 query(
                     Project_seqrun_info_file.file_path,
                     Project_seqrun_info_data.project_id).\
                 join(Project_seqrun_info_data, Project_seqrun_info_data.project_seqrun_info_data_id==Project_seqrun_info_file.project_seqrun_info_data_id).\
                 filter(Project_seqrun_info_file.project_seqrun_info_file_id==id).\
                 one_or_none()
+        if record is None:
+            log.warning(f"Missing data for id {id}")
+            return '', ''
+        (file_path, project_id) = record
         return file_path, project_id
     except Exception as e:
         log.error(e)
 
 def get_path_for_project_analysis_info_file(id):
     try:
-        (file_path, project_id) = \
+        record = \
             db.session.\
                 query(
                     Project_analysis_info_file.file_path,
                     Project_analysis_info_data.project_id).\
                 join(Project_analysis_info_data, Project_analysis_info_data.project_analysis_info_data_id==Project_analysis_info_file.project_analysis_info_data_id).\
                 filter(Project_analysis_info_file.project_analysis_info_file_id==id).\
                 one_or_none()
+        if record is None:
+            log.warning(f"Missing data for id {id}")
+            return '', ''
+        (file_path, project_id) = record
         return file_path, project_id
     except Exception as e:
         log.error(e)
 
 
+def get_path_for_predemult_report(id):
+    try:
+        record = \
+            db.session.\
+                query(PreDeMultiplexingData.file_path).\
+                filter(PreDeMultiplexingData.demult_id==id).\
+                one_or_none()
+        if record is None:
+            log.warning(
+                f"Missing pre-demult data for id {id}")
+            return ''
+        (file_path,) = \
+            record
+        return file_path
+    except Exception as e:
+        raise ValueError(
+            f"Failed to get report for predemult entry {id}, error: {e}")
+
+
 class IFrameView(BaseView):
     route_base = "/"
 
@@ -57,7 +86,7 @@ def view_seqrun_report(self, id):
         # return self.render_template("iframe.html", url=file_path, project_url=project_url)
         with open(file_path, 'r') as fp:
             html_data = fp.read()
-        return self.render_template("iframe.html", html_data=html_data, project_url=project_url)
+        return self.render_template("iframe.html", html_data=html_data, url_link=project_url)
 
     @expose("/static/analysis/<int:id>")
     @has_access
@@ -70,4 +99,16 @@ def view_analysis_report(self, id):
         # return self.render_template("iframe.html", url=file_path, project_url=project_url)
         with open(file_path, 'r') as fp:
             html_data = fp.read()
-        return self.render_template("iframe.html", html_data=html_data, project_url=project_url)
+        return self.render_template("iframe.html", html_data=html_data, url_link=project_url)
+
+    @expose("/static/predemult/<int:id>")
+    @has_access
+    @cache.cached(timeout=600)
+    def view_predemult_report(self, id):
+        file_path = \
+            get_path_for_predemult_report(id=id)
+        url_link = \
+            url_for('PreDeMultiplexingDataView.list')
+        with open(file_path, 'r') as fp:
+            html_data = fp.read()
+        return self.render_template("iframe.html", html_data=html_data, url_link=url_link)

app/metadata_api.py

@@ -8,14 +8,16 @@
 from . import app, db, celery
 from .metadata.metadata_util import cleanup_and_load_new_data_to_metadata_tables
 
+log = logging.getLogger(__name__)
+
 @celery.task(bind=True)
 def async_cleanup_and_load_new_data_to_metadata_tables(
     self, json_file: str) -> dict:
     try:
         cleanup_and_load_new_data_to_metadata_tables(json_file)
         return {"message": "success"}
     except Exception as e:
-        logging.error(
+        log.error(
             "Failed to run celery job, error: {0}".\
                 format(e))
 
@@ -51,6 +53,7 @@ def submit_cleanup_job(self):
                     apply_async(args=[json_file])
             return self.response(200, message='successfully submitted metadata update job')
         except Exception as e:
-            logging.error(e)
+            log.error(e)
+            return self.response_500('failed to submit metadata update job')
 
 

app/models.py

@@ -138,25 +138,18 @@ def __repr__(self):
 class PreDeMultiplexingData(Model):
     __tablename__ = 'pre_demultiplexing_data'
     __table_args__ = (
-        UniqueConstraint('run_name', 'samplesheet_tag'),
+        UniqueConstraint('run_name', 'samplesheet_tag', 'date_stamp'),
         { 'mysql_engine':'InnoDB', 'mysql_charset':'utf8' })
     demult_id = Column(INTEGER(unsigned=True), primary_key=True, nullable=False)
     run_name = Column(String(50), nullable=False)
-    samplesheet_tag = Column(String(50), nullable=False)
-    flowcell_cluster_plot = Column(TEXT())
-    project_summary_table = Column(TEXT())
-    project_summary_plot = Column(TEXT())
-    sample_table = Column(TEXT())
-    sample_plot= Column(TEXT())
-    undetermined_table = Column(TEXT())
-    undetermined_plot = Column(TEXT())
-    file_path = Column(String(500), nullable=True)
-    status = Column(Enum("ACTIVE", "WITHDRAWN", "UNKNOWN"), nullable=False, server_default='UNKNOWN')
+    samplesheet_tag = Column(String(200), nullable=False)
+    file_path = Column(String(500), nullable=False)
+    status = Column(Enum("ACTIVE", "WITHDRAWN", "UNKNOWN"), nullable=False, server_default='ACTIVE')
     date_stamp = Column(TIMESTAMP(), nullable=False, server_default=current_timestamp(), onupdate=datetime.datetime.now)
     def __repr__(self):
         return self.run_name
     def report(self):
-        return Markup('<a href="'+url_for('PreDeMultiplexingDataView.get_report', id=self.demult_id)+'">report</a>')
+        return Markup('<a href="'+url_for('IFrameView.view_predemult_report', id=self.demult_id)+'">report</a>')
 
 """
   Admin home view