Merge pull request #484 from AndersenLab/fix/phenotype-db

Updating Phenotype DB with updated SQL tables

src/modules/db_operations/module.env

@@ -1,2 +1,2 @@
 MODULE_NAME=caendr-db-operations
-MODULE_VERSION=v1.0.41
+MODULE_VERSION=v1.0.42

src/modules/db_operations/requirements.txt

@@ -1,4 +1,5 @@
 backoff==2.2.1
+bleach==4.1.0
 Flask==1.1.2
 Flask_SQLAlchemy==2.5.1
 SQLAlchemy==1.3.18

src/modules/site-v2/base/static/js/plot.js

@@ -411,6 +411,12 @@ function render_ranked_barplot(container_selector, data, config={}) {
   // Read values from config, filling in default values when not supplied
   const fill_color    = config['fill_color']    || 'black';
 
+  // Create a template function for the tooltip
+  // By default, show label & value for each axis
+  const tooltip_id       = config['tooltip_id']       || null;
+  const tooltip_template = config['tooltip_template'] || ((d) => `
+    <p class="tooltip-body">${d[0]}: ${d[1]}</p>
+  `);
 
   // Sort data
   data.sort(function(b, a) {

src/modules/site-v2/module.env

@@ -1,5 +1,5 @@
 MODULE_NAME=caendr-site-v2
-MODULE_VERSION=v2.0.95
+MODULE_VERSION=v2.0.96
 
 PORT=8080
 FLASK_APP=main:app

src/modules/site-v2/templates/_includes/phenotype-database-table.html

@@ -191,7 +191,7 @@
                     $('#{{ offcanvas_id }} .btn-close').click()
                     flashErrorResponse(error.responseJSON, 'There was a problem retrieving this trait. Please try again later.')
                 })
-        })
+            })
 
 
         // Filter table by tag links

src/modules/site-v2/templates/_scripts/trait_utils.js

@@ -32,7 +32,7 @@ function queryTraitByName(trait_id, csrf_token=null) {
   // Construct the data object, using the optional CSRF token if provided
   let data = {trait_id};
   if (csrf_token !== null) data['csrf_token'] = csrf_token;
-
+  
   // Return the AJAX request as a Promise object
   return $.ajax({
       type:        "POST",

src/modules/site-v2/templates/tools/phenotype_database/report.html

@@ -228,6 +228,11 @@ <h4 class="h5">Description:</h4>
         fill_color:    '#0719BC',
         bins_per_tick: 2,
         x_label:       trait_label,
+        tooltip_id:    'tooltip-single-histogram',
+        tooltip_template: (d, labels) => `
+            <p class="tooltip-head"><b>Strain: ${d[0]}</b></p>
+            <p class="tooltip-body">${labels[0]}: ${d[1]}</p>
+        `,
     });
 } catch (err) {
     console.error(`Could not construct histogram. ${err}`)
@@ -238,6 +243,11 @@ <h4 class="h5">Description:</h4>
         width:         1200,
         fill_color:    '#0719BC',
         y_label:       trait_label,
+        tooltip_id:    'tooltip-single-barplot',
+        tooltip_template: (d) => `
+            <p class="tooltip-head"><b>${d[0]}</b></p>
+            <p class="tooltip-body">Value = ${d[1].toFixed(4)}</p>
+        `,
     });
 } catch (err) {
     console.error(`Could not construct ranked bar plot. ${err}`)
@@ -262,6 +272,12 @@ <h4 class="h5">Description:</h4>
         y_label:       `${trait_label_2}`,
         opacity:       0.5,
         opacity_hover: 1,
+        tooltip_id:    'tooltip-double-scatterplot',
+        tooltip_template: (d, labels) => `
+            <p class="tooltip-head"><b>${d[0]}</b></p>
+            <p class="tooltip-body">x = ${d[1].toFixed(4)}</p>
+            <p class="tooltip-body">y = ${d[2].toFixed(4)}</p>
+        `,
     });
 } catch (err) {
     console.error(`Could not construct scatterplot. ${err}`)

src/pkg/caendr/caendr/models/datastore/phenotype_report.py

@@ -286,7 +286,7 @@ def compute_display_name(cls, trait: Union[Trait, TraitFile], trait_name: Option
       raise ValueError()
 
     # Use the Trait object to compute the display name
-    return list(trait.display_name)
+    return [trait.name,] if trait.dataset == 'zhang' else list(trait.display_name)
 
 
   @classmethod

src/pkg/caendr/caendr/models/trait.py

@@ -3,7 +3,9 @@
 
 from caendr.models.datastore import TraitFile
 from caendr.models.sql       import PhenotypeMetadata, PhenotypeDatabase
+from caendr.models.error     import NotFoundError
 from caendr.utils.data       import dataframe_cols_to_dict
+from caendr.api.phenotype    import get_trait
 
 from caendr.services.cloud.postgresql import db
 
@@ -57,9 +59,11 @@ def __init__(self, dataset = None, trait_name = None, trait_file_id = None, trai
       raise ValueError('Could not identify a unique trait from the given information')
 
     # Store the dataset value of the trait file
-    if dataset and self.file['dataset'] and dataset != self.file['dataset']:
-      raise ValueError('Mismatched dataset values')
-    self.dataset = self.file['dataset']
+    # if dataset and self.file['dataset'].value and dataset != self.file['dataset'].value:
+    #   raise ValueError('Mismatched dataset values')
+    self.dataset = self.file['dataset'].value
+
+    self.sql_row = PhenotypeMetadata.query.filter_by(trait_name_caendr = self.name, dataset = self.dataset).one()
 
 
   #
@@ -104,6 +108,24 @@ def from_sql(sql_row: PhenotypeMetadata) -> 'Trait':
       dataset    = sql_row.dataset,
       trait_name = sql_row.trait_name_caendr,
     )
+
+  @classmethod
+  def from_id(cls, trait_id: str) -> 'Trait':
+    '''
+      Instantiate a `Trait` object from a unique trait ID.
+      The given ID must exist in the PhenotypeMetadata SQL table, otherwise a `ValueError` will be raised.
+    '''
+
+    # Get the SQL row with the given trait ID
+    sql_row = PhenotypeMetadata.query.get(trait_id)
+    if sql_row is None:
+      raise NotFoundError(PhenotypeMetadata, {'id': trait_id})
+
+    # Construct a Trait object using the data in the SQL row
+    return cls(
+      trait_name = sql_row.trait_name_caendr,
+      dataset    = sql_row.dataset,
+    )
 
 
   #
@@ -145,4 +167,4 @@ def display_name(self):
     '''
 
     # For bulk files, store the single trait name, otherwise convert the display_name fields to a list
-    return (self.name,) if self.file['is_bulk_file'] else self.file.display_name
+    return (self.sql_row.trait_name_caendr,) if self.file['is_bulk_file'] else self.file.display_name

src/pkg/caendr/caendr/services/sql/etl/phenotype_metadata.py

@@ -58,7 +58,7 @@ def parse_phenotype_metadata(species: Species, **files: LocalDatastoreFile):
              'capture_date':         md['capture_date'],
              'created_on':           md.created_on,
              'modified_on':          md.modified_on,
-             'dataset':              md['dataset'],
+             'dataset':              md['dataset'].value,
              'is_bulk_file':         md['is_bulk_file'],
             } 
     else:
@@ -83,6 +83,6 @@ def parse_phenotype_metadata(species: Species, **files: LocalDatastoreFile):
       'capture_date':         md['capture_date'],
       'created_on':           md.created_on,
       'modified_on':          md.modified_on,
-      'dataset':              md['dataset'],
+      'dataset':              md['dataset'].value,
       'is_bulk_file':         md['is_bulk_file'],
       }