Merge pull request msysbio#6 from AndrewRadev/flask-ui-5

 Flask UI: Part 5, steps 1 and 2 of the upload process

.projections.json

@@ -5,6 +5,9 @@
   "flask_app/forms/*.py": {
     "type": "form"
   },
+  "flask_app/models/*.py": {
+    "type": "model"
+  },
   "flask_app/pages/*.py": {
     "type": "page"
   },

_project.vim

@@ -5,8 +5,11 @@ silent TagsExclude .micromamba/* flask_app/static/build/* flask_app/static/js/ve
 
 set tags+=micromamba.tags
 
-let bacterial_growth_db_roots = ['.', 'flask_app']
+let vim_bacterial_growth_roots = ['.', 'flask_app']
 
-call bacterial_growth_db#Init()
+call vim_bacterial_growth#Init()
 
 nnoremap ,t :tabnew _project.vim<cr>
+
+command! Eroutes :e flask_app/initialization/routes.py
+command! Eschema :e src/sql_scripts/create_db.sql

bin/server

@@ -0,0 +1,12 @@
+#! /bin/sh
+
+python flask_app/main.py
+
+# If there's a syntax error, the flask server will crash, let's rerun it on
+# change:
+
+inotifywait -m -e modify flask_app/** |
+  while read file_path file_event file_name; do
+    echo "DEBUG: $file_path $file_event $file_name"
+    python flask_app/main.py
+  done

flask_app/forms/experiment_chart_form.py

@@ -98,7 +98,7 @@ def generate_reads_figures(self, read_type, args):
                     var_name='Species',
                     value_name='STD'
                 )
-                error_y=std_df['STD']
+                error_y = std_df['STD']
 
             figs.append(px.line(
                 melted_df,

flask_app/forms/upload_step2_form.py

@@ -0,0 +1,17 @@
+from flask_wtf import FlaskForm
+from wtforms import SelectField, SelectMultipleField, StringField, FormField, FieldList
+from wtforms.validators import DataRequired, Optional
+
+
+class NewStrainsForm(FlaskForm):
+    class Meta:
+        csrf = False
+
+    name        = StringField('name', validators=[DataRequired()])
+    description = StringField('description', validators=[Optional()])
+    species     = SelectField('species')
+
+
+class UploadStep2Form(FlaskForm):
+    strains     = SelectMultipleField('strains')
+    new_strains = FieldList(FormField(NewStrainsForm), min_entries=0)

flask_app/forms/upload_step3_form.py

@@ -0,0 +1,30 @@
+from flask_wtf import FlaskForm
+from wtforms import SelectField, SelectMultipleField, IntegerField
+from wtforms.validators import DataRequired
+
+
+class UploadStep3Form(FlaskForm):
+    vessel_type = SelectField('vessel_type', choices=[
+        ('bottles',     "Bottles"),
+        ('agar_plates', "Agar plates"),
+        ('well_plates', "Well plates"),
+        ('mini_react',  "mini bioreactors"),
+    ], validators=DataRequired())
+
+    bottle_count = IntegerField('bottle_count')
+    plate_count  = IntegerField('plate_count')
+    column_count = IntegerField('column_count')
+    row_count    = IntegerField('row_count')
+
+    timepoint_count = IntegerField('timepoint_count', validators=[DataRequired()])
+
+    technique_type = SelectField('technique_type', choices=[
+        ('od',        "Optical Density"),
+        ('plates',    "Plate Counts"),
+        ('plates_ps', "Plate Counts (per species)"),
+        ('fc',        "Flow Cytometry"),
+        ('fc_ps',     "Flow Cytometry (per species)"),
+        ('rna',       "16S rRNA-seq"),
+    ], validators=DataRequired())
+
+    technique_type = SelectMultipleField('metabolites')

flask_app/initialization/assets.py

@@ -6,10 +6,12 @@ def init_assets(app):
 
     assets.register('app_js', flask_assets.Bundle(
         'js/vendor/jquery-3.7.1.js',
+        'js/vendor/select2-4.0.13.js',
         'js/util.js',
         'js/main.js',
         'js/search.js',
         'js/dashboard.js',
+        'js/upload.js',
         filters='rjsmin',
         output='build/app.js'
     ))
@@ -20,12 +22,15 @@ def init_assets(app):
     ))
 
     assets.register('app_css', flask_assets.Bundle(
+        'css/vendor/select2-4.0.13.css',
+        'css/select2-custom.css',
         'css/reset.css',
         'css/utils.css',
         'css/main.css',
         'css/sidebar.css',
         'css/search.css',
         'css/dashboard.css',
+        'css/upload.css',
         filters='cssmin',
         output='build/app.css'
     ))

flask_app/initialization/routes.py

@@ -15,12 +15,17 @@ def init_routes(app):
     app.add_url_rule("/dashboard",       view_func=dashboard_pages.dashboard_index_page)
     app.add_url_rule("/dashboard/chart", view_func=dashboard_pages.dashboard_chart_fragment)
 
-    app.add_url_rule("/upload",    view_func=upload_pages.upload_index_page)
+    app.add_url_rule("/upload/1", view_func=upload_pages.upload_step1_page, methods=["GET", "POST"])
+    app.add_url_rule("/upload/2", view_func=upload_pages.upload_step2_page, methods=["GET", "POST"])
+    app.add_url_rule("/upload/3", view_func=upload_pages.upload_step3_page, methods=["GET", "POST"])
+    app.add_url_rule("/upload/4", view_func=upload_pages.upload_step4_page, methods=["GET", "POST"])
 
     app.add_url_rule("/study/<string:studyId>",     view_func=study_pages.study_show_page)
     app.add_url_rule("/study/<string:studyId>.zip", view_func=study_pages.study_download_page)
 
-    app.add_url_rule("/strain/<int:id>",             view_func=strain_pages.strain_show_page)
+    app.add_url_rule("/strain/<int:id>",    view_func=strain_pages.strain_show_page)
+    app.add_url_rule("/strains/completion", view_func=strain_pages.taxa_completion_json)
+
     app.add_url_rule("/metabolite/<string:cheb_id>", view_func=metabolite_pages.metabolite_show_page)
 
     app.add_url_rule(

flask_app/models/submission.py

@@ -0,0 +1,116 @@
+from uuid import uuid4
+
+import sqlalchemy as sql
+
+
+class Submission:
+    def __init__(self, data, current_step=None, db_conn=None):
+        self.step = current_step or 1
+        self.db_conn = db_conn
+
+        # Step 1:
+        self.type         = data.get('type',         None)
+        self.project_uuid = data.get('project_uuid', None)
+        self.study_uuid   = data.get('study_uuid',   None)
+
+        self.project = data.get('project', {'name': None, 'description': None})
+
+        # Step 2:
+        self.strains     = data.get('strains', [])
+        self.new_strains = data.get('new_strains', [])
+
+    def update_project(self, data):
+        self.type = data['submission_type']
+
+        if self.type == 'new_project':
+            self.project_uuid = uuid4()
+            self.study_uuid = uuid4()
+
+            self.project = {
+                'name':        data['project_name'],
+                'description': data['project_description'],
+            }
+        elif self.type == 'new_study':
+            self.project = _get_project_data(self.db_conn, data['project_uuid'])
+            if self.project:
+                self.project_uuid = data['project_uuid']
+
+            self.study_uuid = uuid4()
+        elif self.type == 'update_study':
+            self.project = _get_project_data(self.db_conn, data['project_uuid'])
+            if self.project:
+                self.project_uuid = data['project_uuid']
+
+            self.study_uuid = data['study_uuid']
+        else:
+            raise KeyError("Unknown self type: {}".format(self.submission_type))
+
+    def update_strains(self, data):
+        self.strains     = data['strains']
+        self.new_strains = data['new_strains']
+
+    def update_study_design(self, data):
+        pass
+
+    def fetch_strains(self):
+        if len(self.strains) == 0:
+            return []
+
+        # TODO (2024-09-22) Figure out a sensible way to bind ids
+
+        query = f"""
+            SELECT
+                tax_id AS id,
+                tax_names AS name
+            FROM Taxa
+            WHERE tax_id IN ({','.join(self.strains)})
+        """
+        result = self.db_conn.execute(sql.text(query)).all()
+
+        return [(entry.id, entry.name) for entry in result]
+
+    def fetch_new_strains(self):
+        if len(self.new_strains) == 0:
+            return []
+
+        new_strains = sorted(self.new_strains, key=lambda s: int(s['species']))
+        species_ids = [s['species'] for s in new_strains]
+
+        query = f"""
+            SELECT tax_names
+            FROM Taxa
+            WHERE tax_id IN ({','.join(species_ids)})
+            ORDER BY tax_id
+        """
+        species_names = self.db_conn.execute(sql.text(query)).scalars()
+
+        for strain, name in zip(new_strains, species_names):
+            strain['species_name'] = name
+
+        return new_strains
+
+    def _asdict(self):
+        return {
+            'type':         self.type,
+            'project_uuid': self.project_uuid,
+            'study_uuid':   self.study_uuid,
+            'project':      self.project,
+            'strains':      self.strains,
+            'new_strains':  self.new_strains,
+        }
+
+
+def _get_project_data(db_conn, uuid):
+    query = """
+        SELECT
+            projectName AS name,
+            projectDescription AS description
+        FROM Project
+        WHERE projectUniqueID = :uuid
+    """
+    result = db_conn.execute(sql.text(query), {'uuid': uuid}).one_or_none()
+
+    if result is None:
+        return None
+    else:
+        return result._asdict()

flask_app/pages/strains.py

@@ -1,4 +1,6 @@
-from flask import render_template
+import json
+
+from flask import render_template, request
 import sqlalchemy as sql
 
 from flask_app.db import get_connection
@@ -13,3 +15,42 @@ def strain_show_page(id):
         study = conn.execute(sql.text(query), {'studyId': strain['studyId']}).one()._asdict()
 
         return render_template("pages/strains/show.html", strain=strain, study=study)
+
+
+def taxa_completion_json():
+    term     = request.args.get('term', '').lower()
+    page     = int(request.args.get('page', '1'))
+    per_page = 10
+
+    # TODO (2024-09-21) Extract to model and test
+
+    with get_connection() as conn:
+        query = """
+            SELECT
+                tax_id AS id,
+                tax_names AS text
+            FROM Taxa
+            WHERE LOWER(tax_names) LIKE :term
+            ORDER BY tax_names ASC
+            LIMIT :per_page
+            OFFSET :offset
+        """
+        results = conn.execute(sql.text(query), {
+            'term': f'%{term}%',
+            'per_page': per_page,
+            'offset': (page - 1) * per_page,
+        }).all()
+        results = [row._asdict() for row in results]
+
+        count_query = """
+            SELECT COUNT(*)
+            FROM Taxa
+            WHERE LOWER(tax_names) LIKE LOWER(:term)
+        """
+        total_count = conn.execute(sql.text(count_query), {'term': f'%{term}%'}).scalar()
+        has_more = (page * per_page < total_count)
+
+        return json.dumps({
+            'results': results,
+            'pagination': {'more': has_more},
+        })

flask_app/pages/upload.py

@@ -1,5 +1,71 @@
-from flask import render_template
+from flask import render_template, session, request, redirect, url_for
 
+from flask_app.db import get_connection
+from flask_app.models.submission import Submission
+from flask_app.forms.upload_step2_form import UploadStep2Form
+from flask_app.forms.upload_step3_form import UploadStep3Form
 
-def upload_index_page():
-    return render_template("pages/upload.html")
+
+def upload_step1_page():
+    with get_connection() as conn:
+        submission = Submission(session.get('submission', {}), current_step=1, db_conn=conn)
+        error = None
+
+        if request.method == 'POST':
+            submission.update_project(request.form)
+
+            if submission.project:
+                session['submission'] = submission._asdict()
+                return redirect(url_for('upload_step2_page'))
+            else:
+                error = "No project found with this UUID"
+
+        return render_template(
+            "pages/upload/index.html",
+            submission=submission,
+            error=error
+        )
+
+
+def upload_step2_page():
+    with get_connection() as conn:
+        submission = Submission(session.get('submission', {}), current_step=2, db_conn=conn)
+        form = UploadStep2Form(request.form)
+
+        if request.method == 'POST':
+            submission.update_strains(form.data)
+            session['submission'] = submission._asdict()
+
+            return redirect(url_for('upload_step3_page'))
+
+        return render_template(
+            "pages/upload/index.html",
+            submission=submission,
+        )
+
+
+def upload_step3_page():
+    with get_connection() as conn:
+        submission = Submission(session.get('submission', {}), current_step=3, db_conn=conn)
+        form = UploadStep3Form(request.form)
+
+        if request.method == 'POST':
+            submission.update_study_design(form.data)
+            session['submission'] = submission._asdict()
+
+            return redirect(url_for('upload_step3_page'))
+
+        return render_template(
+            "pages/upload/index.html",
+            submission=submission,
+        )
+
+
+def upload_step4_page():
+    with get_connection() as conn:
+        submission = Submission(session.get('submission', {}), current_step=4, db_conn=conn)
+
+        return render_template(
+            "pages/upload/index.html",
+            submission=submission,
+        )

flask_app/static/css/dashboard.css

@@ -1,7 +1,7 @@
 .dashboard-page {
   details.experiment-container {
     border: 1px solid var(--border-color);
-    border-radius: 8px;
+    border-radius: var(--border-radius);
     padding: 10px;
     margin-top: 20px;
     margin-bottom: 10px;