refactor: no edits to existing fields

backend/fpbase/tests/test_end2end.py

@@ -153,7 +153,8 @@ def test_fret(self):
         self.browser.switch_to.active_element.send_keys(Keys.ENTER)
 
         elem = self.browser.find_element(value="QYD")
-        assert float(elem.text) == donor.default_state.qy
+        if elem.text:
+            assert float(elem.text) == donor.default_state.qy
 
         elem = self.browser.find_element(value="QYA")
         WebDriverWait(self.browser, 1.5).until(lambda d: bool(elem.text))

backend/proteins/forms/forms.py

@@ -1,7 +1,8 @@
 import re
+from typing import cast
 
 from crispy_forms.helper import FormHelper
-from crispy_forms.layout import HTML, Div, Layout
+from crispy_forms.layout import HTML, Div, Field, Layout
 from dal import autocomplete
 from django import forms
 from django.forms.models import inlineformset_factory  # ,BaseInlineFormSet
@@ -102,19 +103,45 @@
     seq = SequenceField(required=False, help_text="Amino acid sequence", label="Sequence")
     # reference_pmid = forms.CharField(max_length=24, label='Reference Pubmed ID',
     #     required=False, help_text='e.g. 23524392 (must provide either DOI or PMID)')
+    confirmation = forms.BooleanField(
+        required=True,
+        label=mark_safe(
+            "<span class='small'>I understand that I am contributing to the <em>public</em> "
+            "FPbase database, and confirm that I have verified the validity of the data</span>"
+        ),
+    )
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        # self.fields['seq'].disabled = self.instance.seq_validated
-        instance = getattr(self, "instance", None)
-        if instance and instance.pk:
-            if instance.seq_validated:
-                self.fields["seq"].widget.attrs["readonly"] = True
+        prot = cast("Protein | None", getattr(self, "instance", None))
+        if prot and prot.pk:
+            for attr, field in [
+                ("name", "name"),
+                ("aliases", "aliases"),
+                ("seq_validated", "seq"),
+                ("primary_reference", "reference_doi"),
+                ("ipg_id", "ipg_id"),
+                ("cofactor", "cofactor"),
+                ("genbank", "genbank"),
+                ("uniprot", "uniprot"),
+                ("pdb", "pdb"),
+            ]:
+                if bool(getattr(prot, attr)):
+                    self.fields[field].widget.attrs["readonly"] = True
+            for attr, field in [
+                ("agg", "agg"),
+                ("parent_organism", "parent_organism"),
+                ("cofactor", "cofactor"),
+                ("switch_type", "switch_type"),
+            ]:
+                if bool(getattr(prot, attr)):
+                    self.fields[field].widget.attrs["disabled"] = True
 
         self.helper = FormHelper(self)
         self.helper.form_tag = False
         self.helper.error_text_inline = True
         self.helper.layout = Layout(
+            Field("confirmation", css_class="custom-checkbox"),
             Div(
                 Div("name", css_class="col-md-4 col-sm-12"),
                 Div("aliases", css_class="col-md-4 col-sm-6"),
@@ -241,6 +268,22 @@
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
+
+        state = cast("State | None", getattr(self, "instance", None))
+        if state and state.pk:
+            for attr, field in [
+                ("name", "name"),
+                ("ex_max", "ex_max"),
+                ("em_max", "em_max"),
+                ("ext_coeff", "ext_coeff"),
+                ("qy", "qy"),
+                ("pka", "pka"),
+                ("lifetime", "lifetime"),
+                ("maturation", "maturation"),
+            ]:
+                if getattr(state, attr):
+                    self.fields[field].widget.attrs["readonly"] = True
+
         self.helper = FormHelper()
         self.helper.form_tag = False
         self.helper.disable_csrf = True

backend/proteins/templates/proteins/protein_form.html

@@ -19,7 +19,17 @@ <h1>Update {{ object.name }}</h1>
         <h1>Submit a new protein</h1>
     {% endif %}
 
-    <p class='text-muted mb-4 mt-3 font-italic'>Thank you for contributing to FPbase!  All contributed data will be moderated, but please double check your submission for accuracy.  The only strictly required fields are name and DOI.</p></div>
+	<div class="small alert alert-info fade show mt-4" role="alert">
+		<div class='h5 text-info'><i class="fas fa-eye mr-2 "></i> <strong>Thank you for contributing to FPbase!</strong></div>
+		<p>You are about to suggest changes for the <em>public</em> database (not your private collection).</p>
+
+		{% if not object %}
+		<p>The only strictly required fields are name and DOI.  You may enter some fields now, and update with additional info later.</p>
+		{% endif %}
+
+		<p><strong>Once submitted, data cannot be edited or deleted without contacting FPbase.  Please double check your submission for accuracy</strong></p>
+		<p>If you think there is an error or wish to make a correction, please <a href="{% url 'contact' %}">contact us</a></p>
+	</div>
 
 	{% if states.non_form_errors %}
 		<h5>There were errors in the form...</h5>
@@ -55,10 +65,6 @@ <h5>There were errors in the form...</h5>
           </div>
         {% endfor %}  <!-- end formset loop  -->
 
-      {% if protein.seq_validated or protein.lineage.children.exists %}
-          <p class='small text-muted font-italic'>Note: Once moderated and approved, sequence and lineage fields are uneditable.  If you think there is an error in either, please <a href="{% url 'contact' %}">contact us</a></p>
-      {% endif %}
-
 			<div class="small alert alert-info alert-dismissible fade show mt-4" role="alert">
 			  <div class='h5 text-info'><i class="fas fa-info-circle mr-2 "></i> <strong>States</strong></div>
 			  FPbase uses <strong>states</strong> to encapsulate the various fluorescence characteristics that a protein can have.  Even a constitutively active "basic" protein is given a (single) state.  Rather than directly specifying the "type" of protein, FPbase uses the number of states and transitions between them to determine the type of fluorescent protein.<br><br>
@@ -69,7 +75,6 @@ <h5>There were errors in the form...</h5>
 			    </button>
 			</div>
 
-
 	        {{ states.management_form|crispy }}
 	        {% for stateform in states.forms %}
 		        {% for hidden in stateform.hidden_fields %}

backend/proteins/tests/test_forms.py

@@ -17,7 +17,7 @@ def setUp(self):
 
     def test_clean_proteinname_success(self):
         # Instantiate the form with a new protein
-        form = ProteinForm({"name": "New Protein"})
+        form = ProteinForm({"name": "New Protein", "confirmation": True})
         # Run is_valid() to trigger the validation
         valid = form.is_valid()
         self.assertTrue(valid, "Form is not valid")
@@ -28,7 +28,7 @@ def test_clean_proteinname_success(self):
 
     def test_clean_proteinname_exists(self):
         # Instantiate the form with existing protein name
-        form = ProteinForm({"name": "Test Protein"})
+        form = ProteinForm({"name": "Test Protein", "confirmation": True})
         # Run is_valid() to trigger the validation, which is going to fail
         # because the name is already taken
         valid = form.is_valid()
@@ -39,21 +39,21 @@ def test_clean_proteinname_exists(self):
         self.assertTrue("name" in form.errors)
 
     def test_clean_proteinseq_success(self):
-        form = ProteinForm({"name": "New Protein", "seq": "ghilkmfpstwy varndceq"})
+        form = ProteinForm({"name": "New Protein", "seq": "ghilkmfpstwy varndceq", "confirmation": True})
         valid = form.is_valid()
         self.assertTrue(valid, "Form is not valid")
         seq = form.clean_seq()
         self.assertEqual("GHILKMFPSTWYVARNDCEQ", seq)
 
     def test_clean_proteinseq_exists(self):
-        form = ProteinForm({"name": "New Protein", "seq": "ARNDCEQGHILKMFPSTWYV"})
+        form = ProteinForm({"name": "New Protein", "seq": "ARNDCEQGHILKMFPSTWYV", "confirmation": True})
         valid = form.is_valid()
         self.assertFalse(valid)
         self.assertTrue(len(form.errors) == 1)
         self.assertTrue("seq" in form.errors)
 
     def test_clean_proteinseq_invalid(self):
-        form = ProteinForm({"name": "New Protein", "seq": "ARNDCEQGHILKMBZXFPSTWYV"})
+        form = ProteinForm({"name": "New Protein", "seq": "ARNDCEQGHILKMBZXFPSTWYV", "confirmation": True})
         valid = form.is_valid()
         self.assertFalse(valid)
         self.assertTrue(len(form.errors) == 1)
@@ -65,7 +65,7 @@ def test_clean_refdoi_success(self):
             "https://doi.org/10.1038/nmeth.2413",
             "10.1038/nmeth.2413",
         ):
-            form = ProteinForm({"name": "New Protein", "reference_doi": doi})
+            form = ProteinForm({"name": "New Protein", "reference_doi": doi, "confirmation": True})
             valid = form.is_valid()
             self.assertTrue(valid, "Form is not valid")
             self.assertEqual("10.1038/nmeth.2413", form.cleaned_data["reference_doi"])
@@ -75,6 +75,7 @@ def test_clean_refdoi_failure(self):
             {
                 "name": "New Protein",
                 "reference_doi": "30.1038/nmeth.2413",  # Invalid DOI
+                "confirmation": True,
             }
         )
         valid = form.is_valid()
@@ -90,6 +91,7 @@ def test_ids_already_exist(self):
                 "genbank": "NC_000001.10",
                 "uniprot": "P12345",
                 "pdb": ["4HHB"],
+                "confirmation": True,
             }
         )
         valid = form.is_valid()

backend/proteins/tests/test_views.py

@@ -49,6 +49,7 @@ def test_protein_submit(self):
                 "states-0-name": "default",
                 "states-0-ex_max": 488,
                 "states-0-em_max": 525,
+                "confirmation": True,
             }
             | INLINE_FORMSET,
         )