Updates from DNAnexus on 20240802

bco-tool/app/services/custom_bco_db.py

@@ -0,0 +1,45 @@
+from typing import Dict
+import requests
+import json
+
+class CustomBcoDB():
+    def __init__(self, host_url: str, credentials: dict):
+        self.__host_url__ = host_url
+        self.__credentials__ = credentials
+
+    def upload(self) -> Dict[str, str]:
+        try:
+            with open("app/schemas/biocompute_export.json", "r") as file:
+                file_content = json.load(file)
+
+            headers = {
+                "Content-type": "application/json; charset=UTF-8",
+            }
+
+            if self.__credentials__ and len(self.__credentials__) > 0:
+                headers.update(self.__credentials__)
+
+            response = requests.post(
+                url=self.__host_url__,
+                data=json.dumps({ "contents": file_content }),
+                headers=headers
+            )
+
+            if response.status_code == 200:
+                print("File uploaded to Custom BCO DB")
+                return {
+                    "code": 200,
+                    "message": "File uploaded to Custom BCO DB",
+                }
+            else:
+                print("Failed to update file to Custom BCO DB", response.__dict__)
+                return {
+                    "code": response.status_code,
+                    "message": "Failed to update file to Custom BCO DB"
+                }
+        except Exception as e:
+            print(f"Error uploading to Custom BCO DB -- {repr(e)}")
+            return {
+                "code": 500,
+                "message": "Internal server error"
+            }

bco-tool/app/static/exportfile_custom_bco_db.js

@@ -0,0 +1,101 @@
+$(document).ready(function() {
+    bindEvents();
+
+    function bindEvents() {
+        // config to show toast on top center
+        toastr.options = { "positionClass": "toast-top-center" };
+
+        // enable/disable the submit button if url is changed
+        $("#bco_custom_db_url").on("input", (event) => {
+            $(".btn-submit-custom-bco-db").prop("disabled", !event.target.value);
+        });
+
+        // handle event when clicking on the "add/remove credential" button
+        $(document).on('click', '.btn-add-credential', addCredential);
+        $(document).on('click', '.btn-remove-credential', removeCredential);
+
+        // handle event when clicking on the submit button
+        $('.btn-submit-custom-bco-db').on('click', exportFileToCustomBcoDb);
+    }
+
+    function exportFileToCustomBcoDb(event) {
+        const btnSubmit = event.target;
+        const url = $("#bco_custom_db_url").val();
+
+        if (!url) {
+            return toastr.error("Please enter data for all fields to upload custom BCO database");
+        }
+
+        const setSubmitting = (isSubmitting) => {
+            if (isSubmitting) {
+                btnSubmit.disabled = true;
+                btnSubmit.innerHTML = "Submitting...";
+            } else {
+                btnSubmit.disabled = false;
+                btnSubmit.innerHTML = "Submit";
+            }
+        };
+
+        // submit form data
+        setSubmitting(true);
+        $.ajax({
+            type: "POST",
+            headers: { "X-CSRFToken": getCookie("csrftoken") },
+            url: "export_to_custom_bco_db",
+            contentType: "application/json; charset=utf-8",
+            data: JSON.stringify({
+                url,
+                credentials: getCredentials(),
+            }),
+            success: (message) => {
+                toastr.success(message)
+                setSubmitting(false);
+                $("#bco_custom_db_export_container").modal("hide");
+            },
+            error: (err) => {
+                toastr.error(err.responseText || err.statusText || "Error when exporting file to custom BCO database");
+                setSubmitting(false);
+            },
+        });
+    }
+
+    function addCredential() {
+        const credentialContainer = $("#credentials-container");
+        const credentialRow = $("<div></div>")
+            .css("display", "flex")
+            .css("gap", "10px")
+            .addClass("mb-2")
+            .html(`
+                <input type="text" class="form-control rounded-lg" placeholder="key" />
+                <input type="text" class="form-control rounded-lg" placeholder="value" />
+                <button 
+                    type="button"
+                    class="btn-remove-credential btn btn-outline-danger rounded-lg"
+                >
+                    Remove
+                </button>
+            `);
+        credentialContainer.append(credentialRow);
+    }
+
+    function removeCredential() {
+        const button = $(this);
+        const credentialRow = button.parent();
+        credentialRow.remove();
+    }
+
+    function getCredentials() {
+        const credentials = {};
+
+        $("#credentials-container > div").each(function() {
+            const credentialKey = $(this).find("input[placeholder='key']").val();
+            const credentialValue = $(this).find("input[placeholder='value']").val();
+
+            if (credentialKey && credentialValue) {
+              credentials[credentialKey] = credentialValue;
+            }
+        });
+
+        return credentials;
+    }
+});

bco-tool/app/static/scripts.js

@@ -522,6 +522,9 @@ $(document).ready(function() {
             $("#user_token").val("")
             $('#bco_db_export_container').modal('show')
         }
+        else if (export_option == "Custom BCO DB") {
+            $('#bco_custom_db_export_container').modal('show');
+        }
         else if (export_option=="PFDA BCO File"){
             $("#pfda_export_space_selector_div").css("visibility", "hidden")
             $("#pfda_export_folder_selector_div").css("visibility", "hidden")

bco-tool/app/static/styles.css

@@ -284,6 +284,9 @@
         border-color: #007bff;
         background-color: #f8f9fa;
     }
+    .rounded-lg {
+        border-radius: 0.5rem;
+    }
     /* .lorem{
         content: '-';
     } */

bco-tool/app/templates/base.html

@@ -35,6 +35,11 @@
     <script type="text/javascript" src="https://cdn.jsdelivr.net/npm/diff2html/bundles/js/diff2html-ui.min.js"></script>
     <link href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/select2.min.css" rel="stylesheet" />
     <script src="https://cdn.jsdelivr.net/npm/[email protected]/dist/js/select2.min.js"></script>
+
+    <!-- toastr -->
+    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/toastr.js/latest/toastr.min.css">
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/toastr.js/latest/toastr.min.js"></script>
+
     <script src="{% static 'scripts.js' %}"></script>
 </head>
 
@@ -75,6 +80,8 @@
                             <a class="dropdown-item" data-value="BCO DB" href="#">BCO Repository</a>
                             <div class="dropdown-divider"></div>
                             <a class="dropdown-item" data-value="PFDA BCO File" href="#">precisionFDA</a>
+                            <div class="dropdown-divider"></div>
+                            <a class="dropdown-item" data-value="Custom BCO DB" href="#">Custom BCO database</a>
                         </div>
                     </li>
                 </ul>
@@ -125,6 +132,7 @@
             {% include "exportfile_dna_nexus.html" %}
             {% include "exportfile_pfda.html" %}
             {% include "exportfile_bco_db.html" %}
+            {% include "exportfile_custom_bco_db.html" %}
             {% include "description_modal.html" %}
             {% include "image_zoom_modal.html" %}
         </div>

bco-tool/app/templates/exportfile_custom_bco_db.html

@@ -0,0 +1,97 @@
+{% load static %}
+{% block file_uploader %}
+{% csrf_token %}
+<div
+  id="bco_custom_db_export_container"
+  class="modal"
+  role="dialog"
+  aria-labelledby="customBCOModalLabel"
+  aria-hidden="true"
+>
+  <div class="modal-dialog" role="document">
+    <div class="modal-content">
+      <div class="modal-header" style="background-color: navy">
+        <h4 class="modal-title" id="customBCOModalLabel" style="color: white">
+          Custom BCO database
+        </h4>
+        <button
+          type="button"
+          class="close"
+          data-dismiss="modal"
+          style="color: white"
+          aria-label="Close"
+        >
+          <span aria-hidden="true">&times;</span>
+        </button>
+      </div>
+      <div class="modal-body">
+        <div class="row mb-2">
+          <div class="col-3 d-flex align-items-center">
+            <label for="bco_custom_db_url" class="mb-0">BCO DB URL</label>
+          </div>
+          <div class="col-9">
+            <input
+              type="text"
+              class="form-control rounded-lg"
+              id="bco_custom_db_url"
+              placeholder="url"
+            />
+          </div>
+        </div>
+        <div class="mb-2 text-left">
+            Credentials
+        </div>
+        <div id="credentials-container">
+          <div
+            class="mb-2"
+            style="
+              display: flex;
+              gap: 10px;
+            "
+          >
+            <input
+              type="text"
+              class="form-control rounded-lg"
+              placeholder="key"
+            />
+            <input
+              type="text"
+              class="form-control rounded-lg"
+              placeholder="value"
+            />
+            <button
+              type="button"
+              class="btn-remove-credential btn btn-outline-danger rounded-lg"
+            >
+              Remove
+            </button>
+          </div>
+        </div>
+        <button
+          type="button"
+          class="btn-add-credential btn btn-outline-primary btn-block mb-2 rounded-lg"
+        >
+          Add
+        </button>
+      </div>
+      <div class="modal-footer">
+        <button
+          type="button"
+          class="btn rounded-lg"
+          data-dismiss="modal"
+        >
+          Close
+        </button>
+        <button
+          type="button"
+          class="btn-submit-custom-bco-db btn btn-primary rounded-lg"
+          disabled
+        >
+          Submit
+        </button>
+      </div>
+    </div>
+  </div>
+</div>
+<script src="{% static 'exportfile_custom_bco_db.js' %}"></script>
+{% endblock %}

bco-tool/app/views.py

@@ -5,6 +5,7 @@
 from collections import OrderedDict
 
 from app.services.bco_db import BcoDB
+from app.services.custom_bco_db import CustomBcoDB
 from app.services.cwl import CWL
 from app.services.dataservices.bco_data_service import \
     BcoDataService, ComparisonBcoDataService
@@ -20,7 +21,7 @@
 from django.contrib import messages
 from django.core.files.base import ContentFile
 from django.core.files.storage import default_storage
-from django.http import HttpResponse, JsonResponse, QueryDict
+from django.http import HttpResponse, HttpResponseNotAllowed, HttpResponseServerError, JsonResponse, QueryDict
 from django.shortcuts import render
 from django.views.decorators.csrf import csrf_protect
 from script import CompileWorkflow
@@ -1287,6 +1288,25 @@ def export_to_bco_db(request):
     except Exception as e:
         return HttpResponse(status=400)
 
+def export_to_custom_bco_db(request) -> HttpResponse:
+    if request.method != "POST":
+        return HttpResponseNotAllowed(permitted_methods="POST")
+
+    try:
+        # create biocompute_export.json file
+        create_export_bco()
+
+        # get request data
+        requestData = json.loads(request.body) 
+        url = requestData.get("url")
+        credentials = requestData.get("credentials")
+
+        # call request
+        response = CustomBcoDB(host_url=url, credentials=credentials).upload()
+        return HttpResponse(status=response.get("code"), content=response.get("message"))
+    except Exception as e:
+        return HttpResponseServerError()
+
 def save_bco_editor(request):
     try:
         if request.method == "POST":

bco-tool/bconexus/settings.py

@@ -26,7 +26,7 @@
 # SECURITY WARNING: don't run with debug turned on in production!
 DEBUG = True
 
-ALLOWED_HOSTS = []
+ALLOWED_HOSTS = ["*"]
 
 
 # Application definition
@@ -102,7 +102,7 @@
             "formatter": 'formatter_1',
             "class": "logging.handlers.RotatingFileHandler",
             "filename": "./Logs/user.log",
-            "maxBytes":10485760, 
+            "maxBytes":10485760,
             "backupCount":1
         },
     },

bco-tool/bconexus/urls.py

@@ -91,6 +91,7 @@
     path('export_dowload_bco', export_dowload_bco, name='export_dowload_bco'),
     path('export_bco_to_dnanexus', export_bco_to_dnanexus, name='export_bco_to_dnanexus'),
     path('export_to_bco_db', export_to_bco_db, name='export_to_bco_db'),
+    path('export_to_custom_bco_db', export_to_custom_bco_db, name='export_to_custom_bco_db'),
     path('search', search, name='search'),
     path('save_bco_editor',save_bco_editor, name='save_bco_editor'),
     path('validate_bco_editor',validate_bco_editor, name='validate_bco_editor'),

bco-tool/requirements.txt

@@ -111,3 +111,4 @@ xhtml2pdf==0.2.1
 xlrd==1.2.0
 xtermcolor==1.3
 zipp==3.1.0
+tzdata==2024.1

bco-tool/requirements_latest.txt

@@ -36,3 +36,4 @@ urllib3==1.26.10
 websocket-client==0.54.0
 xdg==5.1.1
 zipp==3.8.1
+tzdata==2024.1