Update to deploy

.dockerignore

@@ -0,0 +1 @@
+Dockerfile

.github/workflows/release.yml

@@ -0,0 +1,29 @@
+name: Build and push docker images
+
+on:
+  push:
+    branches: [main]
+
+jobs:
+  build-and-push:
+    name: Build image and push to Docker Hub
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      name: Checkout source code
+    - name: Build the Docker image
+      run: |
+        repo_name_lower=$(echo ${{ github.event.repository.name }}| tr [:upper:] [:lower:])
+        tag="synbiohub/${repo_name_lower}:snapshot"
+        echo $tag
+        docker build . --tag $tag
+    - uses: azure/docker-login@v1
+      with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+    - name: Push the image to Docker Hub
+      run: |
+        repo_name_lower=$(echo ${{ github.event.repository.name }}| tr [:upper:] [:lower:])
+        tag="synbiohub/${repo_name_lower}:snapshot"
+        echo $tag
+        docker push $tag

.gitignore

@@ -0,0 +1,2 @@
+__pycache__
+venv

Dockerfile

@@ -0,0 +1,11 @@
+FROM synbiohub/docker-base-python:snapshot
+
+COPY . .
+
+EXPOSE 5000
+
+RUN pip3 install -r requirements.txt
+
+ENV FLASK_APP=app.py
+
+CMD ["waitress-serve", "--port=5000", "app:app" ]

Input_Query.txt

@@ -0,0 +1,29 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX dc: <http://purl.org/dc/elements/1.1/>
+PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
+PREFIX prov: <http://www.w3.org/ns/prov#>
+PREFIX sbol: <http://sbols.org/v2#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX purl: <http://purl.obolibrary.org/obo/>
+
+SELECT
+?def
+?displayId
+?title
+(count(?def) as ?count)
+?role
+WHERE {
+FILTER regex(?role, "identifiers")
+?s sbol:component ?comp .
+?comp sbol:definition <https://synbiohub.org/public/igem/BBa_B0012/1> .
+?s sbol:component ?comp2 .
+?comp2 sbol:definition ?def .
+OPTIONAL {?def sbol:role ?role} .  
+OPTIONAL {?def sbol:displayId ?displayId} .
+OPTIONAL {?def dcterms:title ?title} .
+  }
+ORDER BY DESC (?count) 
+
+#OFFSET 0 LIMIT 50

LICENSE

@@ -0,0 +1,25 @@
+BSD 2-Clause License
+
+Copyright (c) 2020, Zach Zundel
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Most_Used_By_Type_Query.txt

@@ -0,0 +1,27 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX dc: <http://purl.org/dc/elements/1.1/>
+PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
+PREFIX prov: <http://www.w3.org/ns/prov#>
+PREFIX sbol: <http://sbols.org/v2#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX purl: <http://purl.obolibrary.org/obo/>
+
+SELECT
+	?def
+	?displayId
+	?title
+	(count(?def) as ?count)
+	?role
+WHERE {
+FILTER (?role = <http://identifiers.org/so/SO:0000167>) .
+  	?s sbol:component ?comp .
+  	?comp sbol:definition ?def .
+	OPTIONAL {?def sbol:role ?role} .  
+	OPTIONAL {?def sbol:displayId ?displayId} .
+	OPTIONAL {?def dcterms:title ?title} .
+  }
+ORDER BY DESC (?count) 
+
+#OFFSET 0 LIMIT 50

Most_Used_Query.txt

@@ -0,0 +1,27 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX dc: <http://purl.org/dc/elements/1.1/>
+PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
+PREFIX prov: <http://www.w3.org/ns/prov#>
+PREFIX sbol: <http://sbols.org/v2#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX purl: <http://purl.obolibrary.org/obo/>
+
+SELECT
+	?def
+	?displayId
+	?title
+	(count(?def) as ?count)
+	?role
+WHERE {
+  	?s sbol:component ?comp .
+  	?comp sbol:definition ?def .
+        filter (regex(?role, 'http://identifiers.org/so/SO:')) .
+	OPTIONAL {?def sbol:role ?role} .  
+	OPTIONAL {?def sbol:displayId ?displayId} .
+	OPTIONAL {?def dcterms:title ?title} .
+  }
+ORDER BY DESC (?count) 
+
+#OFFSET 0 LIMIT 50

Preceding_Percent_Query.txt

@@ -0,0 +1,49 @@
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX dcterms: <http://purl.org/dc/terms/>
+PREFIX dc: <http://purl.org/dc/elements/1.1/>
+PREFIX sbh: <http://wiki.synbiohub.org/wiki/Terms/synbiohub#>
+PREFIX prov: <http://www.w3.org/ns/prov#>
+PREFIX sbol: <http://sbols.org/v2#>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX purl: <http://purl.obolibrary.org/obo/>
+
+select
+	#?s
+	?def2
+	(COUNT(?def2) AS ?count)
+	?role
+	?title
+	?displayId
+	(AVG(xsd:integer(?preceeding)) AS ?average_preceeding) # 1 means all preceeding, 0 means all following, is percentage preceeding
+	#?preceeding #if negative then component ends before start of queried component
+	#?start
+	#?end 
+	#?startb
+	#?endb
+	#?def
+where {
+	?s sbol:component ?comp .
+	?s sbol:component ?comp2 .
+	?comp sbol:definition ?def .
+	?comp2 sbol:definition ?def2 .
+	?s sbol:sequenceAnnotation ?sa .
+	?sa sbol:component ?comp2 .
+  	?sa sbol:location ?loc .
+	#?loc sbol:start ?start .
+	?loc sbol:end ?end .
+	?s sbol:sequenceAnnotation ?sb .
+  	?sb sbol:component ?comp .
+  	?sb sbol:location ?locb .
+  	?locb sbol:start ?startb .
+  	#?locb sbol:end ?endb .
+  	OPTIONAL {?def2 sbol:role ?role} . 
+  	OPTIONAL {?def2 dcterms:title ?title} .
+	OPTIONAL {?def2 sbol:displayId ?displayId} .
+  	BIND(if(xsd:integer(?end)-xsd:integer(?startb) < 0, "0", "1") AS ?preceeding) .
+	filter(?def = <https://synbiohub.org/public/igem/BBa_E0040/1>) .
+  	filter(?def2 != <https://synbiohub.org/public/igem/BBa_E0040/1>) .
+  	filter (regex(?role, 'http://identifiers.org/so/SO:')) .
+ 	#filter (?role = <http://identifiers.org/so/SO:0000167> || (?role = <http://identifiers.org/so/SO:0000139>)|| (?role = <http://identifiers.org/so/SO:0000316>)|| (?role = <http://identifiers.org/so/SO:0000141>)) .
+    }
+ORDER BY DESC(?count)

README.md

@@ -0,0 +1,8 @@
+# INSTALL 
+## Docker
+Run `docker run --publish 8080:5000 --detach --name component-use-plug synbiohub/plugin-visual-component-use` Check it is up using localhost:8080/sankey/status
+
+## Python
+Using python run `pip install -r requirements.txt` to install the requirements. 
+Then run `FLASK_APP=app python -m flask run`. 
+A flask module will run at localhost:5000/sankey/.

Toggle_Switch_html.txt

@@ -0,0 +1,39 @@
+<html>
+
+<body>
+<input type="checkbox" name="type" id="bytype" /><label for="bytype">Type Matters</label>
+
+<div id="type">
+    <h2>By type</h2>
+</div>
+
+<div id="notype">
+    <h2>Frequency</h2>
+</div>
+
+<script type="text/javascript">
+document.getElementById('type').style.display = 'none';
+document.getElementById('notype').style.display = 'block';
+
+var inputs = document.getElementsByTagName('input');
+
+function dispp() {
+    if (bytype.checked) {
+        document.getElementById('type').style.display = 'block';
+        document.getElementById('notype').style.display = 'none';
+    }
+    else {
+        document.getElementById('type').style.display = 'none';
+        document.getElementById('notype').style.display = 'block';
+    }
+}
+
+for (i = 0; i < inputs.length; i++) {
+    if (inputs[i].type.toLowerCase() == 'checkbox') {
+        inputs[i].onchange = dispp;
+    }
+}
+</script>
+</body>
+
+</html>