now compatible with the latest DNA Weaver version

Edinburgh-Genome-Foundry · Jan 15, 2020 · ef028d2 · ef028d2
1 parent 160a7bc
commit ef028d2
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Showing 9 changed files with 288 additions and 270 deletions.
diff --git a/backend/Dockerfile b/backend/Dockerfile
@@ -41,6 +41,6 @@ RUN pip install -r requirements.txt
 
 ADD . /code/
 
-ARG CACHEBUST=4
+ARG CACHEBUST=5
 RUN pip install --upgrade git+git://github.com/Edinburgh-Genome-Foundry/DnaWeaver
 # RUN pip install biopython==1.70
diff --git a/backend/app/views/generic_solver/GenericSolverView.py b/backend/app/views/generic_solver/GenericSolverView.py
@@ -9,12 +9,12 @@
 from ..serializers import FileSerializer
 import networkx as nx
 from dnaweaver import (CommercialDnaOffer, DnaAssemblyStation, PartsLibrary,
-                       PcrOutStation, DnaSourcesComparator,
+                       PcrExtractionStation,
                        supply_network_from_json)
 from dnaweaver.reports import (JsonQuote, make_folder_report,
                                autocolor_quote_sources, plot_assembly_blocks)
 
-PcrOutStation.dna_banks = {
+PcrExtractionStation.dna_banks = {
     'e_coli': os.path.join("app", "data", "blastdb", "e_coli", "ecoli")
 }
 PartsLibrary.collections_by_id['EMMA'] = dict(

diff --git a/frontend/src/components/SupplyNetwork/json/default-graph.json b/frontend/src/components/SupplyNetwork/json/default-graph.json
@@ -31,7 +31,7 @@
       "cost": 40,
       "duration": 7,
       "overlap": 40,
-      "overhang_type": "tm",
+      "homology_type": "tm",
       "tm_range": [55, 70],
       "overhang_size_range": [15, 30],
       "max_fragments": 10,

diff --git a/frontend/src/components/SupplyNetwork/json/suppliers.json b/frontend/src/components/SupplyNetwork/json/suppliers.json
@@ -29,14 +29,13 @@
     "defaultName": "Assembly station",
     "defaultParameters": {
       "method": "gibson_assembly",
-      "overlap": 40,
       "cost": 20,
       "duration": 7,
       "max_fragments": 10,
       "enzyme": "BsmBI",
       "fragments_size_range": [100, 5000],
       "overlap": 40,
-      "overhang_type": "tm",
+      "homology_type": "tm",
       "tm_range": [55, 70],
       "overhang_size_range": [15, 30],
       "use_astar": true,
@@ -67,7 +66,11 @@
       "pcr_homology_length": 25,
       "max_overhang_length": 40,
       "max_amplicon_length": 10000,
-      "dna_bank": "e_coli"
+      "dna_bank": "e_coli",
+      "homology_size_range": [18, 22],
+      "tm_range": [55, 65],
+      "homology_type": "tm",
+      "homology_size": 20
     }
   },
   "comparator": {

diff --git a/frontend/src/components/SupplyNetwork/supplier-forms/PCR.vue b/frontend/src/components/SupplyNetwork/supplier-forms/PCR.vue
@@ -12,7 +12,14 @@
     el-form-item(label='Max amplicon size (bp)')
       el-input-number(size='small', v-model='form.max_amplicon_length')
     el-form-item(label='Primer homology')
-      el-input-number(size='small', v-model='form.pcr_homology_length')
+      el-select(v-model='form.homology_type')
+        el-option(value='fixed_size', label='Fixed size')
+        el-option(value='tm', label='Target Tm')
+    el-form-item(label='Tm (C)' v-if="(form.homology_type == 'tm')")
+      detail-slider(v-model='form.homology_size_range', :min='10', :max='120' range)
+      detail-slider(v-model='form.tm_range', :min='20', :max='120' range)
+    el-form-item(label='Homology size (bp)' v-if="form.homology_type == 'fixed_size'")
+      el-input-number(size='small', v-model='form.homology_size')
     el-form-item(label='Max overhang size')
       el-input-number(size='small', v-model='form.max_overhang_length')
 </template>

diff --git a/frontend/static/examples/domestication/domestication.json b/frontend/static/examples/domestication/domestication.json
@@ -56,9 +56,12 @@
    "parameters": {
     "cost": 4,
     "duration": 2,
-    "pcr_homology_length": 20,
+    "homology_type": "tm",
+    "homology_size_range": [18, 22],
+    "tm_range": [55, 65],
     "max_overhang_length": 40,
     "max_amplicon_length": 10000,
+    "homology_size": 20,
     "dna_bank": "e_coli"
    }
   },

diff --git a/frontend/static/examples/parts_reuse/parts_reuse.json b/frontend/static/examples/parts_reuse/parts_reuse.json
@@ -91,9 +91,12 @@
    "parameters": {
     "cost": 4,
     "duration": 2,
-    "pcr_homology_length": 25,
+    "homology_type": "tm",
+    "homology_size_range": [18, 22],
+    "tm_range": [55, 65],
     "max_overhang_length": 40,
     "max_amplicon_length": 10000,
+    "homology_size": 20,
     "dna_bank": "e_coli"
    }
   },