From 89de303d3ee8af2e3da48cce50ed12dceade3b36 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 18:29:18 +0000
Subject: [PATCH 01/48] Create main.yml

---
 .github/workflows/main.yml | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 .github/workflows/main.yml

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 000000000..93cc313a6
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,38 @@
+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ debug ]
+  pull_request:
+    branches: [ debug ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  config:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Extract branch name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        id: extract_branch
+
+      # Runs a single command using the runners shell
+      - name: Run a one-line script
+        run: echo ${{ steps.extract_branch.outputs.branch }}
+
+      # Runs a set of commands using the runners shell
+      - name: Run a multi-line script
+        run: |
+          echo Add other actions to build,
+          echo test, and deploy your project.

From 13986413085ded109f4ea349eadb29e0d948d2aa Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 18:31:30 +0000
Subject: [PATCH 02/48] fix branch

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 93cc313a6..4def31e51 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -24,7 +24,7 @@ jobs:
 
       - name: Extract branch name
         shell: bash
-        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
         id: extract_branch
 
       # Runs a single command using the runners shell

From 608bd7f0e5291bc7477ee20f5294f4bb6f1663ee Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 18:39:14 +0000
Subject: [PATCH 03/48] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4def31e51..9bd2b96ff 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -34,5 +34,5 @@ jobs:
       # Runs a set of commands using the runners shell
       - name: Run a multi-line script
         run: |
-          echo Add other actions to build,
+          echo ${GITHUB_REF##*/}
           echo test, and deploy your project.

From 6b25cd5eea2e01550c0dfc3dc20e9d9b5fa9204c Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 19:03:11 +0000
Subject: [PATCH 04/48] Update main.yml

---
 .github/workflows/main.yml | 39 ++++++++++++++++++++++++++++++++++----
 1 file changed, 35 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9bd2b96ff..61df5c4e8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,14 +22,45 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
 
-      - name: Extract branch name
+      - name: Set servers
         shell: bash
-        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF##*/})"
-        id: extract_branch
+        run: |
+          echo "##[set-output name=;]$(echo ${GITHUB_REF##*/})"
+          echo "##[set-output name=VFB_PDB_SERVER;]$(echo http://pdb:7474)"
+          echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl:8080/kbs/vfb/)"
+          echo "##[set-output name=VFB_R_SERVER;]$(echo http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast)"
+          echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.p2.virtualflybrain.org)"
+          echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.p2.virtualflybrain.org/solr/ontology/select)"
+          if [ "${GITHUB_REF##*/}" == debug ]
+          then
+            echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
+            echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl.virtualflybrain.org/kbs/vfb/)"
+            echo "##[set-output name=VFB_R_SERVER;]$(echo http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast)"
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
+          elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ]
+          then
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)"
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-dev.virtualflybrain.org/solr/ontology/select)"
+          elif [ "${GITHUB_REF##*/}" == alpha ]
+          then
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)"
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)"
+          else
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
+          fi
+        id: servers
 
       # Runs a single command using the runners shell
       - name: Run a one-line script
-        run: echo ${{ steps.extract_branch.outputs.branch }}
+        run: |
+          echo PDB:${{ steps.server.outputs.VFB_PDB_SERVER }}
+          echo OWL:${{ steps.server.outputs.VFB_OWL_SERVER }}
+          echo SOLR:${{ steps.server.outputs.SOLR_SERVER }}
+          echo TREE_PDB:${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
+          echo R:${{ steps.server.outputs.VFB_R_SERVER }}
+
 
       # Runs a set of commands using the runners shell
       - name: Run a multi-line script

From 4686538f54e419da40d2d1d1e73258a9663a65d8 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 19:05:52 +0000
Subject: [PATCH 05/48] typo fix

---
 .github/workflows/main.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 61df5c4e8..c1a19b604 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -25,7 +25,6 @@ jobs:
       - name: Set servers
         shell: bash
         run: |
-          echo "##[set-output name=;]$(echo ${GITHUB_REF##*/})"
           echo "##[set-output name=VFB_PDB_SERVER;]$(echo http://pdb:7474)"
           echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl:8080/kbs/vfb/)"
           echo "##[set-output name=VFB_R_SERVER;]$(echo http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast)"

From a8425e8fc9fbe846f38f0d008ec42b489fca8a04 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 19:09:34 +0000
Subject: [PATCH 06/48] Update main.yml

---
 .github/workflows/main.yml | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c1a19b604..bd5b66442 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -30,22 +30,19 @@ jobs:
           echo "##[set-output name=VFB_R_SERVER;]$(echo http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast)"
           echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.p2.virtualflybrain.org)"
           echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.p2.virtualflybrain.org/solr/ontology/select)"
-          if [ "${GITHUB_REF##*/}" == debug ]
-          then
+          if [ "${GITHUB_REF##*/}" == debug ] ; then
             echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl.virtualflybrain.org/kbs/vfb/)"
             echo "##[set-output name=VFB_R_SERVER;]$(echo http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
-          elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ]
-          then
+          elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-dev.virtualflybrain.org/solr/ontology/select)"
-          elif [ "${GITHUB_REF##*/}" == alpha ]
-          then
+          elif [ "${GITHUB_REF##*/}" == alpha ] ; then
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)"
-          else
+          else 
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
           fi

From 84fde8f952783b0cef6cd857925cd372abe7bf60 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 19:15:28 +0000
Subject: [PATCH 07/48] Update main.yml

---
 .github/workflows/main.yml | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index bd5b66442..cf832fac7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -25,24 +25,28 @@ jobs:
       - name: Set servers
         shell: bash
         run: |
-          echo "##[set-output name=VFB_PDB_SERVER;]$(echo http://pdb:7474)"
-          echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl:8080/kbs/vfb/)"
-          echo "##[set-output name=VFB_R_SERVER;]$(echo http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast)"
-          echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.p2.virtualflybrain.org)"
-          echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.p2.virtualflybrain.org/solr/ontology/select)"
-          if [ "${GITHUB_REF##*/}" == debug ] ; then
+          echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474)"
+          echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/)"
+          echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast)"
+          echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.p2.virtualflybrain.org)"
+          echo "::set-output name=SOLR_SERVER::https://solr.p2.virtualflybrain.org/solr/ontology/select)"
+          if [ "${GITHUB_REF##*/}" == master ] ; then
+            echo "::debug::Set to master setup"
             echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl.virtualflybrain.org/kbs/vfb/)"
             echo "##[set-output name=VFB_R_SERVER;]$(echo http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
           elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
+            echo "::debug::Set to dev setup"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-dev.virtualflybrain.org/solr/ontology/select)"
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
+            echo "::debug::Set to alpha setup"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)"
           else 
+            echo "::debug::Set to default setup"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
           fi

From 03de29463d831cb566a9efb92d5fb58ba0d0e0c9 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 20:14:41 +0000
Subject: [PATCH 08/48] Update main.yml

---
 .github/workflows/main.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cf832fac7..5f5462d3f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -25,11 +25,11 @@ jobs:
       - name: Set servers
         shell: bash
         run: |
-          echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474)"
-          echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/)"
-          echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast)"
-          echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.p2.virtualflybrain.org)"
-          echo "::set-output name=SOLR_SERVER::https://solr.p2.virtualflybrain.org/solr/ontology/select)"
+          echo "::set-output name=PDB::http://pdb:7474"
+          echo "::set-output name=OWL::http://owl:8080/kbs/vfb/"
+          echo "::set-output name=R::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
+          echo "::set-output name=TREE::https://pdb.p2.virtualflybrain.org"
+          echo "::set-output name=SOLR::https://solr.p2.virtualflybrain.org/solr/ontology/select"
           if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup"
             echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"

From a4bd8f7f94c501dadb7591abf4f737e980a5d8ae Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 20:27:29 +0000
Subject: [PATCH 09/48] Update main.yml

---
 .github/workflows/main.yml | 35 +++++++++++++++++++----------------
 1 file changed, 19 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5f5462d3f..2d80700fb 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -24,13 +24,8 @@ jobs:
 
       - name: Set servers
         shell: bash
-        run: |
-          echo "::set-output name=PDB::http://pdb:7474"
-          echo "::set-output name=OWL::http://owl:8080/kbs/vfb/"
-          echo "::set-output name=R::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
-          echo "::set-output name=TREE::https://pdb.p2.virtualflybrain.org"
-          echo "::set-output name=SOLR::https://solr.p2.virtualflybrain.org/solr/ontology/select"
-          if [ "${GITHUB_REF##*/}" == master ] ; then
+      - id: pdb
+        run: if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup"
             echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
@@ -39,27 +34,35 @@ jobs:
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
           elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
             echo "::debug::Set to dev setup"
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)"
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-dev.virtualflybrain.org/solr/ontology/select)"
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474"
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/"
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
+            echo "::set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)"
+            echo "::set-output name=SOLR_SERVER:https://solr-dev.virtualflybrain.org/solr/ontology/select)"
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
             echo "::debug::Set to alpha setup"
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474"
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/"
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)"
           else 
             echo "::debug::Set to default setup"
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474"
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/"
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
             echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
             echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
           fi
-        id: servers
-
+        
       # Runs a single command using the runners shell
       - name: Run a one-line script
         run: |
-          echo PDB:${{ steps.server.outputs.VFB_PDB_SERVER }}
-          echo OWL:${{ steps.server.outputs.VFB_OWL_SERVER }}
-          echo SOLR:${{ steps.server.outputs.SOLR_SERVER }}
-          echo TREE_PDB:${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
-          echo R:${{ steps.server.outputs.VFB_R_SERVER }}
+          echo PDB:${{ steps.pdb.outputs.VFB_PDB_SERVER }}
+          echo OWL:${{ steps.pdb.outputs.VFB_OWL_SERVER }}
+          echo SOLR:${{ steps.pdb.outputs.SOLR_SERVER }}
+          echo TREE_PDB:${{ steps.pdb.outputs.VFB_TREE_PDB_SERVER }}
+          echo R:${{ steps.server.pdb.VFB_R_SERVER }}
 
 
       # Runs a set of commands using the runners shell

From 51c9cdf3042edaf47c10b6c1f5fcd8b207ad7e6c Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 20:38:50 +0000
Subject: [PATCH 10/48] Update main.yml

---
 .github/workflows/main.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 2d80700fb..a4ee968ea 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,10 +21,9 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
-
-      - name: Set servers
-        shell: bash
+        
       - id: pdb
+        shell: bash
         run: if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup"
             echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"

From 23f615f93ccc539325edaa0348f164360194702a Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 20:40:48 +0000
Subject: [PATCH 11/48] Update main.yml

---
 .github/workflows/main.yml | 48 +++++++++++++++++++-------------------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a4ee968ea..56326dde3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -25,33 +25,33 @@ jobs:
       - id: pdb
         shell: bash
         run: if [ "${GITHUB_REF##*/}" == master ] ; then
-            echo "::debug::Set to master setup"
-            echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
-            echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl.virtualflybrain.org/kbs/vfb/)"
-            echo "##[set-output name=VFB_R_SERVER;]$(echo http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast)"
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
+            echo "::debug::Set to master setup";
+            echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)";
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)";
+            echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl.virtualflybrain.org/kbs/vfb/)";
+            echo "##[set-output name=VFB_R_SERVER;]$(echo http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast)";
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)";
           elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
-            echo "::debug::Set to dev setup"
-            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474"
-            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/"
-            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
-            echo "::set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)"
-            echo "::set-output name=SOLR_SERVER:https://solr-dev.virtualflybrain.org/solr/ontology/select)"
+            echo "::debug::Set to dev setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)";
+            echo "::set-output name=SOLR_SERVER:https://solr-dev.virtualflybrain.org/solr/ontology/select)";
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
-            echo "::debug::Set to alpha setup"
-            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474"
-            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/"
-            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)"
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)"
+            echo "::debug::Set to alpha setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)";
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)";
           else 
-            echo "::debug::Set to default setup"
-            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474"
-            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/"
-            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast"
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)"
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)"
+            echo "::debug::Set to default setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
+            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)";
+            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)";
           fi
         
       # Runs a single command using the runners shell

From 4edf03227dfa9eb9898dc7df76b14ad1abba5f3c Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 20:51:36 +0000
Subject: [PATCH 12/48] typo fix

---
 .github/workflows/main.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 56326dde3..9d6358d59 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -26,32 +26,32 @@ jobs:
         shell: bash
         run: if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup";
-            echo "##[set-output name=VFB_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)";
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)";
-            echo "##[set-output name=VFB_OWL_SERVER;]$(echo http://owl.virtualflybrain.org/kbs/vfb/)";
-            echo "##[set-output name=VFB_R_SERVER;]$(echo http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast)";
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)";
+            echo "::set-output name=VFB_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
           elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
             echo "::debug::Set to dev setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
             echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
-            echo "::set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org)";
-            echo "::set-output name=SOLR_SERVER:https://solr-dev.virtualflybrain.org/solr/ontology/select)";
+            echo "::set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER:https://solr-dev.virtualflybrain.org/solr/ontology/select";
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
             echo "::debug::Set to alpha setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
             echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-alpha.virtualflybrain.org)";
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr-alpha.virtualflybrain.org/solr/ontology/select)";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-alpha.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-alpha.virtualflybrain.org/solr/ontology/select";
           else 
             echo "::debug::Set to default setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
             echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
-            echo "##[set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb.virtualflybrain.org)";
-            echo "##[set-output name=SOLR_SERVER;]$(echo https://solr.virtualflybrain.org/solr/ontology/select)";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
           fi
         
       # Runs a single command using the runners shell

From 23c907e726ccfd785c71f9f9dff931f089cc8f4f Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 20:57:44 +0000
Subject: [PATCH 13/48] Update main.yml

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9d6358d59..5b2756cfb 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -36,8 +36,8 @@ jobs:
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
             echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
-            echo "::set-output name=VFB_TREE_PDB_SERVER;]$(echo https://pdb-dev.virtualflybrain.org";
-            echo "::set-output name=SOLR_SERVER:https://solr-dev.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-dev.virtualflybrain.org/solr/ontology/select";
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
             echo "::debug::Set to alpha setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";

From f42f798ff28ddd6ba9dc1f964e3311021abd3f01 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 21:21:49 +0000
Subject: [PATCH 14/48] Update main.yml

---
 .github/workflows/main.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5b2756cfb..61d5e3a6a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -22,7 +22,7 @@ jobs:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
         
-      - id: pdb
+      - id: server
         shell: bash
         run: if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup";
@@ -57,10 +57,10 @@ jobs:
       # Runs a single command using the runners shell
       - name: Run a one-line script
         run: |
-          echo PDB:${{ steps.pdb.outputs.VFB_PDB_SERVER }}
-          echo OWL:${{ steps.pdb.outputs.VFB_OWL_SERVER }}
-          echo SOLR:${{ steps.pdb.outputs.SOLR_SERVER }}
-          echo TREE_PDB:${{ steps.pdb.outputs.VFB_TREE_PDB_SERVER }}
+          echo PDB:${{ steps.server.outputs.VFB_PDB_SERVER }}
+          echo OWL:${{ steps.server.outputs.VFB_OWL_SERVER }}
+          echo SOLR:${{ steps.server.outputs.SOLR_SERVER }}
+          echo TREE_PDB:${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
           echo R:${{ steps.server.pdb.VFB_R_SERVER }}
 
 

From 0dcc9a0bb256bd68f4593873ba7bd3dc377244dd Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 21:25:28 +0000
Subject: [PATCH 15/48] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 61d5e3a6a..e13ac37d8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -61,7 +61,7 @@ jobs:
           echo OWL:${{ steps.server.outputs.VFB_OWL_SERVER }}
           echo SOLR:${{ steps.server.outputs.SOLR_SERVER }}
           echo TREE_PDB:${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
-          echo R:${{ steps.server.pdb.VFB_R_SERVER }}
+          echo R:${{ steps.server.outputs.VFB_R_SERVER }}
 
 
       # Runs a set of commands using the runners shell

From 1d5626914fb0e63f4ffc63016de46f3bddbcdeb5 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 22:25:48 +0000
Subject: [PATCH 16/48] adding build

---
 .github/workflows/main.yml | 51 +++++++++++++++++++++++++++++++-------
 1 file changed, 42 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e13ac37d8..c56c9cf50 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -21,8 +21,10 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
-        
-      - id: server
+      
+      # Decide based on branch which servers to use
+      - name: Setup servers
+        id: server
         shell: bash
         run: if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup";
@@ -31,6 +33,7 @@ jobs:
             echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
             echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
           elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
             echo "::debug::Set to dev setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
@@ -38,6 +41,7 @@ jobs:
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-dev.virtualflybrain.org";
             echo "::set-output name=SOLR_SERVER::https://solr-dev.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::development";
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
             echo "::debug::Set to alpha setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
@@ -45,6 +49,7 @@ jobs:
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-alpha.virtualflybrain.org";
             echo "::set-output name=SOLR_SERVER::https://solr-alpha.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::staging";
           else 
             echo "::debug::Set to default setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
@@ -52,10 +57,11 @@ jobs:
             echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
             echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
           fi
         
-      # Runs a single command using the runners shell
-      - name: Run a one-line script
+      # Output the chosen servers
+      - name: Used Servers
         run: |
           echo PDB:${{ steps.server.outputs.VFB_PDB_SERVER }}
           echo OWL:${{ steps.server.outputs.VFB_OWL_SERVER }}
@@ -64,8 +70,35 @@ jobs:
           echo R:${{ steps.server.outputs.VFB_R_SERVER }}
 
 
-      # Runs a set of commands using the runners shell
-      - name: Run a multi-line script
-        run: |
-          echo ${GITHUB_REF##*/}
-          echo test, and deploy your project.
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+      
+      - name: Login to DockerHub
+        uses: docker/login-action@v1 
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: VirtualFlyBrain/geppetto-vfb:${GITHUB_REF##*/}
+          build-args: |
+            VFB_TREE_PDB_SERVER_ARG=${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
+            SOLR_SERVER_ARG=${{ steps.server.outputs.SOLR_SERVER }}
+            VFB_R_SERVER_ARG=${{ steps.server.outputs.VFB_R_SERVER }}
+            VFB_OWL_SERVER_ARG=${{ steps.server.outputs.VFB_OWL_SERVER }}
+            VFB_PDB_SERVER_ARG=${{ steps.server.outputs.VFB_PDB_SERVER }}
+            build_type=${{ steps.server.outputs.BUILD_TYPE }} 
+            targetBranch=${GITHUB_REF##*/} 
+            originBranch=${GITHUB_REF##*/} 
+            defaultBranch=development
+            finalBuild=true
+      
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

From 4f5ee4e2164ab1182314e46a98affe504a681167 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 22:31:57 +0000
Subject: [PATCH 17/48] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c56c9cf50..0091f2672 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -87,7 +87,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          tags: VirtualFlyBrain/geppetto-vfb:${GITHUB_REF##*/}
+          tags: virtualflybrain/geppetto-vfb:${GITHUB_REF##*/}
           build-args: |
             VFB_TREE_PDB_SERVER_ARG=${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
             SOLR_SERVER_ARG=${{ steps.server.outputs.SOLR_SERVER }}

From 5345f64a92c839d46a362e8287f6b64e8f0beaa3 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Mon, 2 Nov 2020 22:34:53 +0000
Subject: [PATCH 18/48] test with fixed

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0091f2672..429dce37b 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -87,7 +87,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          tags: virtualflybrain/geppetto-vfb:${GITHUB_REF##*/}
+          tags: virtualflybrain/geppetto-vfb:debug
           build-args: |
             VFB_TREE_PDB_SERVER_ARG=${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
             SOLR_SERVER_ARG=${{ steps.server.outputs.SOLR_SERVER }}

From e2dbfe72e18920a3e656fa5b538906257bc536a3 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 09:19:22 +0000
Subject: [PATCH 19/48] multiple builds

---
 .github/workflows/main.yml | 86 +++++++++++++++++++++++++++++++-------
 1 file changed, 71 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 429dce37b..94e4ca927 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -23,15 +23,15 @@ jobs:
       - uses: actions/checkout@v2
       
       # Decide based on branch which servers to use
-      - name: Setup servers
-        id: server
+      - name: Setup local servers
+        id: local-servers
         shell: bash
         run: if [ "${GITHUB_REF##*/}" == master ] ; then
             echo "::debug::Set to master setup";
-            echo "::set-output name=VFB_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb:7474";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl:8080/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://ocpu:80/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
-            echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
-            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
             echo "::set-output name=BUILD_TYPE::release";
           elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
@@ -59,6 +59,42 @@ jobs:
             echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
             echo "::set-output name=BUILD_TYPE::release";
           fi
+      - name: Setup remote servers
+        id: remote-servers
+        shell: bash
+        run: if [ "${GITHUB_REF##*/}" == master ] ; then
+            echo "::debug::Set to master setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          elif [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] ; then
+            echo "::debug::Set to dev setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl-dev.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-dev.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-dev.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::development";
+          elif [ "${GITHUB_REF##*/}" == alpha ] ; then
+            echo "::debug::Set to alpha setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb-alpha.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl-alpha.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-alpha.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr-alpha.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::staging";
+          else 
+            echo "::debug::Set to default setup";
+            echo "::set-output name=VFB_PDB_SERVER::http://pdb.virtualflybrain.org";
+            echo "::set-output name=VFB_OWL_SERVER::http://owl.virtualflybrain.org/kbs/vfb/";
+            echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
+            echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb.virtualflybrain.org";
+            echo "::set-output name=SOLR_SERVER::https://solr.virtualflybrain.org/solr/ontology/select";
+            echo "::set-output name=BUILD_TYPE::release";
+          fi
         
       # Output the chosen servers
       - name: Used Servers
@@ -82,23 +118,43 @@ jobs:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       
-      - name: Build and push
-        id: docker_build
+      - name: Build and push local wss
+        id: docker_build_local
         uses: docker/build-push-action@v2
         with:
           push: true
-          tags: virtualflybrain/geppetto-vfb:debug
+          tags: "virtualflybrain/geppetto-vfb:${GITHUB_REF##*/}-local.wss"
           build-args: |
-            VFB_TREE_PDB_SERVER_ARG=${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
-            SOLR_SERVER_ARG=${{ steps.server.outputs.SOLR_SERVER }}
-            VFB_R_SERVER_ARG=${{ steps.server.outputs.VFB_R_SERVER }}
-            VFB_OWL_SERVER_ARG=${{ steps.server.outputs.VFB_OWL_SERVER }}
-            VFB_PDB_SERVER_ARG=${{ steps.server.outputs.VFB_PDB_SERVER }}
-            build_type=${{ steps.server.outputs.BUILD_TYPE }} 
+            VFB_TREE_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_TREE_PDB_SERVER }}
+            SOLR_SERVER_ARG=${{ steps.local-servers.outputs.SOLR_SERVER }}
+            VFB_R_SERVER_ARG=${{ steps.local-servers.outputs.VFB_R_SERVER }}
+            VFB_OWL_SERVER_ARG=${{ steps.local-servers.outputs.VFB_OWL_SERVER }}
+            VFB_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_PDB_SERVER }}
+            build_type=${{ steps.local-servers.outputs.BUILD_TYPE }} 
+            targetBranch=${GITHUB_REF##*/} 
+            originBranch=${GITHUB_REF##*/} 
+            defaultBranch=development
+            finalBuild=true
+      
+      - name: Build and push remote
+        id: docker_build_remote
+        uses: docker/build-push-action@v2
+        with:
+          push: true
+          tags: "virtualflybrain/geppetto-vfb:${GITHUB_REF##*/}-remote"
+          build-args: |
+            VFB_TREE_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_TREE_PDB_SERVER }}
+            SOLR_SERVER_ARG=${{ steps.local-servers.outputs.SOLR_SERVER }}
+            VFB_R_SERVER_ARG=${{ steps.local-servers.outputs.VFB_R_SERVER }}
+            VFB_OWL_SERVER_ARG=${{ steps.local-servers.outputs.VFB_OWL_SERVER }}
+            VFB_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_PDB_SERVER }}
+            build_type=${{ steps.local-servers.outputs.BUILD_TYPE }} 
             targetBranch=${GITHUB_REF##*/} 
             originBranch=${GITHUB_REF##*/} 
             defaultBranch=development
             finalBuild=true
       
       - name: Image digest
-        run: echo ${{ steps.docker_build.outputs.digest }}
+        run: |
+          echo "local:${{ steps.docker_build_local.outputs.digest }}"
+          echo "remote:${{ steps.docker_build_remote.outputs.digest }}"

From 138225bea66e0b27b0fb8a605881fb6f6a21da7a Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 09:30:36 +0000
Subject: [PATCH 20/48] try with step value

---
 .github/workflows/main.yml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 94e4ca927..afa2091ca 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -23,6 +23,9 @@ jobs:
       - uses: actions/checkout@v2
       
       # Decide based on branch which servers to use
+      - name: Pass branch
+        id: branch
+        run: echo "::set-output name=value::${GITHUB_REF##*/} ";
       - name: Setup local servers
         id: local-servers
         shell: bash
@@ -123,7 +126,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          tags: "virtualflybrain/geppetto-vfb:${GITHUB_REF##*/}-local.wss"
+          tags: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-local.wss"
           build-args: |
             VFB_TREE_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_TREE_PDB_SERVER }}
             SOLR_SERVER_ARG=${{ steps.local-servers.outputs.SOLR_SERVER }}
@@ -141,7 +144,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           push: true
-          tags: "virtualflybrain/geppetto-vfb:${GITHUB_REF##*/}-remote"
+          tags: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"
           build-args: |
             VFB_TREE_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_TREE_PDB_SERVER }}
             SOLR_SERVER_ARG=${{ steps.local-servers.outputs.SOLR_SERVER }}

From c4be65ad2207fed30c1a86ba9430718cf578c09e Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 09:41:56 +0000
Subject: [PATCH 21/48] space fix

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index afa2091ca..bd3aff87f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -25,7 +25,7 @@ jobs:
       # Decide based on branch which servers to use
       - name: Pass branch
         id: branch
-        run: echo "::set-output name=value::${GITHUB_REF##*/} ";
+        run: echo "::set-output name=value::${GITHUB_REF##*/}";
       - name: Setup local servers
         id: local-servers
         shell: bash

From a034cf398cbe785395aefec0f50808462eb26bef Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 10:32:04 +0000
Subject: [PATCH 22/48] Update main.yml

---
 .github/workflows/main.yml | 17 +++++++----------
 1 file changed, 7 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index bd3aff87f..cba11e7a3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -6,9 +6,7 @@ name: CI
 # events but only for the master branch
 on:
   push:
-    branches: [ debug ]
-  pull_request:
-    branches: [ debug ]
+    branches: '*'
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
@@ -100,14 +98,13 @@ jobs:
           fi
         
       # Output the chosen servers
-      - name: Used Servers
+      - name: Used remote servers
         run: |
-          echo PDB:${{ steps.server.outputs.VFB_PDB_SERVER }}
-          echo OWL:${{ steps.server.outputs.VFB_OWL_SERVER }}
-          echo SOLR:${{ steps.server.outputs.SOLR_SERVER }}
-          echo TREE_PDB:${{ steps.server.outputs.VFB_TREE_PDB_SERVER }}
-          echo R:${{ steps.server.outputs.VFB_R_SERVER }}
-
+          echo PDB:${{ steps.remote-servers.outputs.VFB_PDB_SERVER }}
+          echo OWL:${{ steps.remote-servers.outputs.VFB_OWL_SERVER }}
+          echo SOLR:${{ steps.remote-servers.outputs.SOLR_SERVER }}
+          echo TREE_PDB:${{ steps.remote-servers.outputs.VFB_TREE_PDB_SERVER }}
+          echo R:${{ steps.remote-servers.outputs.VFB_R_SERVER }}
 
       - name: Set up QEMU
         uses: docker/setup-qemu-action@v1

From 09a64ada60b583ac465b6491422696457448fc30 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 10:32:56 +0000
Subject: [PATCH 23/48] change name

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cba11e7a3..c3c026aa4 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -11,7 +11,7 @@ on:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # This workflow contains a single job called "build"
-  config:
+  deploy:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
 

From 6fd966046b1e2c8ac1a32a203403287d6f6e4b7f Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 10:49:20 +0000
Subject: [PATCH 24/48] add test

---
 .github/workflows/main.yml | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c3c026aa4..a5a6bc4c4 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -10,7 +10,7 @@ on:
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
+  # Deploy the local and remote versions of geppetto-vfb
   deploy:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
@@ -158,3 +158,20 @@ jobs:
         run: |
           echo "local:${{ steps.docker_build_local.outputs.digest }}"
           echo "remote:${{ steps.docker_build_remote.outputs.digest }}"
+          
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Install
+        # NOTE: this pins the action to a specific commit sha for security
+        # reasons but you can also use a version tag if desired. For example:
+        # ianwalter/puppeteer-container@v4.0.0
+        uses: ianwalter/puppeteer-container@acc52cd2334ad9eaf6e1974562d263e0a711b7e8
+        with:
+          args: pnpm i
+      - name: Test
+        uses: ianwalter/puppeteer-container@acc52cd2334ad9eaf6e1974562d263e0a711b7e8
+        with:
+          args: pnpm t

From 852a24dcbc94767fb69bef2693b5f2f56bd1c85a Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 11:01:16 +0000
Subject: [PATCH 25/48] test

---
 .github/workflows/main.yml | 18 +++++-------------
 1 file changed, 5 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a5a6bc4c4..799dff5b4 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -152,7 +152,7 @@ jobs:
             targetBranch=${GITHUB_REF##*/} 
             originBranch=${GITHUB_REF##*/} 
             defaultBranch=development
-            finalBuild=true
+            finalBuild=false
       
       - name: Image digest
         run: |
@@ -162,16 +162,8 @@ jobs:
   test:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v2
+      
       - name: Install
-        # NOTE: this pins the action to a specific commit sha for security
-        # reasons but you can also use a version tag if desired. For example:
-        # ianwalter/puppeteer-container@v4.0.0
-        uses: ianwalter/puppeteer-container@acc52cd2334ad9eaf6e1974562d263e0a711b7e8
-        with:
-          args: pnpm i
-      - name: Test
-        uses: ianwalter/puppeteer-container@acc52cd2334ad9eaf6e1974562d263e0a711b7e8
-        with:
-          args: pnpm t
+        run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
+      - name: Run server
+        uses: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"

From 596f6513e5bcddeb7e6c2d00433401dd165f81b6 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 11:04:44 +0000
Subject: [PATCH 26/48] merged

---
 .github/workflows/main.yml | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 799dff5b4..304c19b65 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -159,11 +159,7 @@ jobs:
           echo "local:${{ steps.docker_build_local.outputs.digest }}"
           echo "remote:${{ steps.docker_build_remote.outputs.digest }}"
           
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      
-      - name: Install
+      - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
-      - name: Run server
+      - name: Run VFB server
         uses: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"

From 269be6a261a9383a7ca9ea9473eade2940c9b9a1 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 11:08:35 +0000
Subject: [PATCH 27/48] remove server

---
 .github/workflows/main.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 304c19b65..b2559b2c2 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -161,5 +161,4 @@ jobs:
           
       - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
-      - name: Run VFB server
-        uses: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"
+      

From 4b51c3367c885167d14e59636e3d82f4042d0112 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 11:37:58 +0000
Subject: [PATCH 28/48] adding server

---
 .github/workflows/main.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b2559b2c2..a552c0375 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -161,4 +161,5 @@ jobs:
           
       - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
-      
+      - name: Start VFB server
+        run: docker run -t -dit --name=$test-server -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"

From f34c305f5d93f5b217444a736e2335b2ac1a87bb Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 11:53:42 +0000
Subject: [PATCH 29/48] typo fix

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index a552c0375..697727c99 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -162,4 +162,4 @@ jobs:
       - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
       - name: Start VFB server
-        run: docker run -t -dit --name=$test-server -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"
+        run: docker run -t -dit --name=$testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"

From 305aa86a52ea321942968c3005bed6b049657a4d Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 12:08:37 +0000
Subject: [PATCH 30/48] start test and stop

---
 .github/workflows/main.yml | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 697727c99..8aff616c6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -162,4 +162,8 @@ jobs:
       - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
       - name: Start VFB server
-        run: docker run -t -dit --name=$testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"
+        run: |
+          docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
+          Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
+          Test;
+          docker stop testServer

From 0316ea2c0191a0b980b5b3c8130f8cc45c0cf516 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 12:10:34 +0000
Subject: [PATCH 31/48] add landing page

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 8aff616c6..cc4c491f5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -163,6 +163,7 @@ jobs:
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
       - name: Start VFB server
         run: |
+          export LANDING_PAGE="http://localhost:8080/org.geppetto.frontend/geppetto"
           docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;

From d1373b776c171710c8a97a2a9dd53bbf4f1ed31e Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 12:50:16 +0000
Subject: [PATCH 32/48] add first batch of tests

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index cc4c491f5..7b2421072 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -167,4 +167,5 @@ jobs:
           docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
+          npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
           docker stop testServer

From 68a318537c80101a0b750da83254f65a23be92e9 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 12:52:03 +0000
Subject: [PATCH 33/48] splitting

---
 .github/workflows/main.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7b2421072..fe80daf0a 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -168,4 +168,7 @@ jobs:
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
           npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
-          docker stop testServer
+      - name: Test batch 2   
+        run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'
+      - name: Stop VFB server   
+        run: docker stop testServer

From 22aeb9f02e62188e62c63d5b017d7c7cdc91f2bf Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 13:44:14 +0000
Subject: [PATCH 34/48] adding delay

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index fe80daf0a..5b7f815be 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -167,6 +167,7 @@ jobs:
           docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
+          sleep 1m;
           npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
       - name: Test batch 2   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'

From 3b9cb068454678d6e7e5137a99a41e470bd4e4ba Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 14:01:33 +0000
Subject: [PATCH 35/48] output logs

---
 .github/workflows/main.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 5b7f815be..3f34450e3 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -168,6 +168,7 @@ jobs:
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
           sleep 1m;
+          docker logs testServer
           npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
       - name: Test batch 2   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'

From 849bf233491121fc206fa694f8758dac0aa425b1 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 15:12:21 +0000
Subject: [PATCH 36/48] typo fix

---
 .github/workflows/main.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3f34450e3..824c2e991 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -78,7 +78,7 @@ jobs:
             echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-dev.virtualflybrain.org";
             echo "::set-output name=SOLR_SERVER::https://solr-dev.virtualflybrain.org/solr/ontology/select";
-            echo "::set-output name=BUILD_TYPE::development";
+            echo "::set-output name=BUILD_TYPE::release";
           elif [ "${GITHUB_REF##*/}" == alpha ] ; then
             echo "::debug::Set to alpha setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb-alpha.virtualflybrain.org";
@@ -86,7 +86,7 @@ jobs:
             echo "::set-output name=VFB_R_SERVER::http://r.virtualflybrain.org/ocpu/library/vfbr/R/vfb_nblast";
             echo "::set-output name=VFB_TREE_PDB_SERVER::https://pdb-alpha.virtualflybrain.org";
             echo "::set-output name=SOLR_SERVER::https://solr-alpha.virtualflybrain.org/solr/ontology/select";
-            echo "::set-output name=BUILD_TYPE::staging";
+            echo "::set-output name=BUILD_TYPE::release";
           else 
             echo "::debug::Set to default setup";
             echo "::set-output name=VFB_PDB_SERVER::http://pdb.virtualflybrain.org";
@@ -143,12 +143,12 @@ jobs:
           push: true
           tags: "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote"
           build-args: |
-            VFB_TREE_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_TREE_PDB_SERVER }}
-            SOLR_SERVER_ARG=${{ steps.local-servers.outputs.SOLR_SERVER }}
-            VFB_R_SERVER_ARG=${{ steps.local-servers.outputs.VFB_R_SERVER }}
-            VFB_OWL_SERVER_ARG=${{ steps.local-servers.outputs.VFB_OWL_SERVER }}
-            VFB_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_PDB_SERVER }}
-            build_type=${{ steps.local-servers.outputs.BUILD_TYPE }} 
+            VFB_TREE_PDB_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_TREE_PDB_SERVER }}
+            SOLR_SERVER_ARG=${{ steps.remote-servers.outputs.SOLR_SERVER }}
+            VFB_R_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_R_SERVER }}
+            VFB_OWL_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_OWL_SERVER }}
+            VFB_PDB_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_PDB_SERVER }}
+            build_type=${{ steps.remote-servers.outputs.BUILD_TYPE }} 
             targetBranch=${GITHUB_REF##*/} 
             originBranch=${GITHUB_REF##*/} 
             defaultBranch=development

From d29395151a1212b8a14b3b5fee4d321ff2f43432 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 15:37:27 +0000
Subject: [PATCH 37/48] adding all tests

---
 .github/workflows/main.yml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 824c2e991..05eef9b62 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -158,7 +158,7 @@ jobs:
         run: |
           echo "local:${{ steps.docker_build_local.outputs.digest }}"
           echo "remote:${{ steps.docker_build_remote.outputs.digest }}"
-          
+                
       - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
       - name: Start VFB server
@@ -167,10 +167,11 @@ jobs:
           docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
-          sleep 1m;
-          docker logs testServer
-          npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
+      - name: Test batch 2   
+        run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
       - name: Test batch 2   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'
+      - name: Test batch 3   
+        run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch3/.*js'
       - name: Stop VFB server   
         run: docker stop testServer

From e770df475f968f906741e30d39b36b4a9bbc1d5f Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 15:51:14 +0000
Subject: [PATCH 38/48] split out wait step

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 05eef9b62..6c5334c13 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -165,6 +165,8 @@ jobs:
         run: |
           export LANDING_PAGE="http://localhost:8080/org.geppetto.frontend/geppetto"
           docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
+      - name: Wait for VFB server to spin up
+        run: |    
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
       - name: Test batch 2   

From ea4ab50efa918973e3c65ec8fa6284356e760f73 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 15:57:32 +0000
Subject: [PATCH 39/48] Rename .travis.yml to NoLongerUsed.travis.yml

---
 .travis.yml => NoLongerUsed.travis.yml | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .travis.yml => NoLongerUsed.travis.yml (100%)

diff --git a/.travis.yml b/NoLongerUsed.travis.yml
similarity index 100%
rename from .travis.yml
rename to NoLongerUsed.travis.yml

From 5bd711fe5fd1d9681111d5d59577a5fc87ec58d4 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 16:11:09 +0000
Subject: [PATCH 40/48] add review section

---
 .github/workflows/main.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 6c5334c13..359e38fdc 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -175,5 +175,10 @@ jobs:
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'
       - name: Test batch 3   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch3/.*js'
+      - name: Test under review  
+        run: |
+          if [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] || [[ "${GITHUB_REF##*/}" =~ ^(fix|feature).* ]] ; then
+            npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/review/.*js';
+          fi
       - name: Stop VFB server   
         run: docker stop testServer

From 65e1764ccde3bc24a3ff1072ee73167986d797cb Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 16:14:07 +0000
Subject: [PATCH 41/48] cleaning up

---
 .github/workflows/main.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 359e38fdc..92f9b88a7 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -2,8 +2,7 @@
 
 name: CI
 
-# Controls when the action will run. Triggers the workflow on push or pull request
-# events but only for the master branch
+# Controls when the action will run. Triggers the workflow on push only. ToDo: handle pull requests for testing only
 on:
   push:
     branches: '*'

From 88ea5ac420a3222ace8c922fbef0258a211c6ff6 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 16:29:29 +0000
Subject: [PATCH 42/48] adding build timeouts

---
 .github/workflows/main.yml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 92f9b88a7..144941840 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -10,12 +10,15 @@ on:
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # Deploy the local and remote versions of geppetto-vfb
-  deploy:
+  deploy-test:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
+    # total job timeout:
+    timeout-minutes: 40
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
+      
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v2
       
@@ -119,6 +122,7 @@ jobs:
       
       - name: Build and push local wss
         id: docker_build_local
+        timeout-minutes: 10
         uses: docker/build-push-action@v2
         with:
           push: true
@@ -137,6 +141,7 @@ jobs:
       
       - name: Build and push remote
         id: docker_build_remote
+        timeout-minutes: 10
         uses: docker/build-push-action@v2
         with:
           push: true

From a860d448d6184117a6308bef5e58fb5e8d178d2b Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 16:45:47 +0000
Subject: [PATCH 43/48] order fix

---
 .github/workflows/main.yml | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 144941840..3def6c672 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -166,11 +166,10 @@ jobs:
       - name: Install Puppeteer
         run: npm install jest@24.8.0 jest-image-snapshot@4.1.0 puppeteer@1.17.0 jest-puppeteer@4.3.0 @babel/preset-env@7.4.5 url-join@4.0.0 @babel/core@7.4.5
       - name: Start VFB server
-        run: |
-          export LANDING_PAGE="http://localhost:8080/org.geppetto.frontend/geppetto"
-          docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
+        run: docker run -t -dit --name=testServer -p 8080:8080 "virtualflybrain/geppetto-vfb:${{ steps.branch.outputs.value }}-remote";
       - name: Wait for VFB server to spin up
-        run: |    
+        run: |  
+          export LANDING_PAGE="http://localhost:8080/org.geppetto.frontend/geppetto"  
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
       - name: Test batch 2   

From 670b2bed7405e1bc873b3e1f45cca37a597d3cfc Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 16:47:32 +0000
Subject: [PATCH 44/48] name fix

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3def6c672..dd26c411f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -172,7 +172,7 @@ jobs:
           export LANDING_PAGE="http://localhost:8080/org.geppetto.frontend/geppetto"  
           Test () { export http_status=$(curl -s -i $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "100" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; }
           Test;
-      - name: Test batch 2   
+      - name: Test batch 1   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch1/.*js'
       - name: Test batch 2   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch2/.*js'

From db3ace096bc03abf4532ed3a2ca934dd035b09e4 Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Tue, 3 Nov 2020 17:19:39 +0000
Subject: [PATCH 45/48] allowing fail on review

---
 .github/workflows/main.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index dd26c411f..77d8be035 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -14,7 +14,7 @@ jobs:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
     # total job timeout:
-    timeout-minutes: 40
+    timeout-minutes: 45
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -179,6 +179,7 @@ jobs:
       - name: Test batch 3   
         run: npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/batch3/.*js'
       - name: Test under review  
+        continue-on-error: true
         run: |
           if [ "${GITHUB_REF##*/}" == debug ] || [ "${GITHUB_REF##*/}" == pipeline2 ] || [ "${GITHUB_REF##*/}" == vfb_geppetto_application ] || [ "${GITHUB_REF##*/}" == development ] || [[ "${GITHUB_REF##*/}" =~ ^(fix|feature).* ]] ; then
             npm test -- --verbose --colors --forceExit --testPathPattern='geppetto-vfb/tests/jest/vfb/review/.*js';

From a18ac831eb68197c16b51672bd7e15efd4c67fe0 Mon Sep 17 00:00:00 2001
From: Rob Court <rcourt@ed.ac.uk>
Date: Tue, 3 Nov 2020 17:28:33 +0000
Subject: [PATCH 46/48] checking branch is passed correctly

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 77d8be035..1b4846223 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -153,8 +153,8 @@ jobs:
             VFB_OWL_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_OWL_SERVER }}
             VFB_PDB_SERVER_ARG=${{ steps.remote-servers.outputs.VFB_PDB_SERVER }}
             build_type=${{ steps.remote-servers.outputs.BUILD_TYPE }} 
-            targetBranch=${GITHUB_REF##*/} 
-            originBranch=${GITHUB_REF##*/} 
+            targetBranch=${{ steps.branch.outputs.value }}
+            originBranch=${{ steps.branch.outputs.value }} 
             defaultBranch=development
             finalBuild=false
       

From da52b769e9807aa155ef5b4f62e11eb8aa7614d4 Mon Sep 17 00:00:00 2001
From: Rob Court <rcourt@ed.ac.uk>
Date: Tue, 3 Nov 2020 17:33:47 +0000
Subject: [PATCH 47/48] fix on all

---
 .github/workflows/main.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 1b4846223..cfca4ac45 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -134,8 +134,8 @@ jobs:
             VFB_OWL_SERVER_ARG=${{ steps.local-servers.outputs.VFB_OWL_SERVER }}
             VFB_PDB_SERVER_ARG=${{ steps.local-servers.outputs.VFB_PDB_SERVER }}
             build_type=${{ steps.local-servers.outputs.BUILD_TYPE }} 
-            targetBranch=${GITHUB_REF##*/} 
-            originBranch=${GITHUB_REF##*/} 
+            targetBranch=${{ steps.branch.outputs.value }} 
+            originBranch=${{ steps.branch.outputs.value }}
             defaultBranch=development
             finalBuild=true
       

From e67a2ef2707321793d6eafc0edac0cc4288a6b72 Mon Sep 17 00:00:00 2001
From: Rob Court <rcourt@ed.ac.uk>
Date: Tue, 3 Nov 2020 17:47:27 +0000
Subject: [PATCH 48/48] swapping to actions

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9c2292d53..8dded7c89 100755
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.org/VirtualFlyBrain/geppetto-vfb.svg?branch=master)](https://travis-ci.org/VirtualFlyBrain/geppetto-vfb)[![Docker Hub](https://www.shippable.com/assets/images/logos/docker-hub.jpg)](https://hub.docker.com/r/virtualflybrain/geppetto-vfb/)
+[![Build Status](https://github.com/VirtualFlyBrain/geppetto-vfb/workflows/CI/badge.svg)](https://github.com/Robbie1977/geppetto-vfb/actions?query=workflow%3ACI)[![Docker Hub](https://www.shippable.com/assets/images/logos/docker-hub.jpg)](https://hub.docker.com/r/virtualflybrain/geppetto-vfb/)
 
 # geppetto-vfb
 Virtual Fly Brain project customised Geppetto build