From e0af92f1a7eb1b2d6071710f533b652c15e17a55 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Wed, 21 Nov 2018 18:36:52 +0000
Subject: [PATCH 01/35] Fixes to mock-test GSK stratcal run

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 5ddc9f7..93c4e38 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -11,7 +11,7 @@ HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 # HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/esrf_id30b"
 CUSTOM_HARDWARE_OBJECTS_PATH=""
 CUSTOM_BRICKS_PATH=""
 

From 2f2892c0aa6344190108e62e673e8671a6bfef97 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Thu, 13 Dec 2018 11:17:52 +0000
Subject: [PATCH 02/35] GPhL configuration updates, various

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 93c4e38..4fdb621 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -7,12 +7,13 @@ CONTAINER=mx3_deb9_qt4_gphl2
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
+HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/esrf_id30b"
-CUSTOM_HARDWARE_OBJECTS_PATH=""
+# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/test/xml:${HO_SERVER}/configuration/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
 CUSTOM_BRICKS_PATH=""
 
 # User and mac address

From 695c2f8def2c4c1c02716330a2d15681544c6b84 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Fri, 14 Dec 2018 10:41:32 +0000
Subject: [PATCH 03/35] Cleanup. Also removed queue_model_objects_v1 reference

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 4fdb621..c297e01 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -11,7 +11,6 @@ HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/test/xml:${HO_SERVER}/configuration/alba_xaloc13"
 HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
 CUSTOM_BRICKS_PATH=""

From f2e8d753273bd5258bf65f8077df63ae91ed57db Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Wed, 19 Dec 2018 11:58:34 +0000
Subject: [PATCH 04/35] Changed to reflect new location of configuration files

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index c297e01..d8f9a06 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,10 +8,9 @@ CONTAINER=mx3_deb9_qt4_gphl2
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-# HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
 CUSTOM_BRICKS_PATH=""
 

From edff34d48a6e7a41f3b08b4a75a421dc790573b4 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Mon, 25 Mar 2019 15:22:55 +0000
Subject: [PATCH 05/35] Finished merging ALBA_gphl 2.3.0 into master.

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index d8f9a06..1ba82d4 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -49,6 +49,8 @@ DATA_ROOT="/scratch_fs1/"
 
 xhost +local:
 # Command needed to run GPhL workflows
+# Add in this for debug
+# -p 8050:8050 \
 exec docker run -it \
 --mac-address $MAC_ADDRESS \
 -p 25333:25333 \

From 1dd8ed678fb0e5da8050a98443baab2cb5a11ede Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Tue, 26 Mar 2019 16:52:49 +0000
Subject: [PATCH 06/35] Cleaned up imports, and bug fixes in latest merge

Regrettably the import cleanup (or a small part of it) was required
for the bug fix, hence the mixing of the two.

The import changes have moved to importing from HardwareRepository. etc.
and to gui. etc. in all cases, avoiding direct imports of e.g.
sample_centring, abstract.xyz, individual HOs etc.

The reason is that importing the same file under two different paths
creates two different copies in memory, so that state_x == state_y
or setting class attributes gives unpredictable results when the
class/instance is not from the same package in different cases.
---
 dev/gphl/Debian9_qt4/Dockerfile    | 6 ++++++
 dev/gphl/Debian9_qt4/start_mxcube2 | 6 +++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index da51a1d..5517a2c 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -5,6 +5,12 @@ RUN apt-get update
 RUN apt-get install python-pip -y
 RUN pip install --upgrade pip
 
+# To get rid of error, that the ps command cannot eb found
+RUN apt-get install procps -y
+
+# Not used in dockers, btu avoids consgtant error message
+RUN pip install redis
+
 # Python-Java bridge - needed for GPhL workflow:
 # Install as root, otehrwise not found in xml parsing
 RUN pip install py4j
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 1ba82d4..77f8d9e 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-CONTAINER=mx3_deb9_qt4_gphl2
+CONTAINER=mx3_deb9_qt4_gphl3
 
 # The following variables should be checked and (re)set as needed
 
@@ -10,8 +10,8 @@ CONTAINER=mx3_deb9_qt4_gphl2
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
-CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/embl_hh_p14"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 CUSTOM_BRICKS_PATH=""
 
 # User and mac address

From aca27c2c75c4c12374e8414d56f3acd845e6a418 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Wed, 21 Nov 2018 18:36:52 +0000
Subject: [PATCH 07/35] Fixes to mock-test GSK stratcal run

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 5ddc9f7..93c4e38 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -11,7 +11,7 @@ HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 # HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/esrf_id30b"
 CUSTOM_HARDWARE_OBJECTS_PATH=""
 CUSTOM_BRICKS_PATH=""
 

From 7808516bae4b4a95b025cb99d2a82097062a2dd3 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Thu, 13 Dec 2018 11:17:52 +0000
Subject: [PATCH 08/35] GPhL configuration updates, various

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 93c4e38..4fdb621 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -7,12 +7,13 @@ CONTAINER=mx3_deb9_qt4_gphl2
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
+HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:/${HO_SERVER}/esrf_id30b"
-CUSTOM_HARDWARE_OBJECTS_PATH=""
+# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/test/xml:${HO_SERVER}/configuration/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
 CUSTOM_BRICKS_PATH=""
 
 # User and mac address

From 5922b7ed3bed458eaceb5340a27c21213621b208 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Fri, 14 Dec 2018 10:41:32 +0000
Subject: [PATCH 09/35] Cleanup. Also removed queue_model_objects_v1 reference

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 4fdb621..c297e01 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -11,7 +11,6 @@ HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/test/xml:${HO_SERVER}/configuration/alba_xaloc13"
 HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
 CUSTOM_BRICKS_PATH=""

From caebe7674d8e8dc0fd326115bec57a18378289fe Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Wed, 19 Dec 2018 11:58:34 +0000
Subject: [PATCH 10/35] Changed to reflect new location of configuration files

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index c297e01..d8f9a06 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,10 +8,9 @@ CONTAINER=mx3_deb9_qt4_gphl2
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-# HARDWARE_REPOSITORY_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml:/MXCuBE/mxcube/repo_test_1"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/test/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
 CUSTOM_BRICKS_PATH=""
 

From b6ecf53a590c9b5982540fff86a316437c0ed026 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Mon, 25 Mar 2019 15:22:55 +0000
Subject: [PATCH 11/35] Finished merging ALBA_gphl 2.3.0 into master.

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index d8f9a06..1ba82d4 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -49,6 +49,8 @@ DATA_ROOT="/scratch_fs1/"
 
 xhost +local:
 # Command needed to run GPhL workflows
+# Add in this for debug
+# -p 8050:8050 \
 exec docker run -it \
 --mac-address $MAC_ADDRESS \
 -p 25333:25333 \

From 6799fae1737cbae2da359e1a9a53f8fadfe79f9c Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Tue, 26 Mar 2019 16:52:49 +0000
Subject: [PATCH 12/35] Cleaned up imports, and bug fixes in latest merge

Regrettably the import cleanup (or a small part of it) was required
for the bug fix, hence the mixing of the two.

The import changes have moved to importing from HardwareRepository. etc.
and to gui. etc. in all cases, avoiding direct imports of e.g.
sample_centring, abstract.xyz, individual HOs etc.

The reason is that importing the same file under two different paths
creates two different copies in memory, so that state_x == state_y
or setting class attributes gives unpredictable results when the
class/instance is not from the same package in different cases.
---
 dev/gphl/Debian9_qt4/Dockerfile    | 6 ++++++
 dev/gphl/Debian9_qt4/start_mxcube2 | 6 +++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index da51a1d..5517a2c 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -5,6 +5,12 @@ RUN apt-get update
 RUN apt-get install python-pip -y
 RUN pip install --upgrade pip
 
+# To get rid of error, that the ps command cannot eb found
+RUN apt-get install procps -y
+
+# Not used in dockers, btu avoids consgtant error message
+RUN pip install redis
+
 # Python-Java bridge - needed for GPhL workflow:
 # Install as root, otehrwise not found in xml parsing
 RUN pip install py4j
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 1ba82d4..77f8d9e 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-CONTAINER=mx3_deb9_qt4_gphl2
+CONTAINER=mx3_deb9_qt4_gphl3
 
 # The following variables should be checked and (re)set as needed
 
@@ -10,8 +10,8 @@ CONTAINER=mx3_deb9_qt4_gphl2
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
-CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/ALBA"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/embl_hh_p14"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 CUSTOM_BRICKS_PATH=""
 
 # User and mac address

From 63bf3ca6a0fc1d3632853dfbb3634c6244165dda Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Thu, 28 Mar 2019 18:07:26 +0000
Subject: [PATCH 13/35] Fixed comment spelling

---
 dev/gphl/Debian9_qt4/Dockerfile | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index 5517a2c..4484d77 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -5,10 +5,10 @@ RUN apt-get update
 RUN apt-get install python-pip -y
 RUN pip install --upgrade pip
 
-# To get rid of error, that the ps command cannot eb found
+# To get rid of error, that the ps command cannot be found
 RUN apt-get install procps -y
 
-# Not used in dockers, btu avoids consgtant error message
+# Not used by gphl in dockers, but avoids constant error message
 RUN pip install redis
 
 # Python-Java bridge - needed for GPhL workflow:

From 45ef007590768c366455eef60a42b41f9f9bcd95 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Thu, 23 May 2019 17:16:37 +0100
Subject: [PATCH 14/35] UI and HO changes prior tio ALBA test 20190528

Added dose_budget and transmission calculation,
multiple characterisation strategies, ...
---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 77f8d9e..97d2523 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -10,7 +10,7 @@ CONTAINER=mx3_deb9_qt4_gphl3
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 CUSTOM_BRICKS_PATH=""
 

From fe81fbff9cc969e8749cf3b35cb9460227e1d318 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Fri, 24 May 2019 19:14:39 +0100
Subject: [PATCH 15/35] Porting to ALBA production branch

Debugging still incomplete
---
 dev/gphl/Debian9_qt4/start_mxcube2 | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 97d2523..caa21b0 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -7,11 +7,15 @@ CONTAINER=mx3_deb9_qt4_gphl3
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+# HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+# For ALBA 201905:
+HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml/"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:${HO_SERVER}/alba_xaloc13"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
-CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+
 CUSTOM_BRICKS_PATH=""
 
 # User and mac address

From 46875e89f644eaa2f73e4c305d92e358266a8fe9 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Wed, 31 Jul 2019 14:50:07 +0100
Subject: [PATCH 16/35] Removed api and added config for xml-qt and embl_p14.
 Not fully tested.

---
 dev/gphl/Debian9_qt4/Dockerfile    |  3 +++
 dev/gphl/Debian9_qt4/start_mxcube2 | 10 +++++-----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index 4484d77..7a28327 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -8,6 +8,9 @@ RUN pip install --upgrade pip
 # To get rid of error, that the ps command cannot be found
 RUN apt-get install procps -y
 
+# Needed for new configuration from July 2019
+RUN pip install ruamel.yaml
+
 # Not used by gphl in dockers, but avoids constant error message
 RUN pip install redis
 
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index caa21b0..3d107a9 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -1,19 +1,19 @@
 #!/usr/bin/env bash
 
-CONTAINER=mx3_deb9_qt4_gphl3
+CONTAINER=mx3_deb9_qt4_gphl4
 
 # The following variables should be checked and (re)set as needed
 
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-# HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # For ALBA 201905:
-HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml/"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:${HO_SERVER}/alba_xaloc13"
+# HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml/"
+# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:${HO_SERVER}/alba_xaloc13"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/embl_hh_p14"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""

From 61a4ef3aac6660deba7596a59e85a380cc9cc018 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Wed, 7 Aug 2019 15:58:15 +0100
Subject: [PATCH 17/35] CHanged over to ALBA config

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 3d107a9..188f6ea 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -13,7 +13,7 @@ HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 # HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:${HO_SERVER}/alba_xaloc13"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""

From 0391b57ce5b3818c0f470d22236b905bd66e4155 Mon Sep 17 00:00:00 2001
From: rhfogh <rhfogh@globalphasing.com>
Date: Thu, 19 Sep 2019 11:38:56 +0100
Subject: [PATCH 18/35] Fixed CODACY style complaints

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 188f6ea..2813c04 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-CONTAINER=mx3_deb9_qt4_gphl4
+CONTAINER=mx3_deb9_qt4_gphl
 
 # The following variables should be checked and (re)set as needed
 

From e079715d27885ccefce5064ee430902f9b2c549b Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Sat, 19 Oct 2019 17:34:49 +0100
Subject: [PATCH 19/35] Set laptop parameters in new branch

---
 dev/gphl/Debian9_qt4/Dockerfile    | 11 ++++++-----
 dev/gphl/Debian9_qt4/start_mxcube2 | 17 +++++++----------
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index 7a28327..d0d448e 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -27,10 +27,10 @@ RUN pip install mgen
 
 # Add user and group so files on main machine get to belong to user instead of root
 # NB this must be adjusted to the test user. TODO move to separate docker
-RUN groupadd -g 3001 gphl
+# RUN groupadd -g 3001 gphl
 #RUN useradd -g gphl -m -s /bin/tcsh -u 1158 rhfogh
 # No longer makes home directory - this must be mounted externally at startup
-RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
+# RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
 
 # Directories:
 #
@@ -38,9 +38,10 @@ RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
 #
 # GPhL code locations. Name is should match external directory structure,
 # so that the same directory names work inside and outside the docker.
-RUN mkdir -p /archive
-RUN mkdir -p /scratch_fs1
-RUN mkdir -p /public/xtal
+# RUN mkdir -p /archive
+# RUN mkdir -p /scratch_fs1
+# RUN mkdir -p /public/xtal
+RUN mkdir -p /mnt/scrstch
 
 
 # Used instead of Entrypoint to allow alternative commands to be run
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 188f6ea..03e04a8 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,13 +8,10 @@ CONTAINER=mx3_deb9_qt4_gphl4
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-# For ALBA 201905:
-# HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml/"
-# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:${HO_SERVER}/alba_xaloc13"
-# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
+#CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
 HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
-# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""
 
@@ -24,8 +21,8 @@ CUSTOM_BRICKS_PATH=""
 MAC_ADDRESS="54:ee:75:b6:8e:d3"
 #
 # User for docker - for giving correct file ownership.
-# DOCKER_USER_ID="1000:100"
-DOCKER_USER_ID="1158:3001"
+DOCKER_USER_ID="1000:100"
+# DOCKER_USER_ID="1158:3001"
 # User name - used only for file names etc.
 USER_NAME="test_user"
 
@@ -41,11 +38,11 @@ OUTPUT_HOME="/home/rhfogh/dockerhome/"
 # GPHL-specific directories for mounting
 # Note: These are the same from insisde and outside the docker
 # and so must be either identical or used on only one side.
-GPHL_RELEASE_ROOT="/public/xtal/"
-GPHL_SETUP_ROOT="/archive/rhfogh/mxcube/"
+GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/gphl_release/"
+GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/mxcube_setup/"
 
 # Location for output data - must be the same inside and outside docker
-DATA_ROOT="/scratch_fs1/"
+DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"
 
 
 # End of settable parameters.

From 34a21fdb64441c58d949ead98e3ae0a7bfaa5496 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Sat, 19 Oct 2019 17:34:49 +0100
Subject: [PATCH 20/35] Set laptop parameters in new branch

---
 dev/gphl/Debian9_qt4/Dockerfile    | 11 ++++++-----
 dev/gphl/Debian9_qt4/start_mxcube2 | 17 +++++++----------
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index 7a28327..d0d448e 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -27,10 +27,10 @@ RUN pip install mgen
 
 # Add user and group so files on main machine get to belong to user instead of root
 # NB this must be adjusted to the test user. TODO move to separate docker
-RUN groupadd -g 3001 gphl
+# RUN groupadd -g 3001 gphl
 #RUN useradd -g gphl -m -s /bin/tcsh -u 1158 rhfogh
 # No longer makes home directory - this must be mounted externally at startup
-RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
+# RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
 
 # Directories:
 #
@@ -38,9 +38,10 @@ RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
 #
 # GPhL code locations. Name is should match external directory structure,
 # so that the same directory names work inside and outside the docker.
-RUN mkdir -p /archive
-RUN mkdir -p /scratch_fs1
-RUN mkdir -p /public/xtal
+# RUN mkdir -p /archive
+# RUN mkdir -p /scratch_fs1
+# RUN mkdir -p /public/xtal
+RUN mkdir -p /mnt/scrstch
 
 
 # Used instead of Entrypoint to allow alternative commands to be run
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 2813c04..ee14924 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,13 +8,10 @@ CONTAINER=mx3_deb9_qt4_gphl
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-# For ALBA 201905:
-# HO_SERVER="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml/"
-# HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/gphl_mock:/${HO_SERVER}:${HO_SERVER}/alba_xaloc13"
-# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
+#CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
 HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
-# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""
 
@@ -24,8 +21,8 @@ CUSTOM_BRICKS_PATH=""
 MAC_ADDRESS="54:ee:75:b6:8e:d3"
 #
 # User for docker - for giving correct file ownership.
-# DOCKER_USER_ID="1000:100"
-DOCKER_USER_ID="1158:3001"
+DOCKER_USER_ID="1000:100"
+# DOCKER_USER_ID="1158:3001"
 # User name - used only for file names etc.
 USER_NAME="test_user"
 
@@ -41,11 +38,11 @@ OUTPUT_HOME="/home/rhfogh/dockerhome/"
 # GPHL-specific directories for mounting
 # Note: These are the same from insisde and outside the docker
 # and so must be either identical or used on only one side.
-GPHL_RELEASE_ROOT="/public/xtal/"
-GPHL_SETUP_ROOT="/archive/rhfogh/mxcube/"
+GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/gphl_release/"
+GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/mxcube_setup/"
 
 # Location for output data - must be the same inside and outside docker
-DATA_ROOT="/scratch_fs1/"
+DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"
 
 
 # End of settable parameters.

From 55dbf015d1baf69cece38490be4e131e047adf3c Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Sat, 28 Mar 2020 16:23:44 +0000
Subject: [PATCH 21/35] Added jsonschema, pyqtgraph

---
 dev/gphl/Debian9_qt4/Dockerfile | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index d0d448e..924812e 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -8,6 +8,10 @@ RUN pip install --upgrade pip
 # To get rid of error, that the ps command cannot be found
 RUN apt-get install procps -y
 
+# Additional requirements - temporarily put here
+RUN apt-get install python2-jsonschema -y
+RUN apt-get install python2-pyqtgraph -y
+
 # Needed for new configuration from July 2019
 RUN pip install ruamel.yaml
 

From f9f9d14824cc703de7a9da1978bb85ac5a926cb1 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Sun, 29 Mar 2020 18:56:48 +0100
Subject: [PATCH 22/35] snake_case, some fixes, some mockup refactoring.
 Program now opens.

---
 dev/gphl/Debian9_qt4/Dockerfile | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/Dockerfile b/dev/gphl/Debian9_qt4/Dockerfile
index 924812e..7a33da4 100755
--- a/dev/gphl/Debian9_qt4/Dockerfile
+++ b/dev/gphl/Debian9_qt4/Dockerfile
@@ -1,4 +1,4 @@
-FROM mx3_deb9_qt4
+FROM mx3_deb9b_qt4
 
 RUN apt-get update
 
@@ -9,8 +9,8 @@ RUN pip install --upgrade pip
 RUN apt-get install procps -y
 
 # Additional requirements - temporarily put here
-RUN apt-get install python2-jsonschema -y
-RUN apt-get install python2-pyqtgraph -y
+RUN apt-get install python-jsonschema -y
+RUN apt-get install python-pyqtgraph -y
 
 # Needed for new configuration from July 2019
 RUN pip install ruamel.yaml

From 5033c0782c5031a0ca4ecd6ae52ca6fd21499650 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Thu, 28 May 2020 17:18:27 +0100
Subject: [PATCH 23/35] Set config directories etc. to ALBA production values

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index ee14924..51165a4 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-CONTAINER=mx3_deb9_qt4_gphl
+CONTAINER=mx3_deb9_qt4_gphl5
 
 # The following variables should be checked and (re)set as needed
 
@@ -8,9 +8,12 @@ CONTAINER=mx3_deb9_qt4_gphl
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+# HO_CONFIGURATION=${HO_SERVER}/configuration
+HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 #CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_SERVER}/configuration/gphl_mock:/${HO_SERVER}/configuration/xml-qt:${HO_SERVER}/configuration/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""
@@ -23,6 +26,7 @@ MAC_ADDRESS="54:ee:75:b6:8e:d3"
 # User for docker - for giving correct file ownership.
 DOCKER_USER_ID="1000:100"
 # DOCKER_USER_ID="1158:3001"
+# CONSIDER SOMETHING LKE --user $(id -u):$(id -g)
 # User name - used only for file names etc.
 USER_NAME="test_user"
 

From e920d733b24f9aa0b39f81d233f70aecd2be5cf2 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Thu, 4 Jun 2020 15:19:53 +0100
Subject: [PATCH 24/35] Change standard directory structure

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 51165a4..f60c034 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -42,8 +42,8 @@ OUTPUT_HOME="/home/rhfogh/dockerhome/"
 # GPHL-specific directories for mounting
 # Note: These are the same from insisde and outside the docker
 # and so must be either identical or used on only one side.
-GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/gphl_release/"
-GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/mxcube_setup/"
+GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/GPhL/"
+GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/GPhL/mxcube_setup/"
 
 # Location for output data - must be the same inside and outside docker
 DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"

From d0a933d0e4209d50e79a1d551df23ac4f43c1f52 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Tue, 11 Aug 2020 16:02:59 +0100
Subject: [PATCH 25/35] Ported GPhL code from ALBA branch, Pre-test

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index f60c034..ee8f42e 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,12 +8,12 @@ CONTAINER=mx3_deb9_qt4_gphl5
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-# HO_CONFIGURATION=${HO_SERVER}/configuration
-HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
+HO_CONFIGURATION=${HO_SERVER}/configuration
+# HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 #CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/alba_xaloc13"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""

From 327f3f499dfb4499e24214b5fcdc60c32be765ba Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Thu, 15 Oct 2020 17:31:46 +0100
Subject: [PATCH 26/35] Updating GPhL code

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index ee8f42e..138804a 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -13,7 +13,8 @@ HO_CONFIGURATION=${HO_SERVER}/configuration
 #CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
 # HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""

From b9ec525d3e396b28fda9e4436ff1e4c951192839 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Wed, 21 Oct 2020 13:14:38 +0100
Subject: [PATCH 27/35] Addressed points raised by Gleb

(that do not rquire java code changes)
---
 dev/gphl/Debian9_qt4/start_mxcube2 | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 138804a..adec73e 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -12,9 +12,9 @@ HO_CONFIGURATION=${HO_SERVER}/configuration
 # HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 #CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/alba_xaloc13"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""

From 2ec33193041fa9c789bf53a40ff9892df6d6fdda Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Thu, 17 Dec 2020 16:28:55 +0000
Subject: [PATCH 28/35] Refactored from HardwareRepository/ to mx3core/

---
 dev/Debian9_qt4/Dockerfile         | 2 +-
 dev/gphl/Debian9_qt4/README.md     | 2 +-
 dev/gphl/Debian9_qt4/start_mxcube2 | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/dev/Debian9_qt4/Dockerfile b/dev/Debian9_qt4/Dockerfile
index 551a474..18dec9d 100755
--- a/dev/Debian9_qt4/Dockerfile
+++ b/dev/Debian9_qt4/Dockerfile
@@ -24,7 +24,7 @@ WORKDIR /MXCuBE/mxcube
 #RUN git submodule update
 #WORKDIR /MXCuBE/mxcube/HardwareObjects
 #RUN git checkout master
-#WORKDIR /MXCuBE/mxcube/HardwareRepository
+#WORKDIR /MXCuBE/mxcube/mx3core
 #RUN git checkout master
 #WORKDIR /MXCuBE/mxcube/Blissframework
 #RUN git checkout master
diff --git a/dev/gphl/Debian9_qt4/README.md b/dev/gphl/Debian9_qt4/README.md
index 082253c..ae2208e 100755
--- a/dev/gphl/Debian9_qt4/README.md
+++ b/dev/gphl/Debian9_qt4/README.md
@@ -14,7 +14,7 @@ Set environment variable, e.g. (in ~/.bashrc for bash):
 
     export MXCUBE2_ROOT=/path/to/dir/containing/mxcube/repository
 
-Edit the start_mxcube2 file to set MXCuBE HO and HardwareRepository paths,
+Edit the start_mxcube2 file to set MXCuBE HO and mx3core paths,
 User ID to use (for file permissions), output data directory,
 and directories and license info for Global Phasing software.
 
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index adec73e..1da3e81 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -7,15 +7,15 @@ CONTAINER=mx3_deb9_qt4_gphl5
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+HO_SERVER="/MXCuBE/mxcube/mx3core/"
 HO_CONFIGURATION=${HO_SERVER}/configuration
 # HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 #CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
 # HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/alba_xaloc13"
 # HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
-CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/mx3core/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""
 

From fe597a609d09296b316981ad6d660b9352b7688b Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Thu, 17 Dec 2020 17:36:27 +0000
Subject: [PATCH 29/35] Revert "Refactored from HardwareRepository/ to
 mx3core/"

This reverts commit 2ec33193
---
 dev/Debian9_qt4/Dockerfile         | 2 +-
 dev/gphl/Debian9_qt4/README.md     | 2 +-
 dev/gphl/Debian9_qt4/start_mxcube2 | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/dev/Debian9_qt4/Dockerfile b/dev/Debian9_qt4/Dockerfile
index 18dec9d..551a474 100755
--- a/dev/Debian9_qt4/Dockerfile
+++ b/dev/Debian9_qt4/Dockerfile
@@ -24,7 +24,7 @@ WORKDIR /MXCuBE/mxcube
 #RUN git submodule update
 #WORKDIR /MXCuBE/mxcube/HardwareObjects
 #RUN git checkout master
-#WORKDIR /MXCuBE/mxcube/mx3core
+#WORKDIR /MXCuBE/mxcube/HardwareRepository
 #RUN git checkout master
 #WORKDIR /MXCuBE/mxcube/Blissframework
 #RUN git checkout master
diff --git a/dev/gphl/Debian9_qt4/README.md b/dev/gphl/Debian9_qt4/README.md
index ae2208e..082253c 100755
--- a/dev/gphl/Debian9_qt4/README.md
+++ b/dev/gphl/Debian9_qt4/README.md
@@ -14,7 +14,7 @@ Set environment variable, e.g. (in ~/.bashrc for bash):
 
     export MXCUBE2_ROOT=/path/to/dir/containing/mxcube/repository
 
-Edit the start_mxcube2 file to set MXCuBE HO and mx3core paths,
+Edit the start_mxcube2 file to set MXCuBE HO and HardwareRepository paths,
 User ID to use (for file permissions), output data directory,
 and directories and license info for Global Phasing software.
 
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 1da3e81..adec73e 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -7,15 +7,15 @@ CONTAINER=mx3_deb9_qt4_gphl5
 # MXCuBE additional lookup directories
 #
 # Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/mx3core/"
+HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
 HO_CONFIGURATION=${HO_SERVER}/configuration
 # HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 #CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
 # HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/alba_xaloc13"
 # HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
-CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/mx3core/HardwareObjects/mockup"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""
 

From 91b26937aabb6a6d5a11b4a385a25cd67c2efafc Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Wed, 17 Feb 2021 10:23:53 +0000
Subject: [PATCH 30/35] First cut - porting changes from P14 branch to ALBA
 branch

---
 dev/gphl/Debian9_qt4/start_mxcube2 | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index adec73e..0a0cb2f 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,12 +8,12 @@ CONTAINER=mx3_deb9_qt4_gphl5
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-HO_CONFIGURATION=${HO_SERVER}/configuration
-# HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
-#CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
+# HO_CONFIGURATION=${HO_SERVER}/configuration
+HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
+# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/alba_xaloc13"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
 # HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 

From e44afc2852a1accead6dd22a48a876b40242ff86 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Mon, 10 May 2021 16:15:35 +0100
Subject: [PATCH 31/35] First draft qt5 docker file

---
 dev/Ubuntu_qt5/Dockerfile | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100755 dev/Ubuntu_qt5/Dockerfile

diff --git a/dev/Ubuntu_qt5/Dockerfile b/dev/Ubuntu_qt5/Dockerfile
new file mode 100755
index 0000000..43b77ae
--- /dev/null
+++ b/dev/Ubuntu_qt5/Dockerfile
@@ -0,0 +1,19 @@
+FROM ubuntu:focal
+RUN apt-get update
+
+RUN apt-get install -y gevent==1.3.7
+RUN apt-get install -y suds-py3
+RUN apt-get install -y jsonpickle
+RUN apt-get install -y ruamel.yaml
+RUN apt-get install -y PyDispatcher
+RUN apt-get install -y numpy
+RUN apt-get install -y scipy
+RUN apt-get install -y matplotlib
+RUN apt-get install -y Pillow
+RUN apt-get install -y pylint
+RUN apt-get install -y lxml
+RUN apt-get install -y pyqtgraph
+
+
+RUN mkdir -p /MXCuBE/mxcube
+WORKDIR /MXCuBE/mxcube

From eda999a30d3f2035393fd4b9773eabf358cb0786 Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Tue, 25 May 2021 17:30:12 +0100
Subject: [PATCH 32/35] Docker for Python3/Qt5 - WIP

---
 dev/Ubuntu_qt5/Dockerfile              | 59 ++++++++++++++-----
 dev/gphl/Debian9_qt4/start_mxcube2     |  9 ++-
 dev/gphl/Ubuntu_focal_qt5/Dockerfile   | 59 +++++++++++++++++++
 dev/gphl/Ubuntu_focal_qt5/start_mxcube | 78 ++++++++++++++++++++++++++
 4 files changed, 186 insertions(+), 19 deletions(-)
 create mode 100755 dev/gphl/Ubuntu_focal_qt5/Dockerfile
 create mode 100755 dev/gphl/Ubuntu_focal_qt5/start_mxcube

diff --git a/dev/Ubuntu_qt5/Dockerfile b/dev/Ubuntu_qt5/Dockerfile
index 43b77ae..a944114 100755
--- a/dev/Ubuntu_qt5/Dockerfile
+++ b/dev/Ubuntu_qt5/Dockerfile
@@ -1,19 +1,50 @@
 FROM ubuntu:focal
-RUN apt-get update
-
-RUN apt-get install -y gevent==1.3.7
-RUN apt-get install -y suds-py3
-RUN apt-get install -y jsonpickle
-RUN apt-get install -y ruamel.yaml
-RUN apt-get install -y PyDispatcher
-RUN apt-get install -y numpy
-RUN apt-get install -y scipy
-RUN apt-get install -y matplotlib
-RUN apt-get install -y Pillow
-RUN apt-get install -y pylint
-RUN apt-get install -y lxml
-RUN apt-get install -y pyqtgraph
 
+ENV TERM linux
+ENV TZ Europe/London
+RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
+# Install system packages - from Marcus O mxcub3
+
+RUN apt-get update && apt-get -y upgrade && \
+    apt-get install -y apt-utils curl git sudo wget python
+RUN apt-get install -y build-essential
 
 RUN mkdir -p /MXCuBE/mxcube
 WORKDIR /MXCuBE/mxcube
+
+# Qt5 install - from install_pyqt5.sh
+# RUN add-apt-repository --yes ppa:ubuntu-sdk-team/ppa
+# RUN apt-get update -qq
+
+# Install Qt5, QtMultimedia and QtSvg
+RUN apt-get install -qq qtdeclarative5-dev
+ENV  QMAKE /usr/lib/x86_64-linux-gnu/qt5/bin/qmake
+
+# Library versions
+# PYTHON_VERSION=3
+# PYQT_VERSION=5.7.1
+# SIP_VERSION=4.19
+
+# Install sip
+RUN wget --retry-connrefused https://sourceforge.net/projects/pyqt/files/sip/sip-4.19/sip-4.19.tar.gz
+RUN tar -xzf sip-4.19.tar.gz
+RUN pwd
+RUN ls -l
+WORKDIR /MXCuBE/mxcube/sip-4.19
+RUN pwd
+RUN ls -l
+RUN  cat configure.py
+RUN python3 configure.py
+RUN make
+RUN sudo make install
+WORKDIR /MXCuBE/mxcube
+
+# Install PyQt5
+RUN wget --retry-connrefused https://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-5.7.1/PyQt5_gpl-5.7.1.tar.gz
+RUN tar -xzf PyQt5_gpl-5.7.1.tar.gz
+WORKDIR /MXCuBE/mxcube/PyQt5_gpl-5.7.1
+RUN python3 configure.py --confirm-license --qmake=/usr/lib/x86_64-linux-gnu/qt5/bin/qmake
+RUN make
+RUN make install
+WORKDIR /MXCuBE/mxcube
+
diff --git a/dev/gphl/Debian9_qt4/start_mxcube2 b/dev/gphl/Debian9_qt4/start_mxcube2
index 0a0cb2f..20ea61a 100755
--- a/dev/gphl/Debian9_qt4/start_mxcube2
+++ b/dev/gphl/Debian9_qt4/start_mxcube2
@@ -8,13 +8,12 @@ CONTAINER=mx3_deb9_qt4_gphl5
 #
 # Examples of alternative path settings:
 HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-# HO_CONFIGURATION=${HO_SERVER}/configuration
-HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
+HO_CONFIGURATION=${HO_SERVER}/configuration
+# HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
 # CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
 # CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/mockup/gphl:${HO_CONFIGURATION}/mockup/qt:${HO_CONFIGURATION}/mockup:${HO_CONFIGURATION}/embl_hh_p14"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
 CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
 
 CUSTOM_BRICKS_PATH=""
diff --git a/dev/gphl/Ubuntu_focal_qt5/Dockerfile b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
new file mode 100755
index 0000000..24b3d36
--- /dev/null
+++ b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
@@ -0,0 +1,59 @@
+FROM ubuntu_focal_qt5
+
+RUN apt-get update
+
+RUN apt-get install python3-pip -y
+RUN pip install --upgrade pip
+
+# Requirement list
+RUN pip install gevent==1.3.7
+RUN pip install suds-py3
+RUN pip install jsonpickle
+RUN pip install ruamel.yaml
+RUN pip install PyDispatcher
+RUN pip install numpy
+RUN pip install scipy
+RUN pip install matplotlib
+RUN pip install Pillow
+RUN pip install pylint
+RUN pip install lxml
+RUN pip install pyqtgraph
+
+# To get rid of error, that the ps command cannot be found
+# RUN apt-get install procps -y
+
+# Additional requirements - temporarily put here
+# RUN apt-get install python-jsonschema -y
+# RUN apt-get install python-pyqtgraph -y
+
+# Not used by gphl in dockers, but avoids constant error message
+# RUN pip install redis
+
+# Python-Java bridge - needed for GPhL workflow:
+# Install as root, otehrwise not found in xml parsing
+RUN pip install py4j
+# Needed for GPhL simcal
+RUN pip install f90nml
+# Needed for GPhL stratcal rotation matrices
+RUN pip install mgen
+
+# Add user and group so files on main machine get to belong to user instead of root
+# NB this must be adjusted to the test user. TODO move to separate docker
+# RUN groupadd -g 3001 gphl
+#RUN useradd -g gphl -m -s /bin/tcsh -u 1158 rhfogh
+# No longer makes home directory - this must be mounted externally at startup
+# RUN useradd -g gphl -s /bin/tcsh -u 1158 rhfogh
+
+# Directories:
+#
+# /MXCuBE/mxcube - MXCuBE code location is made in mx3_deb9_qt4
+#
+# GPhL code locations. Name is should match external directory structure,
+# so that the same directory names work inside and outside the docker.
+# RUN mkdir -p /archive
+# RUN mkdir -p /scratch_fs1
+# RUN mkdir -p /public/xtal
+RUN mkdir -p /mnt/scrstch
+
+# Used instead of Entrypoint to allow alternative commands to be run
+CMD ["bin/mxcube"]
diff --git a/dev/gphl/Ubuntu_focal_qt5/start_mxcube b/dev/gphl/Ubuntu_focal_qt5/start_mxcube
new file mode 100755
index 0000000..9b649ac
--- /dev/null
+++ b/dev/gphl/Ubuntu_focal_qt5/start_mxcube
@@ -0,0 +1,78 @@
+#!/usr/bin/env bash
+
+CONTAINER=mxcube_ubuntu_focal_qt5
+
+# The following variables should be checked and (re)set as needed
+
+# MXCuBE additional lookup directories
+#
+# Examples of alternative path settings:
+HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
+HO_CONFIGURATION=${HO_SERVER}/configuration
+# HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
+# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
+# CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
+HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
+# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
+CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
+
+CUSTOM_BRICKS_PATH=""
+
+# User and mac address
+#
+# Mac address for docker - nededed for GPhL license
+MAC_ADDRESS="54:ee:75:b6:8e:d3"
+#
+# User for docker - for giving correct file ownership.
+DOCKER_USER_ID="1000:100"
+# DOCKER_USER_ID="1158:3001"
+# CONSIDER SOMETHING LKE --user $(id -u):$(id -g)
+# User name - used only for file names etc.
+USER_NAME="test_user"
+
+# Directories set-up
+#
+# MXCuBE installation is in /MXCuBE/mxcube, as per standard
+#
+# Home directory, used for e.g. .config and .ssh. Externally mounted.
+DOCKER_HOME="/home/rhfogh/"
+OUTPUT_HOME="/home/rhfogh/dockerhome/"
+# GPhL software.
+
+# GPHL-specific directories for mounting
+# Note: These are the same from insisde and outside the docker
+# and so must be either identical or used on only one side.
+GPHL_RELEASE_ROOT="/mnt/scratch/rhfogh/GPhL/"
+GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/GPhL/mxcube_setup/"
+
+# Location for output data - must be the same inside and outside docker
+DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"
+
+
+# End of settable parameters.
+
+
+xhost +local:
+# Command needed to run GPhL workflows
+# Add in this for debug
+# -p 8050:8050 \
+exec docker run -it \
+--mac-address $MAC_ADDRESS \
+-p 25333:25333 \
+-p 25334:25334 \
+-h=$CONTAINER \
+-u $DOCKER_USER_ID \
+-e HOME=$DOCKER_HOME \
+-e USER=$USER_NAME \
+-e DISPLAY=$DISPLAY \
+-e QT_X11_NO_MITSHM=1 \
+-e HARDWARE_REPOSITORY_SERVER=$HARDWARE_REPOSITORY_SERVER \
+-e CUSTOM_HARDWARE_OBJECTS_PATH=$CUSTOM_HARDWARE_OBJECTS_PATH \
+-e CUSTOM_BRICKS_PATH=$CUSTOM_BRICKS_PATH \
+-v $MXCUBE2_ROOT:/MXCuBE/mxcube \
+-v $GPHL_RELEASE_ROOT:$GPHL_RELEASE_ROOT \
+-v $GPHL_SETUP_ROOT:$GPHL_SETUP_ROOT \
+-v $DATA_ROOT:$DATA_ROOT \
+-v $OUTPUT_HOME:$DOCKER_HOME \
+-v /tmp/.X11-unix:/tmp/.X11-unix \
+$CONTAINER

From b12f1391fc6c4ea8a6a3b9f7405ea42f7872376d Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Tue, 1 Jun 2021 15:25:57 +0100
Subject: [PATCH 33/35] Added Ubuntu qt5 docker and updated to use it

---
 dev/Ubuntu_qt5/Dockerfile              | 71 +++++++++++---------------
 dev/gphl/Ubuntu_focal_qt5/Dockerfile   | 42 ++-------------
 dev/gphl/Ubuntu_focal_qt5/start_mxcube | 27 +++++-----
 3 files changed, 47 insertions(+), 93 deletions(-)

diff --git a/dev/Ubuntu_qt5/Dockerfile b/dev/Ubuntu_qt5/Dockerfile
index a944114..35edc5f 100755
--- a/dev/Ubuntu_qt5/Dockerfile
+++ b/dev/Ubuntu_qt5/Dockerfile
@@ -1,50 +1,41 @@
 FROM ubuntu:focal
 
+# Set terminal and time zone, to catch installer interactoin attempts
 ENV TERM linux
 ENV TZ Europe/London
 RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone
-# Install system packages - from Marcus O mxcub3
 
+# Install system packages - from Marcus O mxcub3
 RUN apt-get update && apt-get -y upgrade && \
     apt-get install -y apt-utils curl git sudo wget python
 RUN apt-get install -y build-essential
 
-RUN mkdir -p /MXCuBE/mxcube
-WORKDIR /MXCuBE/mxcube
-
-# Qt5 install - from install_pyqt5.sh
-# RUN add-apt-repository --yes ppa:ubuntu-sdk-team/ppa
-# RUN apt-get update -qq
-
-# Install Qt5, QtMultimedia and QtSvg
-RUN apt-get install -qq qtdeclarative5-dev
-ENV  QMAKE /usr/lib/x86_64-linux-gnu/qt5/bin/qmake
-
-# Library versions
-# PYTHON_VERSION=3
-# PYQT_VERSION=5.7.1
-# SIP_VERSION=4.19
-
-# Install sip
-RUN wget --retry-connrefused https://sourceforge.net/projects/pyqt/files/sip/sip-4.19/sip-4.19.tar.gz
-RUN tar -xzf sip-4.19.tar.gz
-RUN pwd
-RUN ls -l
-WORKDIR /MXCuBE/mxcube/sip-4.19
-RUN pwd
-RUN ls -l
-RUN  cat configure.py
-RUN python3 configure.py
-RUN make
-RUN sudo make install
-WORKDIR /MXCuBE/mxcube
-
-# Install PyQt5
-RUN wget --retry-connrefused https://sourceforge.net/projects/pyqt/files/PyQt5/PyQt-5.7.1/PyQt5_gpl-5.7.1.tar.gz
-RUN tar -xzf PyQt5_gpl-5.7.1.tar.gz
-WORKDIR /MXCuBE/mxcube/PyQt5_gpl-5.7.1
-RUN python3 configure.py --confirm-license --qmake=/usr/lib/x86_64-linux-gnu/qt5/bin/qmake
-RUN make
-RUN make install
-WORKDIR /MXCuBE/mxcube
-
+# Install 'top-level' packages
+RUN apt-get install -y python3-scipy
+RUN apt-get install -y python3-pyqtgraph
+
+# NB numpy, matplotlib, Pillow, PyQt5, and sip
+# are installed at this point
+
+# Get and update pip
+RUN apt-get install python3-pip -y
+RUN pip install --upgrade pip
+
+# From requirement list
+RUN pip install gevent
+RUN pip install suds-py3
+RUN pip install jsonpickle
+RUN pip install ruamel.yaml
+RUN pip install PyDispatcher
+RUN pip install pylint
+RUN pip install lxml
+RUN pip install jsonschema
+
+# Global Phasing requirements
+# Python-Java bridge - needed for GPhL workflow:
+# Install as root, otehrwise not found in xml parsing
+RUN pip install py4j
+# Needed for GPhL simcal and stratcal
+RUN pip install f90nml
+# Needed for GPhL stratcal rotation matrices
+RUN pip install mgen
diff --git a/dev/gphl/Ubuntu_focal_qt5/Dockerfile b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
index 24b3d36..569fd14 100755
--- a/dev/gphl/Ubuntu_focal_qt5/Dockerfile
+++ b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
@@ -1,41 +1,9 @@
-FROM ubuntu_focal_qt5
+FROM ubuntu_focal_qt5b
 
 RUN apt-get update
 
-RUN apt-get install python3-pip -y
-RUN pip install --upgrade pip
-
-# Requirement list
-RUN pip install gevent==1.3.7
-RUN pip install suds-py3
-RUN pip install jsonpickle
-RUN pip install ruamel.yaml
-RUN pip install PyDispatcher
-RUN pip install numpy
-RUN pip install scipy
-RUN pip install matplotlib
-RUN pip install Pillow
-RUN pip install pylint
-RUN pip install lxml
-RUN pip install pyqtgraph
-
-# To get rid of error, that the ps command cannot be found
-# RUN apt-get install procps -y
-
-# Additional requirements - temporarily put here
-# RUN apt-get install python-jsonschema -y
-# RUN apt-get install python-pyqtgraph -y
-
-# Not used by gphl in dockers, but avoids constant error message
-# RUN pip install redis
-
-# Python-Java bridge - needed for GPhL workflow:
-# Install as root, otehrwise not found in xml parsing
-RUN pip install py4j
-# Needed for GPhL simcal
-RUN pip install f90nml
-# Needed for GPhL stratcal rotation matrices
-RUN pip install mgen
+RUN mkdir -p /MXCuBE
+WORKDIR /MXCuBE
 
 # Add user and group so files on main machine get to belong to user instead of root
 # NB this must be adjusted to the test user. TODO move to separate docker
@@ -46,8 +14,6 @@ RUN pip install mgen
 
 # Directories:
 #
-# /MXCuBE/mxcube - MXCuBE code location is made in mx3_deb9_qt4
-#
 # GPhL code locations. Name is should match external directory structure,
 # so that the same directory names work inside and outside the docker.
 # RUN mkdir -p /archive
@@ -56,4 +22,4 @@ RUN pip install mgen
 RUN mkdir -p /mnt/scrstch
 
 # Used instead of Entrypoint to allow alternative commands to be run
-CMD ["bin/mxcube"]
+CMD ["python3",  "/MXCuBE/mxcube/mxcubeqt/__main__.py", "--pyqt5", "--mockupMode"]
diff --git a/dev/gphl/Ubuntu_focal_qt5/start_mxcube b/dev/gphl/Ubuntu_focal_qt5/start_mxcube
index 9b649ac..95b3473 100755
--- a/dev/gphl/Ubuntu_focal_qt5/start_mxcube
+++ b/dev/gphl/Ubuntu_focal_qt5/start_mxcube
@@ -3,20 +3,17 @@
 CONTAINER=mxcube_ubuntu_focal_qt5
 
 # The following variables should be checked and (re)set as needed
-
-# MXCuBE additional lookup directories
 #
-# Examples of alternative path settings:
-HO_SERVER="/MXCuBE/mxcube/HardwareRepository/"
-HO_CONFIGURATION=${HO_SERVER}/configuration
-# HO_CONFIGURATION="/MXCuBE/mxcube/ExampleFiles/HardwareObjects.xml"
-# CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/extra_HO_test_1:/MXCuBE/mxcube/extra_HO_test_2"
-# CUSTOM_BRICKS_PATH="/MXCuBE/mxcube/extra_brick_test_1:/MXCuBE/mxcube/extra_brick_test_2"
-HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}/xml-qt:${HO_CONFIGURATION}/embl_hh_p14"
-# HARDWARE_REPOSITORY_SERVER="${HO_CONFIGURATION}/gphl_mock:${HO_CONFIGURATION}:${HO_CONFIGURATION}/alba_xaloc13"
-CUSTOM_HARDWARE_OBJECTS_PATH="/MXCuBE/mxcube/HardwareRepository/HardwareObjects/mockup"
-
+MXCUBE_BASE=/MXCuBE
+MXCUBE_CORE=${MXCUBE_BASE}/mxcubecore/mxcubecore
 CUSTOM_BRICKS_PATH=""
+CUSTOM_HARDWARE_OBJECTS_PATH="${MXCUBE_CORE}/HardwareObjects/mockup"
+
+MOCKUP_XML_PATH=${MXCUBE_CORE}/configuration/mockup
+MXCUBE_CORE_CONFIG_PATH="${MOCKUP_XML_PATH}/gphl:${MOCKUP_XML_PATH}/qt:${MOCKUP_XML_PATH}"
+
+# SOLEIL:
+MXCUBE_CORE_CONFIG_PATH=${MXCUBE_CORE_CONFIG_PATH}:${MXCUBE_CORE}/configuration/soleil/px2/mockups
 
 # User and mac address
 #
@@ -48,7 +45,6 @@ GPHL_SETUP_ROOT="/mnt/scratch/rhfogh/GPhL/mxcube_setup/"
 # Location for output data - must be the same inside and outside docker
 DATA_ROOT="/mnt/scratch/rhfogh/mxcube_data"
 
-
 # End of settable parameters.
 
 
@@ -66,10 +62,11 @@ exec docker run -it \
 -e USER=$USER_NAME \
 -e DISPLAY=$DISPLAY \
 -e QT_X11_NO_MITSHM=1 \
--e HARDWARE_REPOSITORY_SERVER=$HARDWARE_REPOSITORY_SERVER \
+-e MXCUBE_CORE_CONFIG_PATH=$MXCUBE_CORE_CONFIG_PATH \
 -e CUSTOM_HARDWARE_OBJECTS_PATH=$CUSTOM_HARDWARE_OBJECTS_PATH \
 -e CUSTOM_BRICKS_PATH=$CUSTOM_BRICKS_PATH \
--v $MXCUBE2_ROOT:/MXCuBE/mxcube \
+-e PYTHONPATH=$MXCUBE_BASE/mxcube:$MXCUBE_BASE/mxcubecore \
+-v $MXCUBE_ROOT:/MXCuBE \
 -v $GPHL_RELEASE_ROOT:$GPHL_RELEASE_ROOT \
 -v $GPHL_SETUP_ROOT:$GPHL_SETUP_ROOT \
 -v $DATA_ROOT:$DATA_ROOT \

From 913d4aa957adaade10736eb70a4faca3ebfa1c9b Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Wed, 9 Jun 2021 20:47:16 +0100
Subject: [PATCH 34/35] Functional Ubuntu dockers.

---
 dev/Ubuntu_qt5/Dockerfile            | 5 ++++-
 dev/gphl/Ubuntu_focal_qt5/Dockerfile | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/dev/Ubuntu_qt5/Dockerfile b/dev/Ubuntu_qt5/Dockerfile
index 35edc5f..02f7305 100755
--- a/dev/Ubuntu_qt5/Dockerfile
+++ b/dev/Ubuntu_qt5/Dockerfile
@@ -22,6 +22,8 @@ RUN apt-get install python3-pip -y
 RUN pip install --upgrade pip
 
 # From requirement list
+#RUN pip install greenlet==0.4.16
+#RUN pip install gevent==1.3.7
 RUN pip install gevent
 RUN pip install suds-py3
 RUN pip install jsonpickle
@@ -33,7 +35,8 @@ RUN pip install jsonschema
 
 # Global Phasing requirements
 # Python-Java bridge - needed for GPhL workflow:
-# Install as root, otehrwise not found in xml parsing
+# Install as root, otherwise not found in xml parsing
+#RUN pip install py4j==0.10.6
 RUN pip install py4j
 # Needed for GPhL simcal and stratcal
 RUN pip install f90nml
diff --git a/dev/gphl/Ubuntu_focal_qt5/Dockerfile b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
index 569fd14..3e7dee5 100755
--- a/dev/gphl/Ubuntu_focal_qt5/Dockerfile
+++ b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
@@ -1,4 +1,4 @@
-FROM ubuntu_focal_qt5b
+FROM ubuntu_focal_qt5
 
 RUN apt-get update
 

From 76d213d61afbeaf77f8c673af0d838099c720e8c Mon Sep 17 00:00:00 2001
From: rhfogh <r.h.fogh@gmail.com>
Date: Fri, 11 Jun 2021 20:10:51 +0100
Subject: [PATCH 35/35] Furher fixes for porting

NB some refactoring for consistency
NB Removed cp parameter for collect (for now)
---
 dev/gphl/Ubuntu_focal_qt5/Dockerfile   | 2 +-
 dev/gphl/Ubuntu_focal_qt5/start_mxcube | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/dev/gphl/Ubuntu_focal_qt5/Dockerfile b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
index 3e7dee5..0cfce08 100755
--- a/dev/gphl/Ubuntu_focal_qt5/Dockerfile
+++ b/dev/gphl/Ubuntu_focal_qt5/Dockerfile
@@ -19,7 +19,7 @@ WORKDIR /MXCuBE
 # RUN mkdir -p /archive
 # RUN mkdir -p /scratch_fs1
 # RUN mkdir -p /public/xtal
-RUN mkdir -p /mnt/scrstch
+RUN mkdir -p /mnt/scratch
 
 # Used instead of Entrypoint to allow alternative commands to be run
 CMD ["python3",  "/MXCuBE/mxcube/mxcubeqt/__main__.py", "--pyqt5", "--mockupMode"]
diff --git a/dev/gphl/Ubuntu_focal_qt5/start_mxcube b/dev/gphl/Ubuntu_focal_qt5/start_mxcube
index 95b3473..e7ca88b 100755
--- a/dev/gphl/Ubuntu_focal_qt5/start_mxcube
+++ b/dev/gphl/Ubuntu_focal_qt5/start_mxcube
@@ -4,16 +4,16 @@ CONTAINER=mxcube_ubuntu_focal_qt5
 
 # The following variables should be checked and (re)set as needed
 #
-MXCUBE_BASE=/MXCuBE
-MXCUBE_CORE=${MXCUBE_BASE}/mxcubecore/mxcubecore
+MXCUBE_BASE="/MXCuBE"
+MXCUBE_CORE="${MXCUBE_BASE}/mxcubecore/mxcubecore"
 CUSTOM_BRICKS_PATH=""
 CUSTOM_HARDWARE_OBJECTS_PATH="${MXCUBE_CORE}/HardwareObjects/mockup"
 
-MOCKUP_XML_PATH=${MXCUBE_CORE}/configuration/mockup
+MOCKUP_XML_PATH="${MXCUBE_CORE}/configuration/mockup"
 MXCUBE_CORE_CONFIG_PATH="${MOCKUP_XML_PATH}/gphl:${MOCKUP_XML_PATH}/qt:${MOCKUP_XML_PATH}"
 
 # SOLEIL:
-MXCUBE_CORE_CONFIG_PATH=${MXCUBE_CORE_CONFIG_PATH}:${MXCUBE_CORE}/configuration/soleil/px2/mockups
+MXCUBE_CORE_CONFIG_PATH="${MXCUBE_CORE_CONFIG_PATH}:${MXCUBE_CORE}/configuration/soleil/px2/mockups"
 
 # User and mac address
 #