fix remote vs. local for vlass

• also updates vlass workflows for using the DSOC vlass partition

shared/workspaces/alembic/versions/55e5b37d1ccf_fix_remote_vs_local_vlass_templates.py

+"""fix remote vs local cube templates
+
+Revision ID: 55e5b37d1ccf
+Revises: 5dd6938d2307
+Create Date: 2022-09-12 14:31:55.228979
+
+"""
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "55e5b37d1ccf"
+down_revision = "5dd6938d2307"
+branch_labels = None
+depends_on = None
+
+seci_condor = """executable = vlass_seci.sh
+arguments = metadata.json PPR.xml
+
+output = seci.out
+error = seci.err
+log = condor.log
+
+VLASS_DIR = {{data_location}}
+SBIN_PATH = /lustre/aoc/cluster/pipeline/$ENV(CAPO_PROFILE)/workspaces/sbin
+should_transfer_files = yes
+transfer_input_files = $ENV(HOME)/.ssh/condor_transfer, nraorsync://$(SBIN_PATH)/.matplotlib, nraorsync://$(SBIN_PATH)/pycapo, nraorsync://$(SBIN_PATH)/vela, nraorsync://$(SBIN_PATH)/casa_envoy, nraorsync://$(VLASS_DIR)/working, nraorsync://$(VLASS_DIR)/rawdata, nraorsync://$(VLASS_DIR)/products{{#remote}}, nraorsync://$(VLASS_DIR)/{{profile}}.properties{{/remote}}, nraorsync://$(VLASS_DIR)/PPR.xml, nraorsync://$(VLASS_DIR)/metadata.json
+when_to_transfer_output = ON_EXIT
+transfer_output_files = .job.ad
++nrao_output_files = "working products"
+output_destination = nraorsync://$(VLASS_DIR)
++WantIOProxy = True
+
+request_memory = 50G
+getenv = True
+
+{{^remote}}
+environment = "CAPO_PATH=/home/casa/capo"
+requirements = (VLASS == True) && (HasLustre == True)
++partition = "VLASS"
+{{/remote}}
+{{#remote}}
+requirements = (VLASS == True)
++partition = "VLASS"
+Rank = (TARGET.VLASS == True) + (TARGET.VLASSTEST =!= True)
+{{/remote}}
+
+queue
+
+"""
+old_seci_condor = """executable = vlass_seci.sh
+arguments = metadata.json PPR.xml
+
+output = seci.out
+error = seci.err
+log = condor.log
+
+VLASS_DIR = {{data_location}}
+SBIN_PATH = /lustre/aoc/cluster/pipeline/$ENV(CAPO_PROFILE)/workspaces/sbin
+should_transfer_files = yes
+transfer_input_files = $ENV(HOME)/.ssh/condor_transfer, nraorsync://$(SBIN_PATH)/.matplotlib, nraorsync://$(SBIN_PATH)/pycapo, nraorsync://$(SBIN_PATH)/framework.sh, nraorsync://$(SBIN_PATH)/vela, nraorsync://$(SBIN_PATH)/casa_envoy, nraorsync://$(VLASS_DIR)/working, nraorsync://$(VLASS_DIR)/rawdata, nraorsync://$(VLASS_DIR)/products, nraorsync://$(VLASS_DIR)/{{profile}}.properties, nraorsync://$(VLASS_DIR)/PPR.xml, nraorsync://$(VLASS_DIR)/metadata.json
+when_to_transfer_output = ON_EXIT
+transfer_output_files = .job.ad
++nrao_output_files = "rawdata working products"
+output_destination = nraorsync://$(VLASS_DIR)
++WantIOProxy = True
+
+request_memory = 50G
+getenv = True
+environment = "CAPO_PATH=."
+
+{{#remote}}
+requirements = (VLASS == True)
++partition = "VLASS"
+Rank = (TARGET.VLASS == True) + (TARGET.VLASSTEST =!= True)
+{{/remote}}
+
+queue
+
+"""
+seci_script = """#!/bin/sh
+
+export HOME=$TMPDIR
+{{#remote}}
+export CAPO_PATH=.
+export CAPO_PROFILE={{profile}}
+{{/remote}}
+
+set -o errexit
+
+./casa_envoy --vlass-img $1 $2
+
+"""
+old_seci_script = """#!/bin/sh
+
+export HOME=$TMPDIR
+
+set -o errexit
+
+./casa_envoy --vlass-img $1 $2
+
+"""
+
+cube_condor = """executable = vlass_coarse_envoy.sh
+arguments = metadata.json PPR.xml {{requested_parallel}}
+
+output = vlass_coarse_envoy.out
+error = vlass_coarse_envoy.err
+log = condor.log
+
+VLASS_DIR = {{data_location}}
+SBIN_PATH = /lustre/aoc/cluster/pipeline/$ENV(CAPO_PROFILE)/workspaces/sbin
+should_transfer_files = yes
+transfer_input_files = $ENV(HOME)/.ssh/condor_transfer, nraorsync://$(SBIN_PATH)/.matplotlib, nraorsync://$(SBIN_PATH)/pycapo, nraorsync://$(SBIN_PATH)/vela, nraorsync://$(SBIN_PATH)/casa_envoy, nraorsync://$(VLASS_DIR)/working, nraorsync://$(VLASS_DIR)/rawdata, nraorsync://$(VLASS_DIR)/products{{#remote}}, nraorsync://$(VLASS_DIR)/{{profile}}.properties{{/remote}}, nraorsync://$(VLASS_DIR)/PPR.xml, nraorsync://$(VLASS_DIR)/metadata.json
+when_to_transfer_output = ON_EXIT
+transfer_output_files = .job.ad
++nrao_output_files = "working products"
+output_destination = nraorsync://$(VLASS_DIR)
++WantIOProxy = True
+
+request_cpus = {{requested_parallel}}
+request_memory = 150G
+request_disk = 850G
+getenv = True
+
+{{^remote}}
+environment = "CAPO_PATH=/home/casa/capo"
+requirements = (VLASS == True) && (HasLustre == True)
++partition = "VLASS"
+{{/remote}}
+{{#remote}}
+requirements = (VLASS == True)
++partition = "VLASS"
+Rank = (TARGET.VLASS == True) + (TARGET.VLASSTEST =!= True)
+{{/remote}}
+
+queue
+
+"""
+old_cube_condor = """executable = vlass_coarse_envoy.sh
+arguments = metadata.json PPR.xml {{requested_parallel}}
+
+output = vlass_coarse_envoy.out
+error = vlass_coarse_envoy.err
+log = condor.log
+
+VLASS_DIR = {{data_location}}
+SBIN_PATH = /lustre/aoc/cluster/pipeline/$ENV(CAPO_PROFILE)/workspaces/sbin
+should_transfer_files = yes
+transfer_input_files = $ENV(HOME)/.ssh/condor_transfer, nraorsync://$(SBIN_PATH)/.matplotlib, nraorsync://$(SBIN_PATH)/pycapo, nraorsync://$(SBIN_PATH)/framework.sh, nraorsync://$(SBIN_PATH)/vela, nraorsync://$(SBIN_PATH)/casa_envoy, nraorsync://$(VLASS_DIR)/working, nraorsync://$(VLASS_DIR)/rawdata, nraorsync://$(VLASS_DIR)/products, nraorsync://$(VLASS_DIR)/{{profile}}.properties, nraorsync://$(VLASS_DIR)/PPR.xml, nraorsync://$(VLASS_DIR)/metadata.json
+when_to_transfer_output = ON_EXIT
+transfer_output_files = .job.ad
++nrao_output_files = "rawdata working products"
+output_destination = nraorsync://$(VLASS_DIR)
++WantIOProxy = True
+
+request_cpus = {{requested_parallel}}
+request_memory = 150G
+request_disk = 850G
+getenv = True
+environment = "CAPO_PATH=."
+
+{{#remote}}
+requirements = (VLASS == True)
++partition = "VLASS"
+Rank = (TARGET.VLASS == True) + (TARGET.VLASSTEST =!= True)
+{{/remote}}
+
+queue
+
+"""
+cube_script = """#!/bin/sh
+
+export HOME=$TMPDIR
+{{#remote}}
+export CAPO_PATH=.
+export CAPO_PROFILE={{profile}}
+{{/remote}}
+
+set -o errexit
+
+./casa_envoy --vlass-img $1 $2 --parallel $3
+"""
+old_cube_script = """#!/bin/sh
+
+export HOME=$TMPDIR
+
+set -o errexit
+
+./casa_envoy --vlass-img $1 $2 --parallel $3
+"""
+
+ql_condor = """executable = vlass_ql_envoy.sh
+arguments = metadata.json PPR.xml {{request_id}}
+
+output = ql_envoy.out
+error = ql_envoy.err
+log = condor.log
+
+SBIN_PATH = /lustre/aoc/cluster/pipeline/$ENV(CAPO_PROFILE)/workspaces/sbin
+VLASS_DIR = {{data_location}}
+should_transfer_files = yes
+transfer_input_files = $ENV(HOME)/.ssh/condor_transfer, nraorsync://$(SBIN_PATH)/.matplotlib, nraorsync://$(SBIN_PATH)/pycapo, nraorsync://$(SBIN_PATH)/casa_envoy, nraorsync://$(SBIN_PATH)/vela, nraorsync://$(VLASS_DIR)/working, nraorsync://$(VLASS_DIR)/rawdata, nraorsync://$(VLASS_DIR)/products{{#remote}}, nraorsync://$(VLASS_DIR)/{{profile}}.properties{{/remote}}, nraorsync://$(VLASS_DIR)/PPR.xml, nraorsync://$(VLASS_DIR)/metadata.json{{files_to_transfer}}
+transfer_output_files = .job.ad
++nrao_output_files = "working products"
+when_to_transfer_output = ON_EXIT
+output_destination = nraorsync://$(VLASS_DIR)
++WantIOProxy = True
+
+request_memory = {{ramInGb}}
+getenv = True
+
+{{^remote}}
+environment = "CAPO_PATH=/home/casa/capo"
+requirements = (VLASS == True) && (HasLustre == True)
++partition = "VLASS"
+{{/remote}}
+{{#remote}}
+requirements = (VLASS == True)
++partition = "VLASS"
+Rank = (TARGET.VLASS == True) + (TARGET.VLASSTEST =!= True)
+{{/remote}}
+
+queue
+"""
+old_ql_condor = """executable = vlass_ql_envoy.sh
+arguments = metadata.json PPR.xml {{request_id}}
+
+output = ql_envoy.out
+error = ql_envoy.err
+log = condor.log
+
+SBIN_PATH = /lustre/aoc/cluster/pipeline/$ENV(CAPO_PROFILE)/workspaces/sbin
+VLASS_DIR = {{data_location}}
+should_transfer_files = yes
+transfer_input_files = $ENV(HOME)/.ssh/condor_transfer, nraorsync://$(SBIN_PATH)/.matplotlib, nraorsync://$(SBIN_PATH)/pycapo, nraorsync://$(SBIN_PATH)/casa_envoy, nraorsync://$(SBIN_PATH)/vela, nraorsync://$(VLASS_DIR)/working, nraorsync://$(VLASS_DIR)/rawdata, nraorsync://$(VLASS_DIR)/products{{#remote}}, nraorsync://$(VLASS_DIR)/{{profile}}.properties{{/remote}}, nraorsync://$(VLASS_DIR)/PPR.xml, nraorsync://$(VLASS_DIR)/metadata.json{{files_to_transfer}}
+transfer_output_files = .job.ad
++nrao_output_files = "working rawdata products"
+when_to_transfer_output = ON_EXIT
+output_destination = nraorsync://$(VLASS_DIR)
++WantIOProxy = True
+
+request_memory = {{ramInGb}}
+getenv = True
+
+{{^remote}}
+environment = "CAPO_PATH=/home/casa/capo"
+requirements = HasLustre == True
+{{/remote}}
+{{#remote}}
+requirements = (VLASS == True)
++partition = "VLASS"
+Rank = (TARGET.VLASS == True) + (TARGET.VLASSTEST =!= True)
+{{/remote}}
+
+queue
+"""
+ql_script = """#!/bin/sh
+
+export HOME=$TMPDIR
+{{#remote}}
+export CAPO_PATH=.
+export CAPO_PROFILE={{profile}}
+{{/remote}}
+
+set -o errexit
+
+./casa_envoy --vlass-img $1 $2
+"""
+old_ql_script = """#!/bin/sh
+
+export HOME=$TMPDIR
+
+set -o errexit
+
+./casa_envoy --vlass-img $1 $2
+"""
+
+
+def upgrade():
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{seci_condor}' WHERE filename='vlass_seci.condor'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{seci_script}' WHERE filename='vlass_seci.sh'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{cube_condor}' WHERE filename='vlass_coarse_envoy.condor'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{cube_script}' WHERE filename='vlass_coarse_envoy.sh'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{ql_condor}' WHERE filename='vlass_ql_envoy.condor'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{ql_script}' WHERE filename='vlass_ql_envoy.sh'
+        """
+    )
+
+
+def downgrade():
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{old_seci_condor}' WHERE filename='vlass_seci.condor'
+        """
+    )
+    op.execute(
+        f"""
+            UPDATE workflow_templates
+            SET content=E'{old_seci_script}' WHERE filename='vlass_seci.sh'
+            """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{old_cube_condor}' WHERE filename='vlass_coarse_envoy.condor'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{old_cube_script}' WHERE filename='vlass_coarse_envoy.sh'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{old_ql_condor}' WHERE filename='vlass_ql_envoy.condor'
+        """
+    )
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{old_ql_script}' WHERE filename='vlass_ql_envoy.sh'
+        """
+    )