update scripts when copying from templates

apps/dashboard/app/models/project.rb

@@ -76,9 +76,6 @@ def templates
   validate :project_directory_exist, on: [:create]
   validate :project_template_invalid, on: [:create]
 
-  # the template you created this project from
-  attr_accessor :template
-
   def initialize(attributes = {})
     @id = attributes.delete(:id)
     @directory = attributes.delete(:directory)
@@ -194,15 +191,39 @@ def sync_template
     return true if template.blank?
 
     # Sync the template files over
-    oe, s = Open3.capture2e("rsync", "-a", "#{template}/", "#{project_dataroot}")
+    oe, s = Open3.capture2e(*rsync_args)
     raise oe unless s.success?
 
-    true
+    save_new_scripts
   rescue StandardError => e
     errors.add(:save, "Failed to sync template: #{e.message}")
     false
   end
 
+  # When copying a project from a template, we need new Script objects
+  # that point to the _new_ project directory, not the template's directory.
+  # This creates them _and_ serializes them to yml in the new directory.
+  def save_new_scripts
+    dir = Script.scripts_dir(template)
+    Dir.glob("#{dir}/*/form.yml").map do |script_yml|
+      Script.from_yaml(script_yml, project_dataroot)
+    end.map do |script|
+      saved_successfully = script.save
+      errors.add(:save, script.errors.full_messages) unless saved_successfully
+
+      saved_successfully
+    end.none? do |saved_successfully|
+      saved_successfully == false
+    end
+  end
+
+  def rsync_args
+    [
+      'rsync', '-rltp', '--exclude', 'scripts/*',
+      "#{template}/", project_dataroot.to_s
+    ]
+  end
+
   def project_directory_exist
     if !directory.blank? && Project.lookup_table.map { |_id, directory| directory }.map(&:to_s).include?(directory.to_s)
       errors.add(:directory, :used)

apps/dashboard/app/models/script.rb

@@ -309,9 +309,8 @@ def add_required_fields(form: [], attributes: {})
   end
 
   def add_script_to_form(form: [], attributes: {})
-    return if form.include?('auto_scripts')
+    form << 'auto_scripts' unless form.include?('auto_scripts')
 
-    form << 'auto_scripts'
     attributes[:auto_scripts] = {
       directory: project_dir
     }

apps/dashboard/test/fixtures/projects/chemistry-5533/.ondemand/manifest.yml

@@ -0,0 +1,4 @@
+---
+name: Chemistry 5533
+description: This is a template for a fake chemistry class - 5533.
+icon: fas://atom

apps/dashboard/test/fixtures/projects/chemistry-5533/.ondemand/scripts/8woi7ghd/form.yml

@@ -0,0 +1,54 @@
+---
+title: Assignment 1
+created_at: 1699454963
+form:
+- auto_accounts
+- auto_scripts
+- auto_batch_clusters
+attributes:
+  auto_accounts:
+    options:
+    - - pzs0715
+      - pzs0715
+      - {}
+    - - pzs1118
+      - pzs1118
+      - {}
+    - - pzs0714
+      - pzs0714
+      - {}
+    - - pzs1117
+      - pzs1117
+      - data-option-for-cluster-ascend: false
+    - - pas1604
+      - pas1604
+      - data-option-for-cluster-ascend: false
+    value: pzs0715
+    fixed: true
+    label: Account
+    help: ''
+    required: false
+  auto_scripts:
+    options:
+    - - assignment_1.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_1.sh"
+    - - assignment_2.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_2.sh"
+    - - assignment_3.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_3.sh"
+    directory: "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi"
+    value: "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_1.sh"
+    fixed: true
+    label: Script
+    help: ''
+    required: false
+  auto_batch_clusters:
+    options:
+    - ascend
+    - owens
+    - pitzer
+    value: owens
+    fixed: true
+    label: Cluster
+    help: ''
+    required: false

apps/dashboard/test/fixtures/projects/chemistry-5533/.ondemand/scripts/gtqxzsek/form.yml

@@ -0,0 +1,57 @@
+---
+title: Assignment 2
+created_at: 1699455963
+form:
+- auto_accounts
+- auto_scripts
+- auto_batch_clusters
+attributes:
+  auto_accounts:
+    options:
+    - - pzs0715
+      - pzs0715
+      - {}
+    - - pzs1118
+      - pzs1118
+      - {}
+    - - pzs0714
+      - pzs0714
+      - {}
+    - - pzs1117
+      - pzs1117
+      - data-option-for-cluster-ascend: false
+    - - pas1604
+      - pas1604
+      - data-option-for-cluster-ascend: false
+    value: pzs0715
+    fixed: true
+    label: Account
+    help: ''
+    required: false
+  auto_scripts:
+    options:
+    - - assignment_1.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_1.sh"
+    - - assignment_2.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_2.sh"
+    - - assignment_3.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_3.sh"
+    directory: "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi"
+    value: "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_2.sh"
+    exclude_options:
+    - assignment_3.sh
+    - assignment_1.sh
+    fixed: true
+    label: Script
+    help: ''
+    required: false
+  auto_batch_clusters:
+    options:
+    - ascend
+    - owens
+    - pitzer
+    value: owens
+    fixed: true
+    label: Cluster
+    help: ''
+    required: false

apps/dashboard/test/fixtures/projects/chemistry-5533/.ondemand/scripts/jxbrz2vm/form.yml

@@ -0,0 +1,57 @@
+---
+title: Assignment 3
+created_at: 1699456963
+form:
+- auto_accounts
+- auto_scripts
+- auto_batch_clusters
+attributes:
+  auto_accounts:
+    options:
+    - - pzs0715
+      - pzs0715
+      - {}
+    - - pzs1118
+      - pzs1118
+      - {}
+    - - pzs0714
+      - pzs0714
+      - {}
+    - - pzs1117
+      - pzs1117
+      - data-option-for-cluster-ascend: false
+    - - pas1604
+      - pas1604
+      - data-option-for-cluster-ascend: false
+    value: pzs0715
+    fixed: true
+    label: Account
+    help: ''
+    required: false
+  auto_scripts:
+    options:
+    - - assignment_1.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_1.sh"
+    - - assignment_2.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_2.sh"
+    - - assignment_3.sh
+      - "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_3.sh"
+    directory: "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi"
+    value: "/users/PZS0714/johrstrom/ondemand/src/apps/dashboard/data/projects/cmtgfxfi/assignment_3.sh"
+    exclude_options:
+    - assignment_2.sh
+    - assignment_1.sh
+    fixed: true
+    label: Script
+    help: ''
+    required: false
+  auto_batch_clusters:
+    options:
+    - ascend
+    - owens
+    - pitzer
+    value: owens
+    fixed: true
+    label: Cluster
+    help: ''
+    required: false

apps/dashboard/test/fixtures/projects/chemistry-5533/assignment_1.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+#SBATCH --tasks-per-node 4
+
+
+INPUT_FILE=$PWD/input_data/assignment_1.inp
+OUTPUT_DIR=$PWD/output_data
+
+module load intel
+module load mvapich2
+module load qchem
+
+set -x
+
+# copy input file to $TMPDIR
+cp $INPUT_FILE $TMPDIR
+cd $TMPDIR
+INPUT_FILE="$TMPDIR/assignment_1.inp"
+
+qchem -np $SLURM_NPROCS $INPUT_FILE
+ls -lrta
+cp assignment_1.fchk $OUTPUT_DIR

apps/dashboard/test/fixtures/projects/chemistry-5533/assignment_2.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+#SBATCH --tasks-per-node 4
+
+INPUT_FILE=$PWD/input_data/assignment_1.inp
+OUTPUT_DIR=$PWD/output_data
+
+module load intel
+module load mvapich2
+module load qchem
+
+set -x
+
+# copy input file to $TMPDIR
+cp $INPUT_FILE $TMPDIR/assignment_2.inp
+cd $TMPDIR
+INPUT_FILE="$TMPDIR/assignment_2.inp"
+
+qchem -np $SLURM_NPROCS $INPUT_FILE
+ls -lrta
+cp assignment_2.fchk $OUTPUT_DIR

apps/dashboard/test/fixtures/projects/chemistry-5533/assignment_3.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+#SBATCH --tasks-per-node 4
+
+INPUT_FILE=$PWD/input_data/assignment_1.inp
+OUTPUT_DIR=$PWD/output_data
+
+module load intel
+module load mvapich2
+module load qchem
+
+set -x
+
+# copy input file to $TMPDIR
+cp $INPUT_FILE $TMPDIR/assignment_3.inp
+cd $TMPDIR
+INPUT_FILE="$TMPDIR/assignment_3.inp"
+
+qchem -np $SLURM_NPROCS $INPUT_FILE
+ls -lrta
+cp assignment_3.fchk $OUTPUT_DIR

apps/dashboard/test/fixtures/projects/chemistry-5533/input_data/assignment_1.inp

@@ -0,0 +1,34 @@
+$comment
+ethene
+$end
+
+$molecule
+0 1
+  C   -2.3620772    0.9207308    0.2821606
+  C   -1.0130626    0.5278664   -0.2865418
+  H   -2.6220345    1.9481860   -0.0474867
+  H   -3.1392310    0.2143160   -0.0767561
+  H   -0.7529560   -0.4993875    0.0434971
+  H   -0.2358785    1.2345592    0.0718086
+$end
+
+$rem
+   BASIS  =  6-31G*
+   EXCHANGE  =  HF
+   GUI  =  2
+   JOB_TYPE  =  Optimization
+   PURECART  =  2222
+$end
+
+@@@
+
+$molecule
+read
+$end
+
+$rem
+basis   6-31G*
+exchange   hf
+molden_format true
+print_orbitals true
+$end

apps/dashboard/test/system/jobs_app_test.rb

@@ -716,4 +716,57 @@ def add_bc_num_hours(project_id, script_id)
       end
     end
   end
+
+  test 'creating project from template updates forms' do
+    Dir.mktmpdir do |dir|
+      Project.stubs(:dataroot).returns(Pathname.new(dir))
+      Configuration.stubs(:project_template_dir).returns("#{Rails.root}/test/fixtures/projects")
+
+      visit(projects_root_path)
+      click_on(I18n.t('dashboard.jobs_create_template_project'))
+
+      select('Chemistry 5533', from: 'project_template')
+
+      # nothing in the users' project directory yet.
+      assert_equal(['.project_lookup'], Dir.children(dir))
+      assert_equal('', File.read("#{dir}/.project_lookup"))
+
+      click_on(I18n.t('dashboard.save'))
+
+      assert_equal(2, Dir.children(dir).size)
+      project_dir = Dir.children(dir).select { |path| File.directory?("#{dir}/#{path}") }.first
+      abs_project_dir = "#{dir}/#{project_dir}"
+
+      # 3 shell scripts, 3 forms were copied
+      assert_equal(3, Dir.glob("#{abs_project_dir}/*.sh").size)
+      forms = Dir.glob("#{abs_project_dir}/.ondemand/**/*/form.yml")
+      assert_equal(3, forms.size)
+
+      orig_form = "#{Rails.root}/test/fixtures/projects/chemistry-5533/.ondemand/scripts/8woi7ghd/form.yml"
+      orig_form = YAML.safe_load(File.read(orig_form))
+
+      # ruby 2.7 globs differently
+      new_form = if RUBY_VERSION > '3.0'
+                   YAML.safe_load(File.read(forms.first))
+                 else
+                   YAML.safe_load(File.read(forms[1]))
+                 end
+
+      # 'form' & 'title' are the same
+      assert_equal(orig_form['form'], new_form['form'])
+      assert_equal(orig_form['title'], new_form['title'])
+
+      # every auto_scripts option was copied and has the _new_ project location.
+      new_auto_scripts = new_form['attributes']['auto_scripts']['options']
+      new_auto_scripts.sort_by do |option|
+        # ruby 2.7 doesn't sort the same way
+        option[0].match('\d').to_s.to_i
+      end.each_with_index do |option, idx|
+        filename = "assignment_#{idx + 1}.sh"
+        full_path = "#{abs_project_dir}/#{filename}"
+        assert_equal(filename, option[0])
+        assert_equal(full_path, option[1])
+      end
+    end
+  end
 end