Fixing pulling images out of subdirectories for REAL

schema/versions/0953fe9fb794_fix_subdir_removal.py

+"""fix subdir removal
+
+Revision ID: 0953fe9fb794
+Revises: 42723a9dd85c
+Create Date: 2021-09-13 16:38:13.209103
+
+"""
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision = "0953fe9fb794"
+down_revision = "42723a9dd85c"
+branch_labels = None
+depends_on = None
+
+script_content = """#!/bin/sh
+set -o errexit
+
+export HOME=$TMPDIR
+
+fetch_foundation(){
+  ../productfetcher{{product_locator}}
+
+  echo "Moving images out of subdirectories...."
+  for dir in *.fits; do mv $dir $dir.1; done;
+
+  find . -mindepth 1 -type f -print -exec mv {} . \;
+  find . -mindepth 1 -type d -empty -delete
+  echo "Done. Ready for Carta!"
+}
+
+
+{{#need_data}}
+./framework.sh -r .
+chmod 770 .
+cd rawdata/
+
+fetch_foundation {{^single_image}}&{{/single_image}}
+
+.{{/need_data}}./carta_envoy {{#need_data}}--parallel{{/need_data}} {{#single_image}}--single -i {{imageName}}{{/single_image}} -d $1 -n $2 -wf $3 -r $4
+{{#need_data}}wait{{/need_data}}
+
+"""
+
+old_content = """#!/bin/sh
+set -o errexit
+
+export HOME=$TMPDIR
+
+{{#need_data}}
+./framework.sh -r .
+chmod 770 .
+cd rawdata/
+../productfetcher{{product_locator}} {{^single_image}}&{{/single_image}}
+
+image_subdirs=$(ls)
+
+for i in $image_subdirs; do
+  if [[ -d "./$i" ]]; then
+    mv "./$i"/* .
+    rm -rf "./$i"
+  fi
+done
+
+.{{/need_data}}./carta_envoy {{#need_data}}--parallel{{/need_data}} {{#single_image}}--single -i {{imageName}}{{/single_image}} -d $1 -n $2 -wf $3 -r $4
+{{#need_data}}wait{{/need_data}}
+
+"""
+
+
+def upgrade():
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{script_content}' where filename='carta.sh'
+        """
+    )
+
+
+def downgrade():
+    op.execute(
+        f"""
+        UPDATE workflow_templates
+        SET content=E'{old_content}' where filename='carta.sh'
+        """
+    )