Add liftImported field to existing projects (#815)

* Add liftImported field to existing projects

New script to add liftImported field to documents in ProjectsCollection. 
 Field is set to true if a Compressed Upload ZIP file exists for the 
project; false otherwise.

* Use .lift file instead of .zip to detect import

scripts/add_lift_imported_field.sh

@@ -0,0 +1,52 @@
+#!/bin/bash
+
+# Update CombineDatabase.ProjectsCollection to add the liftImported field.
+#
+# The original design for TheCombine uses the existence of the .zip file used
+# for importing LIFT data as an indicator that LIFT data were imported previously.
+# PR #810 adds a field to documents in the ProjectsCollection, liftImported, for
+# this function.
+# This script adds this field to all current projects and sets it to true if there
+# is a .lift file which is created when the data are imported into a project, and
+# false otherwize.  The zip file that was used in an earlier design of the
+# application is not used because earlier revisions deleted the zip file so this
+# measure is not as reliable as the .lift files.
+
+# Script Strategy
+#  1. use find to find all imported .lift files
+#  2. use list of files to create list of project ObjectIds
+#  3. set liftImported to true for all project ids in list
+#     c.f. https://docs.mongodb.com/manual/reference/operator/query/in/
+#  4. set liftImported to false for all project docs that don't have a liftImported
+#     field
+
+# Function to update documents in the CombineDatabase.ProjectsCollection
+# Expects two arguments:
+#  - mongo selection clause
+#  - mongo update clause
+# Note: In order to aid validation/verification, the function will print the
+#       command that is run.
+update_projects() {
+  mongo_cmd="db.getSiblingDB('CombineDatabase').getCollection('ProjectsCollection').updateMany($1, $2)"
+  echo -e "Running command:\n${mongo_cmd}\n"
+  mongo -eval "${mongo_cmd}"
+}
+
+# set working dorectory
+COMBINE_HOME=${COMBINE_HOME:="/home/combine"}
+cd ${COMBINE_HOME}/.CombineFiles
+
+#  1. use find to find all imported .lift files
+#  2. use list of files to create list of project ObjectIds
+imported_projs="[ $(find . -name "*.lift" | grep Import | xargs | sed "s/\.\/\([0-9a-f]\{24\}\)[^\.]*\.lift/ObjectId\(\"\1\"\),/g" | sed "s/, *\$//") ]"
+
+#  3. set liftImported to true for all project ids in list
+mongo_select="{ \"_id\": { \"\$in\": ${imported_projs}}}"
+mongo_update="{ \"\$set\": { \"liftImported\": true } }"
+update_projects "${mongo_select}" "${mongo_update}"
+
+#  4. set liftImported to false for all project docs that don't have a liftImported
+#     field
+mongo_select="{ \"liftImported\": { \"\$exists\": false }}"
+mongo_update="{ \"\$set\": { \"liftImported\": false } }"
+update_projects "${mongo_select}" "${mongo_update}"