queries.clj

(ns clj-icat-direct.queries
  (:require [clojure.string :as string])
  (:import  [clojure.lang IPersistentMap ISeq]))


(defn- bad-chars->sql-char-class
  [bad-chars]
  (let [bad-chars (string/replace bad-chars #"'|\[|\]|\\" {"\\" "\\\\"
                                                           "'"  "\\'"
                                                           "["  "\\["
                                                           "]"  "\\]"})]
    (str "[" bad-chars "]")))


(defn- file-bad-chars-cond
  [_ bad-chars]
  (str "d.data_name ~ E'" (bad-chars->sql-char-class bad-chars) "'"))


(defn- folder-bad-chars-cond
  [parent-path bad-chars]
  (str "c.coll_name ~ E'" parent-path "/.*" (bad-chars->sql-char-class bad-chars) "'"))


(defn- file-name-cond
  [_ name]
  (str "d.data_name = '" name "'"))


(defn- file-path-cond
  [parent-path path]
  (str "'" parent-path "' || '/' || d.data_name = '" path "'"))


(defn- folder-name-cond
  [parent-path name]
  (str "c.coll_name = '" parent-path "/" name "'"))


(defn- folder-path-cond
  [_ path]
  (str "c.coll_name = '" path "'"))


(defn- mk-temp-table
  [table-name query]
  (str "CREATE TEMPORARY TABLE " table-name " ON COMMIT DROP AS " query))

(defn- analyze
  [table-name]
  (str "ANALYZE " table-name))

(defn- mk-bad-cond
  [mk-bad-chars-cond mk-bad-name-cond mk-bad-path-cond parent-path bad-chars bad-names bad-paths]
  (let [conds (concat (when-not (empty? bad-chars) [(mk-bad-chars-cond parent-path bad-chars)])
                      (map #(mk-bad-name-cond parent-path %) bad-names)
                      (map #(mk-bad-path-cond parent-path %) bad-paths))
        conds (remove nil? conds)]
    (if (empty? conds)
      "FALSE"
      (string/join " OR " (map #(str "(" % ")") conds)))))


(defn ^String mk-bad-file-cond
  "Returns a WHERE condition for files in the count-bad-items-in-folder query.

   Parameters:
     parent-path - the absolute path to the folder containing the files
     bad-chars   - the characters a name cannot contain
     bad-names   - the bad names
     bad-paths   - the bad paths

   Returns:
     It returns the condition."
  [^String parent-path ^String bad-chars ^ISeq bad-names ^ISeq bad-paths]
  (mk-bad-cond file-bad-chars-cond file-name-cond file-path-cond
               parent-path bad-chars bad-names bad-paths))


(defn ^String mk-bad-folder-cond
  "Returns a WHERE condition for folders in the count-bad-items-in-folder query.

   Parameters:
     parent-path - the absolute path to the folder containing the folders
     bad-chars   - the characters a name cannot contain
     bad-names   - the bad names
     bad-paths   - the bad paths

   Returns:
     It returns the condition."
  [^String parent-path ^String bad-chars ^ISeq bad-names ^ISeq bad-paths]
  (mk-bad-cond folder-bad-chars-cond folder-name-cond folder-path-cond
                  parent-path bad-chars bad-names bad-paths))


(defn prepare-text-set
  "Given a set, it prepares the elements for injection into an SQL query. It returns a string
   containing the quoted values separated by commas."
  [values]
  (string/join ", " (map #(str \' % \') values)))


(defn ^String mk-file-type-cond
  "This function constructs condition for search for files with a given file type.

   Parameters:
     file-types - A list of file types used to filter on. A nil or empty list disables filtering.

   Returns:
     It returns a condition for filtering data objects by file type."
  [^ISeq file-types]
  (let [file-types (mapv string/lower-case file-types)
        fmt-ft     (prepare-text-set file-types)]
    (cond
      (empty? file-types)
      "TRUE"

      (some #(= "unknown" %) file-types)
      (str "f.meta_attr_value IS NULL OR f.meta_attr_value IN ('', " fmt-ft ")")

      :else
      (str "f.meta_attr_value IN (" fmt-ft ")"))))


(def ^IPersistentMap sort-columns
  "This is a mapping of API column keywords to fields in the response document."
  {:type      "type"
   :modify-ts "modify_ts"
   :create-ts "create_ts"
   :data-size "data_size"
   :base-name "base_name"
   :full-path "full_path"})


(def ^IPersistentMap sort-directions
  "This ia a mapping of API sort direction keywords to database sort direction strings."
  {:asc "ASC" :desc "DESC"})

(defn- mk-metaids-by-attr
  [attr]
  (str "SELECT meta_id FROM r_meta_main WHERE meta_attr_name = '" attr "'"))

(defn- mk-metaids-by-value-prefix
  [attr prefix]
  (str (mk-metaids-by-attr attr) " AND meta_attr_value LIKE '" prefix "%'"))

(defn- mk-objids-for-metaids
  [cte]
  (str "SELECT object_id FROM r_objt_metamap WHERE meta_id IN (SELECT meta_id FROM " cte ")"))

(defn- mk-filenames-without-attr
  [objs-cte attr-cte]
  (str "SELECT coll_name || '/' || data_name AS path
          FROM r_data_main JOIN r_coll_main USING (coll_id)
         WHERE data_id IN (SELECT object_id FROM " objs-cte " k
                            WHERE NOT EXISTS (SELECT 1 FROM r_objt_metamap
                                               WHERE r_objt_metamap.object_id = k.object_id
                                                 AND meta_id IN (SELECT meta_id FROM " attr-cte ")))"))

(defn ^ISeq mk-filtered-filenames-without-attr
  [uuid-prefix attr]
  [[(mk-temp-table "attr_metaids" (mk-metaids-by-attr attr))]
   [(mk-temp-table "uuid_metaids" (mk-metaids-by-value-prefix "ipc_UUID" uuid-prefix))]
   [(mk-temp-table "uuid_objids" (mk-objids-for-metaids "uuid_metaids"))]
   [(analyze "attr_metaids")]
   [(analyze "uuid_objids")]
   [(mk-filenames-without-attr "uuid_objids" "attr_metaids")]])

(defn- mk-unique-objs-in-coll
  [coll-path]
  (str "SELECT *
          FROM r_data_main AS d1
          WHERE coll_id = (SELECT coll_id FROM r_coll_main WHERE coll_name = '" coll-path "')
            AND d1.data_repl_num = (SELECT MIN(d2.data_repl_num)
                                      FROM r_data_main AS d2
                                      WHERE d2.data_id = d1.data_id)"))


(defn- mk-obj-avus
  [obj-ids-query]
  (str "SELECT object_id, meta_attr_value, meta_attr_name
          FROM r_objt_metamap AS o JOIN r_meta_main AS m ON o.meta_id = m.meta_id
          WHERE o.object_id = ANY(ARRAY(" obj-ids-query "))"))


(defn- mk-file-types
  [avus-cte]
  (str "SELECT * FROM " avus-cte " WHERE meta_attr_name = 'ipc-filetype'"))

(defn ^ISeq mk-get-item
  [dirname basename group-ids-query]
  [(str "WITH "
     "objs AS ("
       "SELECT c.coll_id AS object_id, 'collection' AS type, c.coll_name AS full_path, regexp_replace(c.coll_name, '.*/', '') AS base_name, 0 as data_size, c.create_ts, c.modify_ts FROM r_coll_main c WHERE coll_name = ? || '/' || ? "
       "UNION "
       "SELECT d.data_id as object_id, 'dataobject' as type, c.coll_name || '/' || d.data_name AS full_path, d.data_name AS base_name, d.data_size, d.create_ts, d.modify_ts FROM r_data_main d JOIN r_coll_main c on d.coll_id = c.coll_id WHERE coll_name = ? AND data_name = ?"
     "), "
     "meta AS ("
       "SELECT object_id, max(CASE WHEN meta_attr_name = 'ipc_UUID' THEN meta_attr_value ELSE NULL END) AS uuid, max(CASE WHEN meta_attr_name = 'ipc-filetype' THEN meta_attr_value ELSE NULL END) as info_type FROM r_objt_metamap mm JOIN r_meta_main m USING (meta_id) WHERE object_id IN (SELECT object_id FROM objs) GROUP BY object_id"
     ") "
     "SELECT objs.object_id, objs.type, meta.uuid, objs.full_path, objs.base_name, meta.info_type, objs.data_size, objs.create_ts, objs.modify_ts, max(a.access_type_id) AS access_type_id FROM objs JOIN meta USING (object_id) JOIN r_objt_access a USING (object_id) WHERE a.user_id IN ("
       group-ids-query
     ") "
     "GROUP BY object_id, type, uuid, full_path, base_name, info_type, data_size, objs.create_ts, objs.modify_ts") dirname basename dirname basename])

(defn- mk-files-in-folder
  [parent-path group-ids-query info-type-cond objs-cte avus-cte include-count?]
  (str "SELECT 'dataobject'                      AS type,
               m.meta_attr_value                 AS uuid,
               '" parent-path "/' || d.data_name AS full_path,
               d.data_name                       AS base_name,
               f.meta_attr_value                 AS info_type,
               d.data_size                       AS data_size,
               d.create_ts                       AS create_ts,
               d.modify_ts                       AS modify_ts,
               MAX(a.access_type_id)             AS access_type_id"
       (if include-count? ",
               COUNT(*) OVER () AS total_count" "")
          " FROM " objs-cte " AS d
            JOIN " avus-cte " AS m ON d.data_id = m.object_id
            JOIN r_objt_access AS a ON d.data_id = a.object_id
            LEFT JOIN (" (mk-file-types avus-cte) ") AS f
              ON d.data_id = f.object_id
          WHERE a.user_id IN (" group-ids-query ")
            AND m.meta_attr_name = 'ipc_UUID'
            AND (" info-type-cond ")
          GROUP BY type, uuid, full_path, base_name, info_type, data_size, d.create_ts,
                   d.modify_ts"))


(defn- mk-folders-in-folder
  [parent-path group-ids-query include-count?]
  (str "SELECT 'collection'                           AS type,
               m.meta_attr_value                      AS uuid,
               c.coll_name                            AS full_path,
               REGEXP_REPLACE(c.coll_name, '.*/', '') AS base_name,
               NULL                                   AS info_type,
               0                                      AS data_size,
               c.create_ts                            AS create_ts,
               c.modify_ts                            AS modify_ts,
               MAX(a.access_type_id)                  AS access_type_id"
       (if include-count? ",
               COUNT(*) OVER () AS total_count" "")
         " FROM r_coll_main AS c
            JOIN r_objt_metamap AS om ON om.object_id = c.coll_id
            JOIN r_meta_main AS m ON m.meta_id = om.meta_id
            JOIN r_objt_access AS a ON c.coll_id = a.object_id
          WHERE c.parent_coll_name = '" parent-path "'
            AND c.coll_type != 'linkPoint'
            AND m.meta_attr_name = 'ipc_UUID'
            AND a.user_id IN (" group-ids-query ")
          GROUP BY type, uuid, full_path, base_name, info_type, data_size, c.create_ts,
                   c.modify_ts"))


(defn mk-user
  [user zone]
  [(str "SELECT user_id, user_name, user_type_name, zone_name, user_info, r_comment, create_ts, modify_ts FROM r_user_main WHERE user_name = ? AND zone_name = ?") user zone])

(defn mk-groups
  [user zone & placeholder-vec?]
  (let [base "SELECT *
               FROM r_user_group
               WHERE user_id IN (SELECT user_id
                                   FROM r_user_main
                                   WHERE user_name = %s AND zone_name = %s)"]
    (if placeholder-vec?
      [(format base "?" "?") user zone]
      (format base (str "'" user "'") (str "'" zone "'")))))

(defn mk-path-for-uuid
  [uuid]
  ["WITH objid AS (SELECT object_id FROM r_objt_metamap
                     JOIN r_meta_main USING (meta_id)
                    WHERE meta_attr_name = 'ipc_UUID'
                      AND meta_attr_value = ?::text)
    SELECT coll_name AS path FROM r_coll_main WHERE coll_id IN (select object_id FROM objid)
     UNION ALL
    SELECT coll_name || '/' || data_name AS path FROM r_data_main JOIN r_coll_main USING (coll_id) WHERE data_id IN (select object_id from objid) LIMIT 1" uuid])

(defn- mk-count-colls-in-coll
  [parent-path group-ids-query & {:keys [cond] :or {cond "TRUE"}}]
  (str "SELECT COUNT(DISTINCT c.coll_id) AS total
          FROM r_coll_main c JOIN r_objt_access AS a ON c.coll_id = a.object_id
          WHERE c.parent_coll_name = '" parent-path "'
            AND c.coll_type != 'linkPoint'
            AND a.user_id IN (" group-ids-query ")
            AND (" cond ")"))


(defn- mk-count-objs-of-type
  [objs-cte avus-cte group-query info-type-cond & {:keys [cond] :or {cond "TRUE"}}]
  (str "SELECT COUNT(DISTINCT d.data_id) AS total
          FROM " objs-cte " AS d
            JOIN r_objt_access AS a ON a.object_id = d.data_id
            LEFT JOIN (" (mk-file-types avus-cte) ") AS f ON f.object_id = d.data_id
          WHERE a.user_id IN (" group-query ")
            AND (" info-type-cond ")
            AND (" cond ")"))


(defn ^String mk-count-bad-files-in-folder
  "This function constructs a query for counting all of the files that are direct members of a given
   folder, accessible to a given user, satisfy a given info type condition, and satisfy a given
   condition indicating the file has an invalid name.

   Parameters:
     user           - username of the user that can access the files
     zone           - iRODS authentication zone of the user
     parent-path    - the folder being inspected
     info-type-cond - a WHERE condition indicating the info types of the files to be counted
     bad-file-cond  - a WHERE condition indicating that a file has an invalid name

  Returns:
    It returns the properly formatted SELECT query."
  [& {:keys [user zone parent-path info-type-cond bad-file-cond]}]
  (let [group-query "SELECT group_user_id FROM groups"
        count-query (mk-count-objs-of-type "objs" "file_avus" group-query info-type-cond
                      :cond bad-file-cond)]
    (str "WITH groups    AS (" (mk-groups user zone) "),
               objs      AS (" (mk-unique-objs-in-coll parent-path) "),
               file_avus AS (" (mk-obj-avus "SELECT data_id FROM objs") ")
         " count-query)))


(defn ^String mk-count-bad-folders-in-folder
  "This function constructs a query for counting all of the folders that are direct members of a
   given folder, accessible to a given user, and satisfy a given condition indicating the folder has
   an invalid name.

   Parameters:
     user            - username of the user that can access the folders
     zone            - iRODS authentication zone of the user
     parent-path     - the folder being inspected
     bad-folder-cond - a WHERE condition indicating that a folder has an invalid name

  Returns:
    It returns the properly formatted SELECT query."
  [& {:keys [user zone parent-path bad-folder-cond]}]
  (let [group-query "SELECT group_user_id FROM groups"]
    (str "WITH groups AS (" (mk-groups user zone) ")
         " (mk-count-colls-in-coll parent-path group-query :cond bad-folder-cond))))


(defn ^String mk-count-bad-items-in-folder
  "This function constructs a query for counting all of the files and folders that are direct
   members of a given folder, accessible to a given user, satisfy a given info type condition, and
   satisfy a given condition indicating the file or folder has an invalid name.

   Parameters:
     user            - username of the user that can access the files and folders
     zone            - iRODS authentication zone of the user
     parent-path     - the folder being inspected
     info-type-cond  - a WHERE condition indicating the info types of the files to be counted
     bad-file-cond   - a WHERE condition indicating that a file has an invalid name
     bad-folder-cond - A WHERE condition indicating that a folder has an invalid name

  Returns:
    It returns the properly formatted SELECT query."
  [& {:keys [user zone parent-path info-type-cond bad-file-cond bad-folder-cond]}]
  (let [group-query  "SELECT group_user_id FROM groups"
        folder-query (mk-count-colls-in-coll parent-path group-query :cond bad-folder-cond)
        file-query   (mk-count-objs-of-type "objs" "file_avus" group-query info-type-cond
                       :cond bad-file-cond)]
    (str "WITH groups    AS (" (mk-groups user zone) "),
               objs      AS (" (mk-unique-objs-in-coll parent-path) "),
               file_avus AS (" (mk-obj-avus "SELECT data_id FROM objs") ")
          SELECT ((" folder-query ") + (" file-query ")) AS total")))


(defn ^ISeq mk-count-files-in-folder
  "This function constructs a query for counting all of the files that are direct members of a given
   folder, accessible to a given user, and satisfy a given info type condition.

   Parameters:
     user           - username of the user that can access the files
     zone           - iRODS authentication zone of the user
     parent-path    - the folder being inspected
     info-type-cond - a WHERE condition indicating the info types of the files to be counted

  Returns:
    It returns the properly formatted SELECT query."
  [^String user ^String zone ^String parent-path ^String info-type-cond]
  (let [group-query "SELECT group_user_id FROM groups"]
    [[(mk-temp-table "groups" (mk-groups user zone))]
     [(analyze "groups")]
     [(mk-temp-table "objs" (mk-unique-objs-in-coll parent-path))]
     [(analyze "objs")]
     [(mk-temp-table "file_avus" (mk-obj-avus "SELECT data_id FROM objs"))]
     [(analyze "file_avus")]
     [(str (mk-count-objs-of-type "objs" "file_avus" group-query info-type-cond))]]))


(defn ^ISeq mk-count-folders-in-folder
  "This function constructs a query for counting all of the folders that are direct members of a
   given folder and accessible to a given user.

   Parameters:
     user        - username of the user that can access the files
     zone        - iRODS authentication zone of the user
     parent-path - the folder being inspected

  Returns:
    It returns the properly formatted SELECT query."
  [^String user ^String zone ^String parent-path]
  (let [group-query "SELECT group_user_id FROM groups"]
    [[(str "WITH groups AS (" (mk-groups user zone) ")
           " (mk-count-colls-in-coll parent-path group-query))]]))


(defn ^ISeq mk-count-items-in-folder
  "This function constructs a set of queries for counting all of the files and folders that are direct
   members of a given folder, accessible to a given user, and satisfy a given info type condition.

   Parameters:
     user           - username of the user that can access the files and folders
     zone           - iRODS authentication zone of the user
     parent-path    - the folder being inspected
     info-type-cond - a WHERE condition indicating the info types of the files to be counted

  Returns:
    It returns the properly formatted SELECT query."
  [^String user ^String zone ^String parent-path ^String info-type-cond]
  (let [group-query   "SELECT group_user_id FROM groups"
        folders-query (mk-count-colls-in-coll parent-path group-query)
        files-query   (mk-count-objs-of-type "objs" "file_avus" group-query info-type-cond)]
    [[(mk-temp-table "groups" (mk-groups user zone))]
     [(analyze "groups")]
     [(mk-temp-table "objs" (mk-unique-objs-in-coll parent-path))]
     [(analyze "objs")]
     [(mk-temp-table "file_avus" (mk-obj-avus "SELECT data_id FROM objs"))]
     [(analyze "file_avus")]
     [(str "SELECT ((" folders-query ") + (" files-query ")) AS total")]]))


(defn ^ISeq mk-paged-files-in-folder
  "This function constructs a parameterized set of queries for returning a sorted page of files that are
   direct members of a given folder, accessible to a given user, and satisfy a given info type
   condition.

   Parameters:
     user           - username of the user that can access the files
     zone           - iRODS authentication zone of the user
     parent-path    - the folder being inspected
     info-type-cond - a WHERE condition indicating the info types of the files to be counted
     sort-column    - the result field to sort on:
                      (type|modify_ts|create_ts|data_size|base_name|full_path)
     sort-direction - the direction of the sort
     limit & offset - limit and offset to pass to the query

  Returns:
    It returns the properly formatted parameterized SELECT query. The query is parameterized over
    the page size and offset, respectively. The query will return a result set sorted by the
    provided sort column. Each row in the result set will have the following columns.

      type           - 'dataobject'
      uuid           - the file's UUID
      full_path      - the absolute path to the file in iRODS
      base_name      - the name of the file
      info_type      - the info type of the file
      data_size      - the size in bytes of the file
      create_ts      - the iRODS timestamp string for when the file was created
      modify_ts      - the iRODS timestamp string for when the file was last modified
      access_type_id - the ICAT DB Id indicating the user's level of access to the file"
  [& {:keys [user zone parent-path info-type-cond sort-column sort-direction limit offset groups-table-query]}]
  (let [group-query "SELECT group_user_id FROM groups"]
    [[(mk-temp-table "objs" (mk-unique-objs-in-coll parent-path))]
     [(analyze "objs")]
     [(mk-temp-table "file_avus" (mk-obj-avus "SELECT data_id FROM objs"))]
     [(analyze "file_avus")]
     [(str "WITH groups AS (" (or groups-table-query (mk-groups user zone)) ") "
           (mk-files-in-folder parent-path group-query info-type-cond "objs" "file_avus" true) "
           ORDER BY " sort-column " " sort-direction "
           LIMIT ?
           OFFSET ?") limit offset]]))


(defn ^ISeq mk-paged-folders-in-folder
  "This function constructs a parameterized set of queries for returning a sorted page of folders that are
   direct members of a given folder and accessible to a given user.

   Parameters:
     user           - username of the user that can access the folders
     zone           - iRODS authentication zone of the user
     parent-path    - the folder being inspected
     sort-column    - the result field to sort on:
                      (type|modify_ts|create_ts|data_size|base_name|full_path)
     sort-direction - the direction of the sort
     limit & offset - limit and offset to pass to the query

  Returns:
    It returns the properly formatted parameterized SELECT query. The query is parameterized over
    the page size and offset, respectively. The query will return a result set sorted by the
    provided sort column. Each row in the result set will have the following columns.

      type           - 'collection'
      uuid           - the folder's UUID
      full_path      - the absolute path to the folder in iRODS
      base_name      - the name of the folder
      info_type      - 'NULL'
      data_size      - '0'
      create_ts      - the iRODS timestamp string for when the folder was created
      modify_ts      - the iRODS timestamp string for when the folder was last modified
      access_type_id - the ICAT DB Id indicating the user's level of access to the folder"
  [& {:keys [user zone parent-path sort-column sort-direction limit offset groups-table-query]}]
  [[(str "WITH groups AS (" (or groups-table-query (mk-groups user zone)) ")
       " (mk-folders-in-folder parent-path "SELECT group_user_id FROM groups" true) "
        ORDER BY " sort-column " " sort-direction "
        LIMIT ?
        OFFSET ?") limit offset]])


(defn ^ISeq mk-paged-folder
  "This function constructs a set of parameterized queries for returning a sorted page of files and folders
   that are direct members of a given folder, accessible to a given user, and satisfy a given info
   type condition.

   Parameters:
     user           - username of the user that can access the files and folders
     zone           - iRODS authentication zone of the user
     parent-path    - the folder being inspected
     info-type-cond - a WHERE condition indicating the info types of the files to be counted
     sort-column    - the result field to sort on:
                      (type|modify_ts|create_ts|data_size|base_name|full_path)
     sort-direction - the direction of the sort
     limit & offset - limit and offset to pass to the query

  Returns:
    It returns the properly formatted parameterized SELECT query. The query is parameterized over
    the page size and offset, respectively. The query will return a result set sorted primary by
    entity type, and secondarily by the provided sort column. Each row in the result set will have
    the following columns.

      type           - (collection|dataobject) collection indicates folder and dataobject indicates
                       file
      uuid           - the file's or folder's UUID
      full_path      - the absolute path to the file or folder in iRODS
      base_name      - the name of the file or folder
      info_type      - the info type of the file or NULL for a folder
      data_size      - the size in bytes of the file or 0 for a folder
      create_ts      - the iRODS timestamp string for when the file or folder was created
      modify_ts      - the iRODS timestamp string for when the file or folder was last modified
      access_type_id - the ICAT DB Id indicating the user's level of access to the file or folder"
  [& {:keys [user zone parent-path info-type-cond sort-column sort-direction limit offset groups-table-query]}]
  (let [group-query   "SELECT group_user_id FROM groups"
        folders-query (mk-folders-in-folder parent-path group-query false)
        files-query   (mk-files-in-folder parent-path group-query info-type-cond "objs"
                                          "file_avus" false)]
    [[(mk-temp-table "objs" (mk-unique-objs-in-coll parent-path))]
     [(analyze "objs")]
     [(mk-temp-table "file_avus" (mk-obj-avus "SELECT data_id FROM objs"))]
     [(analyze "file_avus")]
     [(str "WITH groups AS (" (or groups-table-query (mk-groups user zone)) ") "
           "SELECT *, COUNT(*) OVER () AS total_count
            FROM (" folders-query " UNION " files-query ") AS t
            ORDER BY type ASC, " sort-column " " sort-direction "
            LIMIT ?
            OFFSET ?") limit offset]]))


(defn ^String mk-count-uuids-of-file-type
  "This function constructs a query for returning the number of given uuids that are either folders
   or are files satisfying the given info type WHERE condition.

   Parameter:
     user           - username of the user that can access the files and folders
     zone           - iRODS authentication zone of the user
     uuids          - a comma-separated list of uuids to count
     info-type-cond - a WHERE condition indicating the info types of the files to be counted

  Returns:
    It returns the a single row containing a single 'total' column containing the total."
  [^String user ^String zone ^String uuids ^String info-type-cond]
  (str "WITH groups     AS (" (mk-groups user zone) "),
             uuids      AS (SELECT m.meta_attr_value AS uuid, o.object_id
                              FROM r_meta_main AS m
                                JOIN r_objt_metamap AS o ON m.meta_id = o.meta_id
                              WHERE m.meta_attr_name = 'ipc_UUID'
                                AND m.meta_attr_value IN (" uuids ")
                                AND o.object_id IN (SELECT object_id
                                                      FROM r_objt_access
                                                      WHERE user_id in (SELECT group_user_id
                                                                          FROM groups))),
             file_types AS (SELECT *
                              FROM r_objt_metamap AS o
                                JOIN r_meta_main AS m ON m.meta_id = o.meta_id
                              WHERE o.object_id = ANY(ARRAY(SELECT object_id FROM uuids))
                                AND m.meta_attr_name = 'ipc-filetype')
        SELECT ((SELECT COUNT(*)
                   FROM uuids
                   WHERE object_id IN (SELECT coll_id
                                         FROM r_coll_main
                                         WHERE coll_type != 'linkPoint'))
                +
                (SELECT COUNT(*)
                   FROM uuids
                   WHERE object_id IN (SELECT d.data_id
                                         FROM r_data_main As d
                                           LEFT JOIN file_types AS f on d.data_id = f.object_id
                                         WHERE (" info-type-cond ")))) AS total"))


(def queries
  {:count-all-items-under-folder
   "WITH user_groups AS ( SELECT g.group_user_id
                            FROM r_user_main u
                            JOIN r_user_group g ON g.user_id = u.user_id
                           WHERE u.user_name = ?
                             AND u.zone_name = ? ),

         parent      AS ( SELECT coll_id, coll_name from r_coll_main
                           WHERE coll_name = ?
                              OR coll_name LIKE ? || '/%' ),

         data_objs   AS ( SELECT data_id
                            FROM r_data_main
                           WHERE coll_id = ANY(ARRAY( SELECT coll_id FROM parent )) )

    SELECT ((SELECT count(DISTINCT d.data_id) FROM r_objt_access a
               JOIN data_objs d ON a.object_id = d.data_id
              WHERE a.user_id IN ( SELECT group_user_id FROM user_groups )
                AND a.object_id IN ( SELECT data_id from data_objs ))
            +
            (SELECT count(DISTINCT c.coll_id) FROM r_coll_main c
               JOIN r_objt_access a ON c.coll_id = a.object_id
              WHERE a.user_id IN ( SELECT group_user_id FROM user_groups )
                AND c.parent_coll_name = ANY(ARRAY( SELECT coll_name FROM parent ))
                AND c.coll_type != 'linkPoint')) AS total"

   :list-files-under-folder
   "SELECT DISTINCT c.coll_name || '/' || d.data_name AS path,
           m.meta_attr_value AS uuid
      FROM r_coll_main c
      JOIN r_data_main d ON c.coll_id = d.coll_id
      JOIN r_objt_metamap mm ON d.data_id = mm.object_id
      JOIN r_meta_main m ON mm.meta_id = m.meta_id
     WHERE (c.coll_name = ? OR c.coll_name LIKE ? || '/%')
       AND m.meta_attr_name = 'ipc_UUID'
  ORDER BY path"

   :list-folders-in-folder
   "WITH user_groups AS ( SELECT g.group_user_id FROM r_user_main u
                            JOIN r_user_group g ON g.user_id = u.user_id
                           WHERE u.user_name = ?
                             AND u.zone_name = ? )

    SELECT DISTINCT
           c.parent_coll_name                     as dir_name,
           c.coll_name                            as full_path,
           regexp_replace(c.coll_name, '.*/', '') as base_name,
           c.create_ts                            as create_ts,
           c.modify_ts                            as modify_ts,
           'collection'                           as type,
           0                                      as data_size,
           m.meta_attr_value                      as uuid,
           MAX(a.access_type_id)                  as access_type_id
      FROM r_coll_main c
      JOIN r_objt_access a ON c.coll_id = a.object_id
      JOIN r_objt_metamap mm ON mm.object_id = c.coll_id
      JOIN r_meta_main m ON m.meta_id = mm.meta_id
     WHERE a.user_id IN ( SELECT group_user_id FROM user_groups )
       AND c.coll_type != 'linkPoint'
       AND c.parent_coll_name = ?
       AND m.meta_attr_name = 'ipc_UUID'
  GROUP BY dir_name, full_path, base_name, c.create_ts, c.modify_ts, type, data_size, uuid
  ORDER BY base_name ASC"

   :count-files-in-folder
   "WITH user_groups AS ( SELECT g.group_user_id
                            FROM r_user_main u
                            JOIN r_user_group g ON g.user_id = u.user_id
                           WHERE u.user_name = ?
                             AND u.zone_name = ? ),

         parent      AS ( SELECT coll_id from r_coll_main
                           WHERE coll_name = ? ),

         data_objs   AS ( SELECT data_id
                            FROM r_data_main
                           WHERE coll_id = ANY(ARRAY( SELECT coll_id FROM parent )) )

      SELECT count(DISTINCT d.data_id) FROM r_objt_access a
        JOIN data_objs d ON a.object_id = d.data_id
       WHERE a.user_id IN ( SELECT group_user_id FROM user_groups )
         AND a.object_id IN ( SELECT data_id from data_objs )"

   :count-folders-in-folder
   "WITH user_groups AS ( SELECT g.group_user_id
                            FROM r_user_main u
                            JOIN r_user_group g ON g.user_id = u.user_id
                           WHERE u.user_name = ?
                             AND u.zone_name = ? )

    SELECT count(DISTINCT c.coll_id) FROM r_coll_main c
      JOIN r_objt_access a ON c.coll_id = a.object_id
     WHERE a.user_id IN ( SELECT group_user_id FROM user_groups )
       AND c.coll_type != 'linkPoint'
       AND c.parent_coll_name = ?"

   :file-permissions
   "SELECT DISTINCT o.access_type_id, u.user_name
      FROM r_user_main u,
           r_data_main d,
           r_coll_main c,
           r_tokn_main t,
           r_objt_access o
     WHERE c.coll_name = ?
       AND d.data_name = ?
       AND c.coll_id = d.coll_id
       AND o.object_id = d.data_id
       AND t.token_namespace = 'access_type'
       AND u.user_id = o.user_id
       AND o.access_type_id = t.token_id
     LIMIT ?
    OFFSET ?"

   :folder-permissions
   "SELECT DISTINCT a.access_type_id, u.user_name
     FROM r_coll_main c
     JOIN r_objt_access a ON c.coll_id = a.object_id
     JOIN r_user_main u ON a.user_id = u.user_id
    WHERE c.parent_coll_name = ?
      AND c.coll_name = ?
    LIMIT ?
   OFFSET ?"

   :folder-permissions-for-user
   "WITH user_lookup AS ( SELECT u.user_id as user_id FROM r_user_main u WHERE u.user_name = ?)
    SELECT DISTINCT a.access_type_id
      FROM r_coll_main c
      JOIN r_objt_access a ON c.coll_id = a.object_id
      JOIN r_user_main u ON a.user_id = u.user_id
     WHERE c.coll_name = ?
       AND u.user_id IN ( SELECT g.group_user_id
                           FROM  r_user_group g,
                                 user_lookup
                           WHERE g.user_id = user_lookup.user_id )"

   :file-permissions-for-user
   "WITH user_lookup AS ( SELECT u.user_id as user_id FROM r_user_main u WHERE u.user_name = ? ),
              parent AS ( SELECT c.coll_id as coll_id, c.coll_name as coll_name FROM r_coll_main c WHERE c.coll_name = ? )
    SELECT DISTINCT a.access_type_id
      FROM r_data_main d
      JOIN r_coll_main c ON c.coll_id = d.coll_id
      JOIN r_objt_access a ON d.data_id = a.object_id
      JOIN r_user_main u ON a.user_id = u.user_id,
           user_lookup,
           parent
     WHERE u.user_id IN ( SELECT g.group_user_id
                           FROM  r_user_group g,
                                 user_lookup
                           WHERE g.user_id = user_lookup.user_id )
       AND c.coll_id = parent.coll_id
       AND d.data_name = ?"

   :folder-listing
   "WITH objs AS (SELECT coll_id AS object_id, coll_name AS full_path
                  FROM r_coll_main
                  WHERE parent_coll_name = ?
                    AND coll_type != 'linkPoint'
                  UNION
                  SELECT d.data_id, c.coll_name || '/' || d.data_name
                  FROM r_data_main d
                           JOIN r_coll_main c ON d.coll_id = c.coll_id
                  WHERE c.coll_name = ?),
         user_access AS (SELECT DISTINCT object_id
                         FROM r_objt_access
                         WHERE user_id IN (SELECT g.group_user_id
                                           FROM r_user_main u
                                                    JOIN r_user_group g ON g.user_id = u.user_id
                                           WHERE u.user_name = ? AND u.zone_name = ?)
                           AND object_id IN (SELECT object_id FROM objs))
    SELECT full_path
    FROM objs
    WHERE object_id IN (SELECT object_id FROM user_access)"

   :select-files-with-uuids
   "SELECT DISTINCT m.meta_attr_value                   uuid,
                    (c.coll_name || '/' || d.data_name) path,
                    1000 * CAST(d.create_ts AS BIGINT)  \"date-created\",
                    1000 * CAST(d.modify_ts AS BIGINT)  \"date-modified\",
                    d.data_size                         \"file-size\"
      FROM r_meta_main m
        JOIN r_objt_metamap o ON m.meta_id = o.meta_id
        JOIN r_data_main d ON o.object_id = d.data_id
        JOIN r_coll_main c ON d.coll_id = c.coll_id
      WHERE m.meta_attr_name = 'ipc_UUID' AND m.meta_attr_value IN (%s)"

   :select-folders-with-uuids
   "SELECT m.meta_attr_value                  uuid,
           c.coll_name                        path,
           1000 * CAST(c.create_ts AS BIGINT) \"date-created\",
           1000 * CAST(c.modify_ts AS BIGINT) \"date-modified\"
      FROM r_meta_main m
        JOIN r_objt_metamap o ON m.meta_id = o.meta_id
        JOIN r_coll_main c ON o.object_id = c.coll_id
      WHERE m.meta_attr_name = 'ipc_UUID' AND m.meta_attr_value IN (%s)"

   :paged-uuid-listing
   "WITH groups AS (SELECT group_user_id
                      FROM r_user_group
                      WHERE user_id IN (SELECT user_id
                                          FROM r_user_main
                                          WHERE user_name = ? AND zone_name = ?)),
         uuids AS (SELECT m.meta_attr_value uuid,
                          o.object_id
                     FROM r_meta_main m JOIN r_objt_metamap o ON m.meta_id = o.meta_id
                     WHERE m.meta_attr_name = 'ipc_UUID'
                       AND m.meta_attr_value IN (%s)
                       AND o.object_id IN (SELECT object_id
                                             FROM r_objt_access
                                             WHERE user_id in (SELECT group_user_id FROM groups))),
         file_types AS (SELECT om.object_id, mm.meta_attr_value
                          FROM r_objt_metamap AS om
                            JOIN r_meta_main AS mm ON mm.meta_id = om.meta_id
                          WHERE om.object_id = ANY(ARRAY(SELECT object_id FROM uuids))
                            AND mm.meta_attr_name = 'ipc-filetype')
    SELECT p.type,
           p.uuid,
           p.full_path,
           p.base_name,
           p.info_type,
           p.data_size,
           p.create_ts,
           p.modify_ts,
           MAX(p.access_type_id) AS access_type_id
      FROM (SELECT 'collection'                           AS type,
                   u.uuid                                 AS uuid,
                   c.coll_name                            AS full_path,
                   regexp_replace(c.coll_name, '.*/', '') AS base_name,
                   NULL                                   AS info_type,
                   0                                      AS data_size,
                   c.create_ts                            AS create_ts,
                   c.modify_ts                            AS modify_ts,
                   a.access_type_id                       AS access_type_id
              FROM uuids u
                JOIN r_coll_main c ON u.object_id = c.coll_id
                JOIN r_objt_access AS a ON c.coll_id = a.object_id
              WHERE c.coll_type != 'linkPoint' AND a.user_id IN (SELECT group_user_id FROM groups)
            UNION
            SELECT 'dataobject'                         AS type,
                   u.uuid                               AS uuid,
                   (c.coll_name || '/' || d1.data_name) AS full_path,
                   d1.data_name                         AS base_name,
                   f.meta_attr_value                    AS info_type,
                   d1.data_size                         AS data_size,
                   d1.create_ts                         AS create_ts,
                   d1.modify_ts                         AS modify_ts,
                   a.access_type_id                     AS access_type_id
              FROM uuids u
                JOIN r_data_main AS d1 ON u.object_id = d1.data_id
                JOIN r_coll_main c ON d1.coll_id = c.coll_id
                JOIN r_objt_access AS a ON d1.data_id = a.object_id
                LEFT JOIN file_types AS f ON d1.data_id = f.object_id
              WHERE d1.data_repl_num = (SELECT MIN(d2.data_repl_num)
                                          FROM r_data_main AS d2
                                          WHERE d2.data_id = d1.data_id)
                AND a.user_id IN (SELECT group_user_id FROM groups)
                AND (%s)) AS p
      GROUP BY p.type, p.uuid, p.full_path, p.base_name, p.info_type, p.data_size, p.create_ts,
               p.modify_ts
      ORDER BY p.type ASC, %s %s
      LIMIT ?
      OFFSET ?"})