Merge branch 'stage-019-esFormat' into stage-091-datasetsRucio

Stage 019 transformation

Now it can accept data not only from Stage 016,
but also from 091 (see #79) -- or any other stage,
that produces data in the required format.

---
This merge overrides merge of PR #86

Utils/Dataflow/016_task2es/task2es.py

@@ -26,6 +26,25 @@
     sys.stderr.write("(ERROR) Failed to import pyDKB library: %s\n" % err)
     sys.exit(1)
 
+def add_es_index_info(data):
+    """ Update data with required for ES indexing info.
+
+    Add fields:
+      _id => taskid
+      _type => 'task'
+
+    Return value:
+      False -- update failed, skip the record
+      True  -- update successful
+    """
+    if type(data) is not dict:
+        return False
+    if not data.get('taskid'):
+        return False
+    data['_id'] = data['taskid']
+    data['_type'] = 'task'
+    return True
+
 def get_category(row):
     """
     Each task can be associated with a number of Physics Categories.
@@ -97,6 +116,10 @@ def process(stage, message):
         hashtags = hashtags.lower().split(',')
         data['hashtag_list'] = [x.strip() for x in hashtags]
     data['phys_category'] = get_category(data)
+    if not add_es_index_info(data):
+        sys.stderr.write("(WARN) Skip message (not enough info"
+                         " for ES indexing.\n")
+        return True
     out_message = JSONMessage(data)
     stage.output(out_message)
     return True

Utils/Dataflow/019_oracle2esFormat/README → Utils/Dataflow/019_esFormat/README

@@ -4,13 +4,22 @@
 
 Description
 -----------
-Prepare data, taken by Oracle Connector, before uploading to ElasticSearch:
+Prepare data before uploading to ElasticSearch:
  * turn JSON keys to lower case
  * generate JSON with index information
 
+Use ./run.sh to run stage with common configuration from
+  /Utils/Elasticsearch/config/es
+
 Input
 -----
-...comes from Oracle Connector: JSON documents, one document -- one line.
+Expects data in JSON format with special fields.
+Required:
+* '_id' (ES record identifier);
+* '_type' (ES record type).
+
+Optional:
+* '_parent' (ES identifier for parent type record).
 
 Output
 ------

Utils/Dataflow/019_esFormat/esFormat.php

@@ -0,0 +1,91 @@
+#!/usr/bin/env php
+<?php
+function exception_error_handler($errno, $errstr, $errfile, $errline ) {
+   throw new ErrorException($errstr, 0, $errno, $errfile, $errline);
+}
+set_error_handler("exception_error_handler");
+
+$DEFAULT_INDEX = 'prodsys';
+$ES_INDEX = NULL;
+
+function check_input($row) {
+  $required_fields = array('_id', '_type');
+
+  if (!is_array($row)) {
+    fwrite(STDERR, "(WARN) Failed to decode message.\n");
+    return FALSE;
+  }
+
+  foreach ($required_fields as $field) {
+    if (!(isset($row[$field]))) {
+      fwrite(STDERR, "(WARN) Required field \"$field\" is not set or empty.\n");
+      return FALSE;
+    }
+  }
+
+  return TRUE;
+}
+
+function convertIndexToLowerCase(&$a) {
+  $result = array();
+
+  foreach (array_keys($a) as $i) {
+    $result[strtolower($i)] = $a[$i];
+  }
+
+  $a = $result;
+}
+
+function constructIndexJson(&$row) {
+  global $ES_INDEX;
+  $index = Array(
+    'index' => Array(
+      '_index' => $ES_INDEX,
+      '_type'  => $row['_type'],
+      '_id'    => $row['_id'],
+    )
+  );
+
+  if (isset($row['_parent'])) {
+    $index['index']['_parent'] = $row['_parent'];
+  }
+
+  foreach ($index['index'] as $key => $val) {
+    unset($row[$key]);
+  }
+
+  return $index;
+}
+
+if (isset($argv[1])) {
+  $h = fopen($argv[1], "r");
+} else {
+  $h = fopen('php://stdin', 'r');
+}
+
+$ES_INDEX = getenv('ES_INDEX');
+if (!$ES_INDEX) {
+  $ES_INDEX = $DEFAULT_INDEX;
+}
+
+if ($h) {
+  while (($line = fgets($h)) !== false) {
+    $row = json_decode($line,true);
+
+    if (!check_input($row)) {
+      fwrite(STDERR, "(WARN) Skipping message (\"".substr($line, 0, 1000)."\").\n");
+      continue;
+    }
+
+    convertIndexToLowerCase($row);
+
+    $index = constructIndexJson($row);
+
+    echo json_encode($index)."\n";
+    echo json_encode($row)."\n";
+  }
+}
+
+fclose($h);
+
+?>

Utils/Dataflow/019_esFormat/input/sample.016.ndjson

@@ -0,0 +1 @@
+../../016_task2es/output/sample.ndjson

Utils/Dataflow/019_esFormat/input/sample.091.ndjson

@@ -0,0 +1 @@
+../../091_datasetsRucio/output/datasets.ndjson

Utils/Dataflow/019_esFormat/run.sh

@@ -0,0 +1,15 @@
+#/usr//bin/env bash
+
+base_dir=$(cd "$(dirname "$(readlink -f "$0")")"; pwd)
+
+ES_CONFIG=$base_dir/../../Elasticsearch/config/es
+
+[ -r "$ES_CONFIG" ] \
+  || { echo "Can't access configuration file: $ES_CONFIG" >&2 \
+       && exit 1; }
+
+set -a
+  . "$ES_CONFIG"
+set +a
+
+$base_dir/esFormat.php