update yaml parser to read in arrays and output them

diag_manager/diag_yaml_format.md

@@ -43,14 +43,14 @@ diag_files:
 ### 2.1 Global Section
 The diag_yaml requires “title” and the “baseDate”.
 - The **title** is a string that labels the diag yaml.  The equivalent in the legacy diag_table would be the experiment.  It is recommended that each diag_yaml have a separate title label that is descriptive of the experiment that is using it.
-- The **basedate** is an array of 6 integers indicating the base_date in the format [year month day hour minute second].
+- The **base_date** is a comma-separated array of 6 integers indicating the base_date in the format [year, month, day, hour, minute, second]. Spacing is not significant.
 
 **Example:**
 
 In the YAML format:
 ```yaml
 title: ESM4_piControl
-base_date: 2022 5 26 12 3 1
+base_date: [2022, 5, 26, 12, 3, 1]
 ```
 
 In the legacy ascii format:
@@ -281,7 +281,7 @@ The sub region can be listed under the sub_region section as a dashed array. The
 Bellow is a complete example of diag_table.yaml:
 ```yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: wild_card_name%4yr%2mo%2dy%2hr
   freq: 6 hours

diag_manager/fms_diag_yaml.F90

@@ -1667,13 +1667,14 @@ subroutine fms_diag_yaml_out()
   call fms_f2c_string( keys(1)%key2, 'base_date')
   basedate_loc = diag_yaml%get_basedate()
   tmpstr1 = ''; tmpstr2 = ''
-  tmpstr1 = string(basedate_loc(1))
+  tmpstr1 = '[ '//string(basedate_loc(1))
   tmpstr2 = trim(tmpstr1)
   do i=2, basedate_size
     tmpstr1 = string(basedate_loc(i))
-    tmpstr2 = trim(tmpstr2) // ' ' // trim(tmpstr1)
+    tmpstr2 = trim(tmpstr2) // ', ' // trim(tmpstr1)
   enddo
-  call fms_f2c_string(vals(1)%val2, trim(tmpstr2))
+  tmpstr1 = trim(tmpstr2) // ']'
+  call fms_f2c_string(vals(1)%val2, trim(tmpstr1))
   call yaml_out_add_level2key('diag_files', keys(1))
   key3_i = 0
   !! tier 2 - diag files

parser/yaml_output_functions.c

@@ -89,7 +89,9 @@ void keyerror(yaml_event_t * event, yaml_emitter_t * emitter){
   fprintf(stderr, "WARNING: YAML_OUTPUT: Failed to emit event %d: %s\n", event->type, emitter->problem);
   fprintf(stdout, "WARNING: YAML_OUTPUT: Failed to emit event %d: %s\n", event->type, emitter->problem);
 }
-/* \breif Writes the key/value pairs of the fmsyamloutkeys and fmsyamloutvalues structs
+/* \brief Writes the key/value pairs of the fmsyamloutkeys and fmsyamloutvalues structs
+ * \note If second value (val2) in struct starts with '[' it will be assumed the value is a yaml array
+ * There may be slight differences in spacing for array outputs vs what is read in.
  * \param emitter The libyaml emitter for this file
  * \param event The libyaml eent pointer
  * \param aindex The index of keys and vals that are being written currently
@@ -124,11 +126,58 @@ void write_keys_vals_yaml (yaml_emitter_t * emitter, yaml_event_t * event , int
       keyerror(event, emitter);
       return;
     }
-    yaml_scalar_event_initialize(event, NULL, (yaml_char_t *)YAML_STR_TAG,
-        (yaml_char_t *)vals[aindex].val2, strlen(vals[aindex].val2), 1, 0, YAML_PLAIN_SCALAR_STYLE);
-    if (!yaml_emitter_emit(emitter, event)){
-      keyerror(event, emitter);
-      return;
+
+    // check if we're writing an array
+    if(vals[aindex].val2[0] != '['){
+      yaml_scalar_event_initialize(event, NULL, NULL,
+          (yaml_char_t *)vals[aindex].val2, strlen(vals[aindex].val2), 1, 0, YAML_PLAIN_SCALAR_STYLE);
+      if (!yaml_emitter_emit(emitter, event)){
+        keyerror(event, emitter);
+        return;
+      }
+    } else {
+      // parse the string for individual elements
+      char *buff = vals[aindex].val2;
+      char cbuff[2]; // single char buffer for appending
+      cbuff[1] = '\0';
+      char elements[16][255];
+      int ecount=0; // count of elements
+      strcpy(elements[0], "");
+      for(int i=1; i< strlen(buff)-1; i++){
+        if(buff[i] != ' ' && buff[i] != ','){
+          cbuff[0] = buff[i];
+          strcat(elements[ecount], cbuff);
+        }
+        if(buff[i] == ','){
+          ecount++;
+          if(ecount >= 16) {
+            printf("Error: element count in write_keys_vals_yaml greater than max value of 16");
+            return;
+          }
+          strcpy(elements[ecount], "");
+        }
+      }
+      // start flow sequence
+      yaml_sequence_start_event_initialize(event, NULL, NULL, 1, YAML_FLOW_SEQUENCE_STYLE);
+      if (!yaml_emitter_emit(emitter, event)){
+        keyerror(event, emitter);
+        return;
+      }
+      // loop through and write elements
+      for (int i=0; i <= ecount; i++){
+        yaml_scalar_event_initialize(event, NULL, NULL,
+            (yaml_char_t *)elements[i], strlen(elements[i]), 1, 0, YAML_PLAIN_SCALAR_STYLE);
+        if (!yaml_emitter_emit(emitter, event)){
+          keyerror(event, emitter);
+          return;
+        }
+      }
+      // end flow sequence
+      yaml_sequence_end_event_initialize(event);
+      if (!yaml_emitter_emit(emitter, event)){
+        keyerror(event, emitter);
+        return;
+      }
     }
   }
   if (keys[aindex].key3[0] !='\0')  {

parser/yaml_parser.F90

@@ -70,6 +70,8 @@ module yaml_parser_mod
 interface
 
 !> @brief Private c function that opens and parses a yaml file (see yaml_parser_binding.c)
+!! Any arrays (formatted as [a, b, c] or a multiline '-' tabbed list) will be
+!! read in as a space-separated list of characters
 !! @return Flag indicating if the read was successful
 function open_and_parse_file_wrap(filename, file_id) bind(c) &
    result(error_code)

parser/yaml_parser_binding.c

@@ -316,6 +316,9 @@ int open_and_parse_file_wrap(char *filename, int *file_id)
   char current_layername[255]; /* Name of the current block */
   int i;                       /* To minimize the typing :) */
   int j;                       /* To minimize the typing :) */
+  bool is_flow_sequence = false;/* Flag indicating if within a flow sequence (aka a yaml array ie. [1, 2, 3, 4] or - tabbed list)*/
+  bool is_first = false;        /* Flag indicating if current item is the first item in the flow sequence*/
+  char buff[255];               /* String buffer for individual array values*/
 
   if (nfiles == 0 )
   {
@@ -356,6 +359,19 @@ int open_and_parse_file_wrap(char *filename, int *file_id)
         is_key = false;
         break;
        }
+    case YAML_FLOW_SEQUENCE_START_TOKEN:
+       {
+         is_key = false;
+         is_flow_sequence = true;
+         is_first = true;
+         break;
+       }
+    case YAML_FLOW_SEQUENCE_END_TOKEN:
+       {
+         is_key = false;
+         is_flow_sequence = false;
+         break;
+       }
     case YAML_BLOCK_ENTRY_TOKEN:
        {
         layer = layer + 1;
@@ -386,19 +402,28 @@ int open_and_parse_file_wrap(char *filename, int *file_id)
        {
         if ( ! is_key)
         {
-         current_parent = parent[layer];
-         strcpy(current_layername, "");
-         key_count = key_count + 1;
-         i = key_count;
-         my_files.files[j].keys = realloc(my_files.files[j].keys, (i+1)*sizeof(key_value_pairs));
-         my_files.files[j].keys[i].key_number=i;
-         my_files.files[j].keys[i].parent_key = current_parent;
-         strcpy(my_files.files[j].keys[i].parent_name, current_layername);
-         strcpy(my_files.files[j].keys[i].key, key_value);
-         strcpy(my_files.files[j].keys[i].value, token.data.scalar.value);
-         my_files.files[j].nkeys = key_count;
-         /* printf("----> LAYER:%i LAYER_NAME=%s PARENT:%i, KEYCOUNT:%i KEY: %s VALUE: %s \n", layer, current_layername, current_parent, key_count, key_value, token.data.scalar.value); */
-         strcpy(key_value,"");
+         if (! is_flow_sequence || is_first) // if either a normal value or the first element in a flow sequence
+         {
+            current_parent = parent[layer];
+            strcpy(current_layername, "");
+            key_count = key_count + 1;
+            i = key_count;
+            my_files.files[j].keys = realloc(my_files.files[j].keys, (i+1)*sizeof(key_value_pairs));
+            my_files.files[j].keys[i].key_number=i;
+            my_files.files[j].keys[i].parent_key = current_parent;
+            strcpy(my_files.files[j].keys[i].parent_name, current_layername);
+            strcpy(my_files.files[j].keys[i].key, key_value);
+            strcpy(my_files.files[j].keys[i].value, token.data.scalar.value);
+            my_files.files[j].nkeys = key_count;
+            /* printf("----> LAYER:%i LAYER_NAME=%s PARENT:%i, KEYCOUNT:%i KEY: %s VALUE: %s \n", layer, current_layername, current_parent, key_count, key_value, token.data.scalar.value); */
+            strcpy(key_value,"");
+            is_first = false;
+         } else { // if an item in a flow sequence
+            strcpy(buff, token.data.scalar.value);
+            strcat(my_files.files[j].keys[i].value, " ");
+            strcat(my_files.files[j].keys[i].value, buff);
+         }
+
         }
         else
          {strcpy(key_value,token.data.scalar.value);}

test_fms/diag_manager/test_cell_measures.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 
 diag_files:
 - file_name: static_file

test_fms/diag_manager/test_diag_manager2.sh

@@ -514,7 +514,7 @@ if [ -z "${skipflag}" ]; then
 
   cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [ 2, 1, 1, 0, 0, 0 ]
 diag_files:
 - file_name: wild_card_name%4yr%2mo%2dy%2hr
   filename_time: end
@@ -592,7 +592,7 @@ my_test_count=`expr $my_test_count + 1`
 
   cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0 ]
 diag_files:
 - file_name: wild_card_name%4yr%2mo%2dy%2hr
   filename_time: end
@@ -673,7 +673,7 @@ _EOF
   printf "&diag_manager_nml \n use_modern_diag = .true. \n/" | cat > input.nml
   cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0 ]
 diag_files:
 - file_name: file1
   freq: 6 hours
@@ -722,7 +722,7 @@ _EOF
   printf "&diag_manager_nml \n use_modern_diag = .true. \n do_diag_field_log = .true. \n/" | cat > input.nml
   cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0 ]
 
 diag_files:
 - file_name: static_file
@@ -886,7 +886,7 @@ _EOF
   cat <<_EOF > diag_out_ref.yaml
 ---
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: static_file
   freq: -1
@@ -1296,7 +1296,7 @@ test_expect_success "check modern diag manager yaml output (test $my_test_count)
 printf "&diag_manager_nml \n use_modern_diag = .true. \n use_clock_average = .true. \n /" | cat > input.nml
 cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0 ]
 
 diag_files:
 - file_name: file1_clock
@@ -1318,7 +1318,7 @@ my_test_count=`expr $my_test_count + 1`
 printf "&diag_manager_nml \n use_modern_diag = .true. \n use_clock_average = .false. \n /" | cat > input.nml
 cat <<_EOF > diag_table.yaml
 title: test_diag_manager
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0 ]
 
 diag_files:
 - file_name: file1_forecast

test_fms/diag_manager/test_dm_weights.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_weights
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_weights
   time_units: hours

test_fms/diag_manager/test_flush_nc_file.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_nc_flush
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_flush
   time_units: hours

test_fms/diag_manager/test_multiple_send_data.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_multiple_sends
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_multiple_sends
   time_units: hours

test_fms/diag_manager/test_output_every_freq.sh

@@ -30,7 +30,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_diag_manager_01
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_0days
   time_units: days

test_fms/diag_manager/test_prepend_date.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_prepend_date
-base_date: 1 1 1 0 0 0
+base_date: [1, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_non_static
   time_units: hours

test_fms/diag_manager/test_subregional.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_subregional
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 
 diag_files:
 # This is to test a file with multiple z axis

test_fms/diag_manager/test_time_avg.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_avg
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_avg
   time_units: hours

test_fms/diag_manager/test_time_diurnal.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_diurnal
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_diurnal
   time_units: hours

test_fms/diag_manager/test_time_max.sh

@@ -31,7 +31,7 @@ output_dir
 #TODO replace with yaml diag_table and set diag_manager_nml::use_modern_diag=.true.
 cat <<_EOF > diag_table.yaml
 title: test_max
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_max
   time_units: hours

test_fms/diag_manager/test_time_min.sh

@@ -31,7 +31,7 @@ output_dir
 #TODO replace with yaml diag_table and set diag_manager_nml::use_modern_diag=.true.
 cat <<_EOF > diag_table.yaml
 title: test_min
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_min
   time_units: hours

test_fms/diag_manager/test_time_none.sh

@@ -30,7 +30,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_none
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_none
   freq: 6 hours

test_fms/diag_manager/test_time_pow.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_pow
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_pow
   time_units: hours

test_fms/diag_manager/test_time_rms.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_rms
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_rms
   time_units: hours

test_fms/diag_manager/test_time_sum.sh

@@ -28,7 +28,7 @@ output_dir
 
 cat <<_EOF > diag_table.yaml
 title: test_sum
-base_date: 2 1 1 0 0 0
+base_date: [2, 1, 1, 0, 0, 0]
 diag_files:
 - file_name: test_sum
   time_units: hours