Skip to content

Commit

Permalink
Fix baton-list and baton-do list operation not printing null checksums
Browse files Browse the repository at this point in the history 
Due to an incorrect check for JSON null, the checkum attribute was omitted
from output JSON, even when specifically requested. This change fixes that
behaviour and also rationalises the naming of the checksum flags for the
print, calculate and verify operations so that they are more explicit.
  • Loading branch information
@kjsanger
kjsanger committed Sep 12, 2024
1 parent ac9b658 commit b44d3b6
Show file tree
Hide file tree
Showing 7 changed files with 77 additions and 60 deletions.
4 changes: 2 additions & 2 deletions README.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,15 +48,15 @@ Compatible with iRODS 4.1.x, 4.2.x and 4.3.x
| 3.1.x | 4.2.7 - 4.2.9 |
| 3.2.x | 4.2.7 - 4.2.11 |
| 3.3.x | 4.2.7 - 4.2.11 |
| 4.2.x | 4.2.7 - 4.3.1 |
| 4.2.x | 4.2.7 - 4.3.3 |


Note that building against iRODS 4.3.0 requires

LDFLAGS="-Wl,-z,muldefs"

due to https://github.com/irods/irods/issues/6448 (which is fixed
in iRODS 4.3.1).
in iRODS 4.3.1 and later).

## Installation:

Expand Down
42 changes: 21 additions & 21 deletions src/baton-list.c
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/**
* Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021 Genome Research
* Ltd. All rights reserved.
* Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021, 2024 Genome
* Research Ltd. All rights reserved.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -134,25 +134,25 @@ int main(int argc, char *argv[]) {
" Lists data objects and collections described in a JSON\n"
" input file.\n"
"\n"
" --acl Print access control lists in output.\n"
" --avu Print AVU lists in output.\n"
" --checksum Print data object checksums in output.\n"
" --connect-time The duration in seconds after which a connection\n"
" to iRODS will be refreshed (closed and reopened\n"
" between JSON documents) to allow iRODS server\n"
" resources to be released. Optional, defaults to\n"
" 10 minutes.\n"
" --contents Print collection contents in output.\n"
" --file The JSON file describing the data objects and\n"
" collections. Optional, defaults to STDIN.\n"
" --replicate Print data object replicates.\n"
" --silent Silence warning messages.\n"
" --size Print data object sizes in output.\n"
" --timestamp Print timestamps in output.\n"
" --unbuffered Flush print operations for each JSON object.\n"
" --unsafe Permit unsafe relative iRODS paths.\n"
" --verbose Print verbose messages to STDERR.\n"
" --version Print the version number and exit.\n";
" --acl Print access control lists in output.\n"
" --avu Print AVU lists in output.\n"
" --checksum Print data object checksums in output.\n"
" --connect-time The duration in seconds after which a connection\n"
" to iRODS will be refreshed (closed and reopened\n"
" between JSON documents) to allow iRODS server\n"
" resources to be released. Optional, defaults to\n"
" 10 minutes.\n"
" --contents Print collection contents in output.\n"
" --file The JSON file describing the data objects and\n"
" collections. Optional, defaults to STDIN.\n"
" --replicate Print data object replicates.\n"
" --silent Silence warning messages.\n"
" --size Print data object sizes in output.\n"
" --timestamp Print timestamps in output.\n"
" --unbuffered Flush print operations for each JSON object.\n"
" --unsafe Permit unsafe relative iRODS paths.\n"
" --verbose Print verbose messages to STDERR.\n"
" --version Print the version number and exit.\n";

if (help_flag) {
printf("%s\n",help);
Expand Down
16 changes: 10 additions & 6 deletions src/json.c
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/**
* Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021 Genome Research
* Ltd. All rights reserved.
* Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021, 2024 Genome
* Research Ltd. All rights reserved.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -609,12 +609,16 @@ int op_avu_p(json_t *operation_args) {
return json_is_true(json_object_get(operation_args, JSON_OP_AVU));
}

int op_checksum_p(json_t *operation_args) {
return json_is_true(json_object_get(operation_args, JSON_OP_CHECKSUM));
int op_print_checksum_p(json_t *operation_args) {
return json_is_true(json_object_get(operation_args, JSON_OP_PRINT_CHECKSUM));
}

int op_verify_p(json_t *operation_args) {
return json_is_true(json_object_get(operation_args, JSON_OP_VERIFY));
int op_calculate_checksum_p(json_t *operation_args) {
return json_is_true(json_object_get(operation_args, JSON_OP_CALCULATE_CHECKSUM));
}

int op_verify_checksum_p(json_t *operation_args) {
return json_is_true(json_object_get(operation_args, JSON_OP_VERIFY_CHECKSUM));
}

int op_force_p(json_t *operation_args) {
Expand Down
15 changes: 9 additions & 6 deletions src/json.h
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/**
* Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021 Genome Research
* Ltd. All rights reserved.
* Copyright (C) 2013, 2014, 2015, 2017, 2019, 2021, 2024 Genome
* Research Ltd. All rights reserved.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -118,8 +118,9 @@

#define JSON_OP_ACL "acl"
#define JSON_OP_AVU "avu"
#define JSON_OP_CHECKSUM "checksum"
#define JSON_OP_VERIFY "verify"
#define JSON_OP_PRINT_CHECKSUM "checksum"
#define JSON_OP_CALCULATE_CHECKSUM "checksum"
#define JSON_OP_VERIFY_CHECKSUM "verify"
#define JSON_OP_FORCE "force"
#define JSON_OP_COLLECTION "collection"
#define JSON_OP_CONTENTS "contents"
Expand Down Expand Up @@ -264,9 +265,11 @@ int op_acl_p(json_t *operation_args);

int op_avu_p(json_t *operation_args);

int op_checksum_p(json_t *operation_args);
int op_print_checksum_p(json_t *operation_args);

int op_verify_p(json_t *operation_args);
int op_calculate_checksum_p(json_t *operation_args);

int op_verify_checksum_p(json_t *operation_args);

int op_force_p(json_t *operation_args);

Expand Down
13 changes: 10 additions & 3 deletions src/list.c
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/**
* Copyright (C) 2013, 2014, 2015, 2016, 2017, 2019, 2021, 2023 Genome
* Research Ltd. All rights reserved.
* Copyright (C) 2013, 2014, 2015, 2016, 2017, 2019, 2021, 2023,
* 2024 Genome Research Ltd. All rights reserved.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -229,7 +229,14 @@ json_t *list_checksum(rcComm_t *conn, rodsPath_t *rods_path,
}

json_t *obj = json_array_get(results, 0);
json_t *checksum = json_incref(json_object_get(obj, JSON_CHECKSUM_KEY));
json_t *c = json_object_get(obj, JSON_CHECKSUM_KEY);
json_t *checksum;
if (c != NULL) {
checksum = json_incref(c);
}
else {
checksum = json_null();
}

free_query_input(query_in);
if (results) json_decref(results);
Expand Down
45 changes: 24 additions & 21 deletions src/operations.c
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
/**
* Copyright (C) 2017, 2018, 2019, 2020, 2021, 2022 Genome Research
* Ltd. All rights reserved.
* Copyright (C) 2017, 2018, 2019, 2020, 2021, 2022 , 2024 Genome
* Research Ltd. All rights reserved.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand Down Expand Up @@ -250,25 +250,22 @@ json_t *baton_json_dispatch_op(rodsEnv *env, rcComm_t *conn, json_t *envelope,
if (error->code != 0) goto finally;

option_flags flags = args_copy.flags;
if (op_acl_p(args)) flags = flags | PRINT_ACL;
if (op_avu_p(args)) flags = flags | PRINT_AVU;
if (op_checksum_p(args)) flags = flags |
CALCULATE_CHECKSUM |
PRINT_CHECKSUM;
if (op_verify_p(args)) flags = flags |
VERIFY_CHECKSUM |
PRINT_CHECKSUM;
if (op_contents_p(args)) flags = flags | PRINT_CONTENTS;
if (op_replicate_p(args)) flags = flags | PRINT_REPLICATE;
if (op_size_p(args)) flags = flags | PRINT_SIZE;
if (op_timestamp_p(args)) flags = flags | PRINT_TIMESTAMP;
if (op_raw_p(args)) flags = flags | PRINT_RAW;
if (op_save_p(args)) flags = flags | SAVE_FILES;
if (op_recurse_p(args)) flags = flags | RECURSIVE;
if (op_force_p(args)) flags = flags | FORCE;
if (op_collection_p(args)) flags = flags | SEARCH_COLLECTIONS;
if (op_object_p(args)) flags = flags | SEARCH_OBJECTS;
if (op_single_server_p(args)) flags = flags | SINGLE_SERVER;
if (op_acl_p(args)) flags = flags | PRINT_ACL;
if (op_avu_p(args)) flags = flags | PRINT_AVU;
if (op_print_checksum_p(args)) flags = flags | PRINT_CHECKSUM;
if (op_calculate_checksum_p(args)) flags = flags | CALCULATE_CHECKSUM | PRINT_CHECKSUM;
if (op_verify_checksum_p(args)) flags = flags | VERIFY_CHECKSUM | PRINT_CHECKSUM;
if (op_contents_p(args)) flags = flags | PRINT_CONTENTS;
if (op_replicate_p(args)) flags = flags | PRINT_REPLICATE;
if (op_size_p(args)) flags = flags | PRINT_SIZE;
if (op_timestamp_p(args)) flags = flags | PRINT_TIMESTAMP;
if (op_raw_p(args)) flags = flags | PRINT_RAW;
if (op_save_p(args)) flags = flags | SAVE_FILES;
if (op_recurse_p(args)) flags = flags | RECURSIVE;
if (op_force_p(args)) flags = flags | FORCE;
if (op_collection_p(args)) flags = flags | SEARCH_COLLECTIONS;
if (op_object_p(args)) flags = flags | SEARCH_OBJECTS;
if (op_single_server_p(args)) flags = flags | SINGLE_SERVER;
args_copy.flags = flags;

if (has_operation(args)) {
Expand Down Expand Up @@ -320,6 +317,12 @@ json_t *baton_json_dispatch_op(rodsEnv *env, rcComm_t *conn, json_t *envelope,
}
else if (str_equals(op, JSON_LIST_OP, MAX_STR_LEN)) {
result = baton_json_list_op(env, conn, target, &args_copy, error);
if (error->code != 0) goto finally;

if (args_copy.flags & PRINT_CHECKSUM) {
result = add_checksum_json_object(conn, result, error);
if (error->code != 0) goto finally;
}
}
else if (str_equals(op, JSON_METAMOD_OP, MAX_STR_LEN)) {
result = baton_json_metamod_op(env, conn, target, &args_copy, error);
Expand Down
2 changes: 1 addition & 1 deletion tests/check_baton.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2211,7 +2211,7 @@ START_TEST(test_checksum_data_obj) {
ck_assert_int_eq(list_error.code, 0);
json_t *checksum = json_object_get(result, JSON_CHECKSUM_KEY);

ck_assert_ptr_eq(checksum, NULL);
ck_assert(json_is_null(checksum));
json_decref(result);

baton_error_t flag_conflict_error;
Expand Down

0 comments on commit b44d3b6

Please sign in to comment.