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Merge pull request #305 from kjsanger/fix/print-null-checksum
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Fix baton-list and baton-do list operation not printing null checksums
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@kjsanger
kjsanger authored Sep 16, 2024
2 parents 52df2c1 + b44d3b6 commit 6b299ae
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4 changes: 2 additions & 2 deletions README.md
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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:

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42 changes: 21 additions & 21 deletions src/baton-list.c
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@@ -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);
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16 changes: 10 additions & 6 deletions src/json.c
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@@ -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) {
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15 changes: 9 additions & 6 deletions src/json.h
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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);

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13 changes: 10 additions & 3 deletions src/list.c
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@@ -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);
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45 changes: 24 additions & 21 deletions src/operations.c
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@@ -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);
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2 changes: 1 addition & 1 deletion tests/check_baton.c
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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;
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