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NCBI C++ ToolKit: src/app/pubseq_gateway/server/introspection_html.hpp Source File

1 "<!DOCTYPE HTML><html>\n" 3 " <title>PubSeq Gateway - Help Page</title>\n" 6 " border: 1px solid;\n" 10 " border-collapse: collapse;\n" 13 " background-color: #D8D8D8;\n" 14 " font-size: larger;\n" 15 " font-weight: bold;\n" 17 " table.first-column > tbody > tr > td:nth-of-type(1) {\n" 18 " font-size: larger;\n" 19 " font-weight: bold;\n" 20 " background-color: #F5F5F5;\n" 22 " table.nested td {\n" 23 " border-color: silver;\n" 29 " <h1>PubSeq Gateway</h1>\n" 30 " <p>Accession resolution and retrieval of bio-sequences. Retrieval of named annotations.</p>\n" 37 " <td>build-date</td>\n" 38 " <td>May 8 2025 12:32:53</td>\n" 40 " </table><br><hr><br><br><h2>Commands</h2>\n" 42 " <li><a href=\"#ID_getblob\">ID/getblob</a></li>\n" 43 " <li><a href=\"#ID_get\">ID/get</a></li>\n" 44 " <li><a href=\"#ID_get_tse_chunk\">ID/get_tse_chunk</a></li>\n" 45 " <li><a href=\"#ID_resolve\">ID/resolve</a></li>\n" 46 " <li><a href=\"#ID_get_na\">ID/get_na</a></li>\n" 47 " <li><a href=\"#ID_get_acc_ver_history\">ID/get_acc_ver_history</a></li>\n" 48 " <li><a href=\"#ID_get_sat_mapping\">ID/get_sat_mapping</a></li>\n" 49 " <li><a href=\"#IPG_resolve\">IPG/resolve</a></li>\n" 50 " <li><a href=\"#ADMIN_config\">ADMIN/config</a></li>\n" 51 " <li><a href=\"#ADMIN_info\">ADMIN/info</a></li>\n" 52 " <li><a href=\"#ADMIN_status\">ADMIN/status</a></li>\n" 53 " <li><a href=\"#ADMIN_shutdown\">ADMIN/shutdown</a></li>\n" 54 " <li><a href=\"#ADMIN_get_alerts\">ADMIN/get_alerts</a></li>\n" 55 " <li><a href=\"#ADMIN_ack_alerts\">ADMIN/ack_alerts</a></li>\n" 56 " <li><a href=\"#ADMIN_statistics\">ADMIN/statistics</a></li>\n" 57 " <li><a href=\"#ADMIN_dispatcher_status\">ADMIN/dispatcher_status</a></li>\n" 58 " <li><a href=\"#ADMIN_connections_status\">ADMIN/connections_status</a></li>\n" 59 " <li><a href=\"#hello\">hello</a></li>\n" 60 " <li><a href=\"#healthz\">healthz</a></li>\n" 61 " <li><a href=\"#livez\">livez</a></li>\n" 62 " <li><a href=\"#readyz\">readyz</a></li>\n" 63 " <li><a href=\"#_readyz_cassandra\">/readyz/cassandra</a></li>\n" 64 " <li><a href=\"#_readyz_connections\">/readyz/connections</a></li>\n" 65 " <li><a href=\"#_readyz_lmdb\">/readyz/lmdb</a></li>\n" 66 " <li><a href=\"#_readyz_wgs\">/readyz/wgs</a></li>\n" 67 " <li><a href=\"#_readyz_cdd\">/readyz/cdd</a></li>\n" 68 " <li><a href=\"#_readyz_snp\">/readyz/snp</a></li>\n" 69 " <li><a href=\"#TEST_io\">TEST/io</a></li>\n" 70 " <li><a href=\"#health\">health</a></li>\n" 71 " <li><a href=\"#deep-health\">deep-health</a></li>\n" 72 " <li><a href=\"#favicon.ico\">favicon.ico</a></li>\n" 73 " <li><a href=\"#unknown\">unknown</a></li>\n" 74 " </ul><a id=\"ID_getblob\"></a><h2>ID/getblob</h2>\n" 75 " <p>Retrieves blob chunks basing on the blob identifier</p>\n" 76 " <table class=\"first-column\">\n" 78 " <th>Parameter</th>\n" 79 " <th>Optional</th>\n" 81 " <th>Description</th>\n" 82 " <th>Allowed Values</th>\n" 87 " <td>mandatory</td>\n" 89 " <td class=\"description\"><sat>.<sat_key>. The blob sat and sat key. Both must be positive integers.</td>\n" 90 " <td>Non empty string. The interpretation of the blob id depends on a processor. Cassandra\n" 91 " processor expects the following format: <sat>.<sat key> where boath are integers</td>\n" 96 " <td>optional</td>\n" 98 " <td class=\"description\">TSE option controls what blob is provided:<br><br><table class=\"nested\">\n" 101 " <td>ID2 split available</td>\n" 102 " <td>ID2 split not available</td>\n" 106 " <td>Nothing</td>\n" 107 " <td>Nothing</td>\n" 111 " <td>Split INFO blob only</td>\n" 112 " <td>Nothing</td>\n" 116 " <td>Split INFO blob only</td>\n" 117 " <td>All Cassandra data chunks of the blob itself</td>\n" 121 " <td>All split blobs</td>\n" 122 " <td>All Cassandra data chunks of the blob itself</td>\n" 126 " <td>All Cassandra data chunks of the blob itself</td>\n" 127 " <td>All Cassandra data chunks of the blob itself</td>\n" 131 " <td>none, whole, orig, smart and slim</td>\n" 135 " <td>last_modified</td>\n" 136 " <td>optional</td>\n" 137 " <td>Integer</td>\n" 138 " <td class=\"description\">The blob last modification. If provided then the exact match will be requested with\n" 139 " the Cassandra storage corresponding field value.</td>\n" 140 " <td>Positive integer. Not provided means that the most recent match will be selected.</td>\n" 144 " <td>use_cache</td>\n" 145 " <td>optional</td>\n" 147 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 148 " affects the seq id resolution step and the blob properties lookup step. The following\n" 149 " options are available:<br><br><table class=\"nested\">\n" 152 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 153 " Cassandra database for the lookups.</td>\n" 157 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 158 " only the LMDB cache.</td>\n" 162 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 166 " <td>yes, no and not provided</td>\n" 170 " <td>include_hup</td>\n" 171 " <td>optional</td>\n" 173 " <td class=\"description\">Explicitly tells the server if it should try to retrieve data from HUP keyspaces.\n" 174 " If data are coming from a secure keyspace then the following logic is used. If the\n" 175 " include_hup option is provided then the decision is made basing on the provided value.\n" 176 " Otherwise a decision is made basing on the presence of the WebCubbyUser cookie. If\n" 177 " it was decided that HUP data needs to be provided then the server uses the WebCubbyUser\n" 178 " cookie value to perform an authorization check.</td>\n" 179 " <td>yes and no</td>\n" 183 " <td>client_id</td>\n" 184 " <td>optional</td>\n" 186 " <td class=\"description\">The client identifier. If provided then the exclude blob feature takes place.</td>\n" 187 " <td>A string identifier</td>\n" 191 " <td>send_blob_if_small</td>\n" 192 " <td>optional</td>\n" 193 " <td>Integer</td>\n" 194 " <td class=\"description\"></td>\n" 195 " <td>An integer greater or equal 0</td>\n" 200 " <td>optional</td>\n" 202 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 203 " <td>yes and no</td>\n" 208 " <td>optional</td>\n" 209 " <td>Integer</td>\n" 210 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n" 211 " <td>An integer greater or equal 0</td>\n" 215 " <td>enable_processor</td>\n" 216 " <td>optional</td>\n" 218 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 219 " repeated as many times as needed.</td>\n" 220 " <td>A string</td>\n" 224 " <td>disable_processor</td>\n" 225 " <td>optional</td>\n" 227 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 228 " be repeated as many times as needed.</td>\n" 229 " <td>A string</td>\n" 233 " <td>processor_events</td>\n" 234 " <td>optional</td>\n" 236 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 237 " <td>yes and no</td>\n" 242 " <p>The PSG protocol is used in the HTTP body. The blob properties and chunks are provided.</p>\n" 243 " <hr><br><br><a id=\"ID_get\"></a><h2>ID/get</h2>\n" 244 " <p>Retrieves blob chunks basing on the seq_id and seq_id_type</p>\n" 245 " <table class=\"first-column\">\n" 247 " <th>Parameter</th>\n" 248 " <th>Optional</th>\n" 250 " <th>Description</th>\n" 251 " <th>Allowed Values</th>\n" 252 " <th>Default</th>\n" 256 " <td>mandatory</td>\n" 258 " <td class=\"description\">Sequence identifier</td>\n" 259 " <td>A string identifier</td>\n" 263 " <td>seq_id_type</td>\n" 264 " <td>optional</td>\n" 265 " <td>Integer</td>\n" 266 " <td class=\"description\">Sequence identifier type</td>\n" 267 " <td>Integer type greater than 0</td>\n" 271 " <td>use_cache</td>\n" 272 " <td>optional</td>\n" 274 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 275 " affects the seq id resolution step and the blob properties lookup step. The following\n" 276 " options are available:<br><br><table class=\"nested\">\n" 279 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 280 " Cassandra database for the lookups.</td>\n" 284 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 285 " only the LMDB cache.</td>\n" 289 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 293 " <td>yes, no and not provided</td>\n" 298 " <td>optional</td>\n" 300 " <td class=\"description\">TSE option controls what blob is provided:<br><br><table class=\"nested\">\n" 303 " <td>ID2 split available</td>\n" 304 " <td>ID2 split not available</td>\n" 308 " <td>Nothing</td>\n" 309 " <td>Nothing</td>\n" 313 " <td>Split INFO blob only</td>\n" 314 " <td>Nothing</td>\n" 318 " <td>Split INFO blob only</td>\n" 319 " <td>All Cassandra data chunks of the blob itself</td>\n" 323 " <td>All split blobs</td>\n" 324 " <td>All Cassandra data chunks of the blob itself</td>\n" 328 " <td>All Cassandra data chunks of the blob itself</td>\n" 329 " <td>All Cassandra data chunks of the blob itself</td>\n" 333 " <td>none, whole, orig, smart and slim</td>\n" 337 " <td>exclude_blobs</td>\n" 338 " <td>optional</td>\n" 340 " <td class=\"description\">A comma separated list of blob identifiers which client already has. If provided then\n" 341 " if the resolution of sequence identifier/sequence identifier type matches one of the\n" 342 " blob identifiers in the list then the blob will not be sent. The format of the blob\n" 343 " identifier depends on a processor. For example, a Cassandra processor expects the\n" 344 " format as <sat>.<sat key> where both of them are integers. Note: it works in conjunction\n" 345 " with the client_id parameter.</td>\n" 346 " <td>A list of blob indentifiers</td>\n" 350 " <td>client_id</td>\n" 351 " <td>optional</td>\n" 353 " <td class=\"description\">The client identifier. If provided then the exclude blob feature takes place.</td>\n" 354 " <td>A string identifier</td>\n" 358 " <td>acc_substitution</td>\n" 359 " <td>optional</td>\n" 361 " <td class=\"description\">The option controls how the bioseq info accession substitution is done. If the substitution\n" 362 " is needed then the seq_ids list is analyzed. If there is one with Gi then it is taken\n" 363 " for substitution. Otherwise an arbitrary one is picked. The supported policy values\n" 364 " are:<br><br><table class=\"nested\">\n" 366 " <td>default</td>\n" 367 " <td>substitute if version value (version <= 0) or seq_id_type is Gi(12)</td>\n" 370 " <td>limited</td>\n" 371 " <td>substitute only if the resolved record's seq_id_type is GI(12)</td>\n" 375 " <td>the accession substitution is never done</td>\n" 379 " <td>limited, never or default</td>\n" 380 " <td>default</td>\n" 383 " <td>send_blob_if_small</td>\n" 384 " <td>optional</td>\n" 385 " <td>Integer</td>\n" 386 " <td class=\"description\"></td>\n" 387 " <td>An integer greater or equal 0</td>\n" 391 " <td>resend_timeout</td>\n" 392 " <td>optional</td>\n" 394 " <td class=\"description\">If the blob has already been sent to the client more than this time ago then the blob\n" 395 " will be sent anyway. If less then the 'already sent' reply will have an additional\n" 396 " field 'sent_seconds_ago' with the corresponding value. The special value 0 means that\n" 397 " the blob will be sent regardless when it was already sent.</td>\n" 398 " <td>Floating point value greater or equal 0.0</td>\n" 399 " <td>Taken from [SERVER]/resend_timeout configuration setting</td>\n" 402 " <td>seq_id_resolve</td>\n" 403 " <td>optional</td>\n" 405 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n" 406 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n" 407 " <td>yes and no</td>\n" 411 " <td>include_hup</td>\n" 412 " <td>optional</td>\n" 414 " <td class=\"description\">Explicitly tells the server if it should try to retrieve data from HUP keyspaces.\n" 415 " If data are coming from a secure keyspace then the following logic is used. If the\n" 416 " include_hup option is provided then the decision is made basing on the provided value.\n" 417 " Otherwise a decision is made basing on the presence of the WebCubbyUser cookie. If\n" 418 " it was decided that HUP data needs to be provided then the server uses the WebCubbyUser\n" 419 " cookie value to perform an authorization check.</td>\n" 420 " <td>yes and no</td>\n" 425 " <td>optional</td>\n" 427 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 428 " <td>yes and no</td>\n" 433 " <td>optional</td>\n" 434 " <td>Integer</td>\n" 435 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n" 436 " <td>An integer greater or equal 0</td>\n" 440 " <td>enable_processor</td>\n" 441 " <td>optional</td>\n" 443 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 444 " repeated as many times as needed.</td>\n" 445 " <td>A string</td>\n" 449 " <td>disable_processor</td>\n" 450 " <td>optional</td>\n" 452 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 453 " be repeated as many times as needed.</td>\n" 454 " <td>A string</td>\n" 458 " <td>processor_events</td>\n" 459 " <td>optional</td>\n" 461 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 462 " <td>yes and no</td>\n" 467 " <p>The PSG protocol is used in the HTTP body. The bioseq info, blob properties and chunks\n" 468 " are provided.</p>\n" 469 " <hr><br><br><a id=\"ID_get_tse_chunk\"></a><h2>ID/get_tse_chunk</h2>\n" 470 " <p>Retrieves a TSE blob chunk</p>\n" 471 " <table class=\"first-column\">\n" 473 " <th>Parameter</th>\n" 474 " <th>Optional</th>\n" 476 " <th>Description</th>\n" 477 " <th>Allowed Values</th>\n" 478 " <th>Default</th>\n" 481 " <td>id2_chunk</td>\n" 482 " <td>mandatory</td>\n" 483 " <td>Integer</td>\n" 484 " <td class=\"description\">The tse blob chunk number. The Cassandra processor recognizes a special value of 999999999\n" 485 " for the parameter. In this case the effective chunk number will be taken from the\n" 486 " id2_info parameter</td>\n" 487 " <td>Integer greater or equal 0. Some processors may introduce more strict rules. For example,\n" 488 " Cassandra processor requires the chunk number to be greater than 0.</td>\n" 492 " <td>id2_info</td>\n" 493 " <td>mandatory</td>\n" 495 " <td class=\"description\">The following formats are recognized:<br><br><table class=\"nested\">\n" 497 " <td>Cassandra processor, option 1</td>\n" 498 " <td>3 or 4 integers separated by '.': <sat>.<info>.<chunks>[.<split version>]</td>\n" 501 " <td>Cassandra processor, option 2</td>\n" 502 " <td>psg~~tse_id-<sat>.<sat key>[~~tse_last_modified-<int>[~~tse_split_version-<int>]</td>\n" 505 " <td>Other processors</td>\n" 506 " <td>id2~~tse_id-<string>~~tse_last_modified-<int>~~tse_split_version-<int></td>\n" 510 " <td>A string in a format recognisable by one of the processors</td>\n" 514 " <td>use_cache</td>\n" 515 " <td>optional</td>\n" 517 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 518 " affects the seq id resolution step and the blob properties lookup step. The following\n" 519 " options are available:<br><br><table class=\"nested\">\n" 522 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 523 " Cassandra database for the lookups.</td>\n" 527 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 528 " only the LMDB cache.</td>\n" 532 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 536 " <td>yes, no and not provided</td>\n" 540 " <td>include_hup</td>\n" 541 " <td>optional</td>\n" 543 " <td class=\"description\">Explicitly tells the server if it should try to retrieve data from HUP keyspaces.\n" 544 " If data are coming from a secure keyspace then the following logic is used. If the\n" 545 " include_hup option is provided then the decision is made basing on the provided value.\n" 546 " Otherwise a decision is made basing on the presence of the WebCubbyUser cookie. If\n" 547 " it was decided that HUP data needs to be provided then the server uses the WebCubbyUser\n" 548 " cookie value to perform an authorization check.</td>\n" 549 " <td>yes and no</td>\n" 554 " <td>optional</td>\n" 556 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 557 " <td>yes and no</td>\n" 562 " <td>optional</td>\n" 563 " <td>Integer</td>\n" 564 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n" 565 " <td>An integer greater or equal 0</td>\n" 569 " <td>enable_processor</td>\n" 570 " <td>optional</td>\n" 572 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 573 " repeated as many times as needed.</td>\n" 574 " <td>A string</td>\n" 578 " <td>disable_processor</td>\n" 579 " <td>optional</td>\n" 581 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 582 " be repeated as many times as needed.</td>\n" 583 " <td>A string</td>\n" 587 " <td>processor_events</td>\n" 588 " <td>optional</td>\n" 590 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 591 " <td>yes and no</td>\n" 596 " <p>The PSG protocol is used in the HTTP body. The blob properties and chunks are provided.</p>\n" 597 " <hr><br><br><a id=\"ID_resolve\"></a><h2>ID/resolve</h2>\n" 598 " <p>Resolve seq_id and provide bioseq info</p>\n" 599 " <table class=\"first-column\">\n" 601 " <th>Parameter</th>\n" 602 " <th>Optional</th>\n" 604 " <th>Description</th>\n" 605 " <th>Allowed Values</th>\n" 606 " <th>Default</th>\n" 610 " <td>mandatory</td>\n" 612 " <td class=\"description\">Sequence identifier</td>\n" 613 " <td>A string identifier</td>\n" 617 " <td>seq_id_type</td>\n" 618 " <td>optional</td>\n" 619 " <td>Integer</td>\n" 620 " <td class=\"description\">Sequence identifier type</td>\n" 621 " <td>Integer type greater than 0</td>\n" 625 " <td>use_cache</td>\n" 626 " <td>optional</td>\n" 628 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 629 " affects the seq id resolution step and the blob properties lookup step. The following\n" 630 " options are available:<br><br><table class=\"nested\">\n" 633 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 634 " Cassandra database for the lookups.</td>\n" 638 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 639 " only the LMDB cache.</td>\n" 643 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 647 " <td>yes, no and not provided</td>\n" 652 " <td>optional</td>\n" 654 " <td class=\"description\">The format of the data sent to the client. Available options:<br><br><table class=\"nested\">\n" 656 " <td>protobuf</td>\n" 657 " <td>bioseq info will be sent as a protobuf binary data</td>\n" 661 " <td>bioseq info will be sent as a serialized JSON dictionary</td>\n" 665 " <td>the server decides what format to use: protobuf or json</td>\n" 669 " <td>protobuf, json or native</td>\n" 673 " <td>all_info</td>\n" 674 " <td>optional</td>\n" 676 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 678 " <td>yes and no</td>\n" 682 " <td>canon_id</td>\n" 683 " <td>optional</td>\n" 685 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 687 " <td>yes and no</td>\n" 691 " <td>seq_ids</td>\n" 692 " <td>optional</td>\n" 694 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 696 " <td>yes and no</td>\n" 700 " <td>mol_type</td>\n" 701 " <td>optional</td>\n" 703 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 705 " <td>yes and no</td>\n" 710 " <td>optional</td>\n" 712 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 714 " <td>yes and no</td>\n" 719 " <td>optional</td>\n" 721 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 723 " <td>yes and no</td>\n" 727 " <td>blob_id</td>\n" 728 " <td>optional</td>\n" 730 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 732 " <td>yes and no</td>\n" 737 " <td>optional</td>\n" 739 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 741 " <td>yes and no</td>\n" 746 " <td>optional</td>\n" 748 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 750 " <td>yes and no</td>\n" 754 " <td>date_changed</td>\n" 755 " <td>optional</td>\n" 757 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 759 " <td>yes and no</td>\n" 764 " <td>optional</td>\n" 766 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 768 " <td>yes and no</td>\n" 773 " <td>optional</td>\n" 775 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 777 " <td>yes and no</td>\n" 781 " <td>seq_state</td>\n" 782 " <td>optional</td>\n" 784 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n" 786 " <td>yes and no</td>\n" 790 " <td>acc_substitution</td>\n" 791 " <td>optional</td>\n" 793 " <td class=\"description\">The option controls how the bioseq info accession substitution is done. If the substitution\n" 794 " is needed then the seq_ids list is analyzed. If there is one with Gi then it is taken\n" 795 " for substitution. Otherwise an arbitrary one is picked. The supported policy values\n" 796 " are:<br><br><table class=\"nested\">\n" 798 " <td>default</td>\n" 799 " <td>substitute if version value (version <= 0) or seq_id_type is Gi(12)</td>\n" 802 " <td>limited</td>\n" 803 " <td>substitute only if the resolved record's seq_id_type is GI(12)</td>\n" 807 " <td>the accession substitution is never done</td>\n" 811 " <td>limited, never or default</td>\n" 812 " <td>default</td>\n" 815 " <td>seq_id_resolve</td>\n" 816 " <td>optional</td>\n" 818 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n" 819 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n" 820 " <td>yes and no</td>\n" 825 " <td>optional</td>\n" 827 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 828 " <td>yes and no</td>\n" 833 " <td>optional</td>\n" 834 " <td>Integer</td>\n" 835 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n" 836 " <td>An integer greater or equal 0</td>\n" 840 " <td>enable_processor</td>\n" 841 " <td>optional</td>\n" 843 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 844 " repeated as many times as needed.</td>\n" 845 " <td>A string</td>\n" 849 " <td>disable_processor</td>\n" 850 " <td>optional</td>\n" 852 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 853 " be repeated as many times as needed.</td>\n" 854 " <td>A string</td>\n" 858 " <td>processor_events</td>\n" 859 " <td>optional</td>\n" 861 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 862 " <td>yes and no</td>\n" 867 " <p>The bioseq info is sent back in the HTTP body as binary protobuf or as PSG protocol\n" 868 " chunks depending on the protocol choice</p>\n" 869 " <hr><br><br><a id=\"ID_get_na\"></a><h2>ID/get_na</h2>\n" 870 " <p>Retrieves named annotations</p>\n" 871 " <table class=\"first-column\">\n" 873 " <th>Parameter</th>\n" 874 " <th>Optional</th>\n" 876 " <th>Description</th>\n" 877 " <th>Allowed Values</th>\n" 878 " <th>Default</th>\n" 882 " <td>optional</td>\n" 884 " <td class=\"description\">Sequence identifier. This or seq_ids parameter value must be provided for the request.</td>\n" 885 " <td>A string identifier</td>\n" 889 " <td>seq_ids</td>\n" 890 " <td>optional</td>\n" 892 " <td class=\"description\">A space separated list of the sequence identifier synonims. This or seq_id parameter\n" 893 " value must be provided for the request.</td>\n" 894 " <td>A list of space separated string identifiers</td>\n" 898 " <td>seq_id_type</td>\n" 899 " <td>optional</td>\n" 900 " <td>Integer</td>\n" 901 " <td class=\"description\">Sequence identifier type</td>\n" 902 " <td>Integer type greater than 0</td>\n" 907 " <td>mandatory</td>\n" 909 " <td class=\"description\">A comma separated list of named annotations to be retrieved.</td>\n" 910 " <td>A string</td>\n" 914 " <td>use_cache</td>\n" 915 " <td>optional</td>\n" 917 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 918 " affects the seq id resolution step and the blob properties lookup step. The following\n" 919 " options are available:<br><br><table class=\"nested\">\n" 922 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 923 " Cassandra database for the lookups.</td>\n" 927 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 928 " only the LMDB cache.</td>\n" 932 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 936 " <td>yes, no and not provided</td>\n" 941 " <td>optional</td>\n" 943 " <td class=\"description\">The format of the data sent to the client. Available options:<br><br><table class=\"nested\">\n" 945 " <td>protobuf</td>\n" 946 " <td>bioseq info will be sent as a protobuf binary data</td>\n" 950 " <td>bioseq info will be sent as a serialized JSON dictionary</td>\n" 954 " <td>the server decides what format to use: protobuf or json</td>\n" 958 " <td>protobuf, json or native</td>\n" 963 " <td>optional</td>\n" 965 " <td class=\"description\">TSE option controls what blob is provided:<br><br><table class=\"nested\">\n" 968 " <td>ID2 split available</td>\n" 969 " <td>ID2 split not available</td>\n" 973 " <td>Nothing</td>\n" 974 " <td>Nothing</td>\n" 978 " <td>Split INFO blob only</td>\n" 979 " <td>Nothing</td>\n" 983 " <td>Split INFO blob only</td>\n" 984 " <td>All Cassandra data chunks of the blob itself</td>\n" 988 " <td>All split blobs</td>\n" 989 " <td>All Cassandra data chunks of the blob itself</td>\n" 993 " <td>All Cassandra data chunks of the blob itself</td>\n" 994 " <td>All Cassandra data chunks of the blob itself</td>\n" 998 " <td>none, whole, orig, smart and slim</td>\n" 1002 " <td>client_id</td>\n" 1003 " <td>optional</td>\n" 1004 " <td>String</td>\n" 1005 " <td class=\"description\">The client identifier. If provided then the exclude blob feature takes place.</td>\n" 1006 " <td>A string identifier</td>\n" 1010 " <td>send_blob_if_small</td>\n" 1011 " <td>optional</td>\n" 1012 " <td>Integer</td>\n" 1013 " <td class=\"description\"></td>\n" 1014 " <td>An integer greater or equal 0</td>\n" 1018 " <td>seq_id_resolve</td>\n" 1019 " <td>optional</td>\n" 1020 " <td>String</td>\n" 1021 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n" 1022 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n" 1023 " <td>yes and no</td>\n" 1027 " <td>resend_timeout</td>\n" 1028 " <td>optional</td>\n" 1030 " <td class=\"description\">If the blob has already been sent to the client more than this time ago then the blob\n" 1031 " will be sent anyway. If less then the 'already sent' reply will have an additional\n" 1032 " field 'sent_seconds_ago' with the corresponding value. The special value 0 means that\n" 1033 " the blob will be sent regardless when it was already sent.</td>\n" 1034 " <td>Floating point value greater or equal 0.0</td>\n" 1035 " <td>Taken from [SERVER]/resend_timeout configuration setting</td>\n" 1038 " <td>snp_scale_limit</td>\n" 1039 " <td>optional</td>\n" 1040 " <td>String</td>\n" 1041 " <td class=\"description\">GenBank ID2 SNP reader parameter</td>\n" 1042 " <td>chromosome, contig, supercontig, unit and not provided</td>\n" 1047 " <td>optional</td>\n" 1048 " <td>String</td>\n" 1049 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 1050 " <td>yes and no</td>\n" 1055 " <td>optional</td>\n" 1056 " <td>Integer</td>\n" 1057 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n" 1058 " <td>An integer greater or equal 0</td>\n" 1062 " <td>enable_processor</td>\n" 1063 " <td>optional</td>\n" 1064 " <td>String</td>\n" 1065 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 1066 " repeated as many times as needed.</td>\n" 1067 " <td>A string</td>\n" 1071 " <td>disable_processor</td>\n" 1072 " <td>optional</td>\n" 1073 " <td>String</td>\n" 1074 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 1075 " be repeated as many times as needed.</td>\n" 1076 " <td>A string</td>\n" 1080 " <td>processor_events</td>\n" 1081 " <td>optional</td>\n" 1082 " <td>String</td>\n" 1083 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 1084 " <td>yes and no</td>\n" 1089 " <p>The PSG protocol is used in the HTTP body. The bioseq info and named annotation chunks\n" 1090 " are provided.</p>\n" 1091 " <hr><br><br><a id=\"ID_get_acc_ver_history\"></a><h2>ID/get_acc_ver_history</h2>\n" 1092 " <p>Retrieves accession version history</p>\n" 1093 " <table class=\"first-column\">\n" 1095 " <th>Parameter</th>\n" 1096 " <th>Optional</th>\n" 1098 " <th>Description</th>\n" 1099 " <th>Allowed Values</th>\n" 1100 " <th>Default</th>\n" 1103 " <td>seq_id</td>\n" 1104 " <td>mandatory</td>\n" 1105 " <td>String</td>\n" 1106 " <td class=\"description\">Sequence identifier</td>\n" 1107 " <td>A string identifier</td>\n" 1111 " <td>seq_id_type</td>\n" 1112 " <td>optional</td>\n" 1113 " <td>Integer</td>\n" 1114 " <td class=\"description\">Sequence identifier type</td>\n" 1115 " <td>Integer type greater than 0</td>\n" 1119 " <td>use_cache</td>\n" 1120 " <td>optional</td>\n" 1121 " <td>String</td>\n" 1122 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 1123 " affects the seq id resolution step and the blob properties lookup step. The following\n" 1124 " options are available:<br><br><table class=\"nested\">\n" 1127 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 1128 " Cassandra database for the lookups.</td>\n" 1132 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 1133 " only the LMDB cache.</td>\n" 1137 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 1141 " <td>yes, no and not provided</td>\n" 1146 " <td>optional</td>\n" 1147 " <td>String</td>\n" 1148 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 1149 " <td>yes and no</td>\n" 1154 " <td>optional</td>\n" 1155 " <td>Integer</td>\n" 1156 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n" 1157 " <td>An integer greater or equal 0</td>\n" 1161 " <td>enable_processor</td>\n" 1162 " <td>optional</td>\n" 1163 " <td>String</td>\n" 1164 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 1165 " repeated as many times as needed.</td>\n" 1166 " <td>A string</td>\n" 1170 " <td>disable_processor</td>\n" 1171 " <td>optional</td>\n" 1172 " <td>String</td>\n" 1173 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 1174 " be repeated as many times as needed.</td>\n" 1175 " <td>A string</td>\n" 1179 " <td>processor_events</td>\n" 1180 " <td>optional</td>\n" 1181 " <td>String</td>\n" 1182 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 1183 " <td>yes and no</td>\n" 1188 " <p>The PSG protocol is used in the HTTP body. The bioseq info and accession version history\n" 1189 " chunks are provided.</p>\n" 1190 " <hr><br><br><a id=\"ID_get_sat_mapping\"></a><h2>ID/get_sat_mapping</h2>\n" 1191 " <p>Provides the cassandra sat to keyspace mapping information</p>\n" 1193 " <p>The HTTP body is a JSON dictionary with the cassandra sat to keyspace mapping information.</p>\n" 1194 " <hr><br><br><a id=\"IPG_resolve\"></a><h2>IPG/resolve</h2>\n" 1195 " <p>Resolve nucleotide/protein/ipg and provide ipg info</p>\n" 1196 " <table class=\"first-column\">\n" 1198 " <th>Parameter</th>\n" 1199 " <th>Optional</th>\n" 1201 " <th>Description</th>\n" 1202 " <th>Allowed Values</th>\n" 1203 " <th>Default</th>\n" 1206 " <td>protein</td>\n" 1207 " <td>mandatory</td>\n" 1208 " <td>String</td>\n" 1209 " <td class=\"description\">The protein to be resolved. It may be ommitted if ipg is provided.</td>\n" 1210 " <td>A string identifier</td>\n" 1214 " <td>nucleotide</td>\n" 1215 " <td>optional</td>\n" 1216 " <td>String</td>\n" 1217 " <td class=\"description\">The nucleotide to be resolved.</td>\n" 1218 " <td>A string identifier</td>\n" 1223 " <td>mandatory</td>\n" 1224 " <td>Integer</td>\n" 1225 " <td class=\"description\">The ipg to be resolved. It may be ommitted if protein is provided.</td>\n" 1226 " <td>An integer greater than 0</td>\n" 1230 " <td>use_cache</td>\n" 1231 " <td>optional</td>\n" 1232 " <td>String</td>\n" 1233 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n" 1234 " affects the seq id resolution step and the blob properties lookup step. The following\n" 1235 " options are available:<br><br><table class=\"nested\">\n" 1238 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n" 1239 " Cassandra database for the lookups.</td>\n" 1243 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n" 1244 " only the LMDB cache.</td>\n" 1248 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n" 1252 " <td>yes, no and not provided</td>\n" 1256 " <td>seq_id_resolve</td>\n" 1257 " <td>optional</td>\n" 1258 " <td>String</td>\n" 1259 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n" 1260 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n" 1261 " <td>yes and no</td>\n" 1266 " <td>optional</td>\n" 1267 " <td>String</td>\n" 1268 " <td class=\"description\">The option to include trace messages to the server output</td>\n" 1269 " <td>yes and no</td>\n" 1273 " <td>enable_processor</td>\n" 1274 " <td>optional</td>\n" 1275 " <td>String</td>\n" 1276 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n" 1277 " repeated as many times as needed.</td>\n" 1278 " <td>A string</td>\n" 1282 " <td>disable_processor</td>\n" 1283 " <td>optional</td>\n" 1284 " <td>String</td>\n" 1285 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n" 1286 " be repeated as many times as needed.</td>\n" 1287 " <td>A string</td>\n" 1291 " <td>processor_events</td>\n" 1292 " <td>optional</td>\n" 1293 " <td>String</td>\n" 1294 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n" 1295 " <td>yes and no</td>\n" 1300 " <p>The ipg record(s) is sent baback in the HTTP body as PSG protocol chunks</p>\n" 1301 " <hr><br><br><a id=\"ADMIN_config\"></a><h2>ADMIN/config</h2>\n" 1302 " <p>Provides the server configuration information</p>\n" 1304 " <p>The HTTP body is a JSON dictionary with the configuration information. The request\n" 1305 " may be configured as protected in the server settings. If so then the server will\n" 1306 " use the value of the AdminAuthToken cookie to check permissions.</p>\n" 1307 " <hr><br><br><a id=\"ADMIN_info\"></a><h2>ADMIN/info</h2>\n" 1308 " <p>Provides the server run-time information</p>\n" 1310 " <p>The HTTP body is a JSON dictionary with the run-time information like resource consumption.\n" 1311 " The request may be configured as protected in the server settings. If so then the\n" 1312 " server will use the value of the AdminAuthToken cookie to check permissions.</p>\n" 1313 " <hr><br><br><a id=\"ADMIN_status\"></a><h2>ADMIN/status</h2>\n" 1314 " <p>Provides the server event counters</p>\n" 1316 " <p>The HTTP body is a JSON dictionary with various event counters. The request may be\n" 1317 " configured as protected in the server settings. If so then the server will use the\n" 1318 " value of the AdminAuthToken cookie to check permissions.</p>\n" 1319 " <hr><br><br><a id=\"ADMIN_shutdown\"></a><h2>ADMIN/shutdown</h2>\n" 1320 " <p>Performs the server shutdown</p>\n" 1321 " <table class=\"first-column\">\n" 1323 " <th>Parameter</th>\n" 1324 " <th>Optional</th>\n" 1326 " <th>Description</th>\n" 1327 " <th>Allowed Values</th>\n" 1328 " <th>Default</th>\n" 1331 " <td>username</td>\n" 1332 " <td>optional</td>\n" 1333 " <td>String</td>\n" 1334 " <td class=\"description\">The user name who requested the shutdown</td>\n" 1335 " <td>A string identifier</td>\n" 1339 " <td>auth_token</td>\n" 1340 " <td>optional</td>\n" 1341 " <td>String</td>\n" 1342 " <td class=\"description\">Authorization token. If the configuration [ADMIN]/auth_token value is configured then\n" 1343 " the request must have the token value matching the configured to be granted.</td>\n" 1344 " <td>A string identifier</td>\n" 1348 " <td>timeout</td>\n" 1349 " <td>optional</td>\n" 1350 " <td>Integer</td>\n" 1351 " <td class=\"description\">The timeout in seconds within which the shutdown must be performed. If 0 then it leads\n" 1352 " to an immediate shutdown. If 1 or more seconds then the server will reject all new\n" 1353 " requests and wait till the timeout is over or all the pending requests are completed\n" 1354 " and then do the shutdown.</td>\n" 1355 " <td>An integer greater or equal 0</td>\n" 1360 " <p>The standard HTTP protocol is used. The request may be configured as protected in\n" 1361 " the server settings. If so then the server will use the value of the AdminAuthToken\n" 1362 " cookie to check permissions.</p>\n" 1363 " <hr><br><br><a id=\"ADMIN_get_alerts\"></a><h2>ADMIN/get_alerts</h2>\n" 1364 " <p>Provides the server alerts</p>\n" 1366 " <p>The HTTP body is a JSON dictionary with the current server alerts. The request may\n" 1367 " be configured as protected in the server settings. If so then the server will use\n" 1368 " the value of the AdminAuthToken cookie to check permissions.</p>\n" 1369 " <hr><br><br><a id=\"ADMIN_ack_alerts\"></a><h2>ADMIN/ack_alerts</h2>\n" 1370 " <p>Acknowledge an alert</p>\n" 1371 " <table class=\"first-column\">\n" 1373 " <th>Parameter</th>\n" 1374 " <th>Optional</th>\n" 1376 " <th>Description</th>\n" 1377 " <th>Allowed Values</th>\n" 1378 " <th>Default</th>\n" 1382 " <td>mandatory</td>\n" 1383 " <td>String</td>\n" 1384 " <td class=\"description\">The alert identifier to acknowledge</td>\n" 1385 " <td>A string identifier</td>\n" 1389 " <td>username</td>\n" 1390 " <td>mandatory</td>\n" 1391 " <td>String</td>\n" 1392 " <td class=\"description\">The user name who acknowledges the alert</td>\n" 1393 " <td>A string identifier</td>\n" 1398 " <p>The standard HTTP protocol is used. The request may be configured as protected in\n" 1399 " the server settings. If so then the server will use the value of the AdminAuthToken\n" 1400 " cookie to check permissions.</p>\n" 1401 " <hr><br><br><a id=\"ADMIN_statistics\"></a><h2>ADMIN/statistics</h2>\n" 1402 " <p>Provides the server collected statistics</p>\n" 1403 " <table class=\"first-column\">\n" 1405 " <th>Parameter</th>\n" 1406 " <th>Optional</th>\n" 1408 " <th>Description</th>\n" 1409 " <th>Allowed Values</th>\n" 1410 " <th>Default</th>\n" 1414 " <td>optional</td>\n" 1415 " <td>String</td>\n" 1416 " <td class=\"description\">If provided then the collected statistics is rest. Otherwise the collected statistics\n" 1417 " is sent to the client.</td>\n" 1418 " <td>yes and no</td>\n" 1422 " <td>most_recent_time</td>\n" 1423 " <td>optional</td>\n" 1424 " <td>Integer</td>\n" 1425 " <td class=\"description\">Number of seconds in the past for the most recent time range limit</td>\n" 1426 " <td>An integer greater or equal 0</td>\n" 1430 " <td>most_ancient_time</td>\n" 1431 " <td>optional</td>\n" 1432 " <td>Integer</td>\n" 1433 " <td class=\"description\">Number of seconds in the past for the most ancient time range limit</td>\n" 1434 " <td>An integer greater or equal 0</td>\n" 1435 " <td>Effectively infinity, max integer</td>\n" 1438 " <td>histogram_names</td>\n" 1439 " <td>optional</td>\n" 1440 " <td>String</td>\n" 1441 " <td class=\"description\">Comma separated list of the histogram names. If provided then the server returns all\n" 1442 " existing histograms (listed in histogram_names) which intersect with the specified\n" 1443 " time period.</td>\n" 1444 " <td>A comma separated list of string identifiers</td>\n" 1448 " <td>time_series</td>\n" 1449 " <td>optional</td>\n" 1450 " <td>String</td>\n" 1451 " <td class=\"description\">Describes the aggregation of the per-minute data collected by the server. Format:\n" 1452 " <int>:<int>[ <int:<int>]* <int>:\n" 1453 " There are pairs of integers divided by ':'. The pairs are divided by spaces. The first\n" 1454 " integer is how many minutes to be aggregated, the second integer is the last index\n" 1455 " of the data sequence to be aggregated. For each aggregation the server calculates\n" 1456 " the average number of requests per second. The last pair must not have the second\n" 1457 " integer - this is an item which describes the aggregation till the end of the available\n" 1458 " data. A special value is also supported: no. This value means that the server will\n" 1459 " not send time series data at all.</td>\n" 1460 " <td>no or aggregation description string</td>\n" 1461 " <td>1:59 5:1439 60:</td>\n" 1465 " <p>The HTTP body is a JSON dictionary with the collected statistics information. The\n" 1466 " request may be configured as protected in the server settings. If so then the server\n" 1467 " will use the value of the AdminAuthToken cookie to check permissions.</p>\n" 1468 " <hr><br><br><a id=\"ADMIN_dispatcher_status\"></a><h2>ADMIN/dispatcher_status</h2>\n" 1469 " <p>Provides the request dispatcher status</p>\n" 1471 " <p>The HTTP body is a JSON dictionary with the current request dispatcher status.</p>\n" 1472 " <hr><br><br><a id=\"ADMIN_connections_status\"></a><h2>ADMIN/connections_status</h2>\n" 1473 " <p>Provides the connections status</p>\n" 1475 " <p>The HTTP body is a JSON dictionary with the current connections status.</p>\n" 1476 " <hr><br><br><a id=\"hello\"></a><h2>hello</h2>\n" 1477 " <p>Provides the peer id and peer user agent to to the server. These values can be used\n" 1478 " for throttling.</p>\n" 1479 " <table class=\"first-column\">\n" 1481 " <th>Parameter</th>\n" 1482 " <th>Optional</th>\n" 1484 " <th>Description</th>\n" 1485 " <th>Allowed Values</th>\n" 1486 " <th>Default</th>\n" 1489 " <td>peer_id</td>\n" 1490 " <td>mandatory</td>\n" 1491 " <td>String</td>\n" 1492 " <td class=\"description\">The peer identifier</td>\n" 1493 " <td>A non-empty string without white space symbols</td>\n" 1497 " <td>peer_user_agent</td>\n" 1498 " <td>mandatory</td>\n" 1499 " <td>String</td>\n" 1500 " <td class=\"description\">The peer user agent</td>\n" 1501 " <td>A non-empty string without white space symbols</td>\n" 1506 " <p>HTTP status is set to 200 if the peer id and user agent values were accepted and memorized.\n" 1507 " Otherwise the HTTP status is set to 400 and the HTTP body contains a plain text with\n" 1508 " an error message. HTTP status can be set to 500 (with the plain text HTTP body error\n" 1509 " message) in case of exceptions during the execution.</p>\n" 1510 " <hr><br><br><a id=\"healthz\"></a><h2>healthz</h2>\n" 1511 " <p>Performs a functionality check. It can be used by monitoring facilities.</p>\n" 1512 " <table class=\"first-column\">\n" 1514 " <th>Parameter</th>\n" 1515 " <th>Optional</th>\n" 1517 " <th>Description</th>\n" 1518 " <th>Allowed Values</th>\n" 1519 " <th>Default</th>\n" 1522 " <td>verbose</td>\n" 1523 " <td>optional</td>\n" 1525 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1526 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1527 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1532 " <td>exclude</td>\n" 1533 " <td>optional</td>\n" 1534 " <td>String</td>\n" 1535 " <td class=\"description\">A name of a check which should not be performed. The parameter can be repeated as\n" 1536 " many times as needed.</td>\n" 1537 " <td>A string</td>\n" 1542 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n" 1543 " status is set to 500. If verbose flag is provided then the HTTP body contains a JSON\n" 1544 " dictionary with detailed information.</p>\n" 1545 " <hr><br><br><a id=\"livez\"></a><h2>livez</h2>\n" 1546 " <p>Performs a live check. It can be used by monitoring facilities.</p>\n" 1547 " <table class=\"first-column\">\n" 1549 " <th>Parameter</th>\n" 1550 " <th>Optional</th>\n" 1552 " <th>Description</th>\n" 1553 " <th>Allowed Values</th>\n" 1554 " <th>Default</th>\n" 1557 " <td>verbose</td>\n" 1558 " <td>optional</td>\n" 1560 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1561 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1562 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1568 " <p>HTTP status is set to 200 if the live check succeeded. Otherwise the HTTP status is\n" 1569 " set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n" 1570 " with detailed information.</p>\n" 1571 " <hr><br><br><a id=\"readyz\"></a><h2>readyz</h2>\n" 1572 " <p>Performs a functionality check. It can be used by monitoring facilities.</p>\n" 1573 " <table class=\"first-column\">\n" 1575 " <th>Parameter</th>\n" 1576 " <th>Optional</th>\n" 1578 " <th>Description</th>\n" 1579 " <th>Allowed Values</th>\n" 1580 " <th>Default</th>\n" 1583 " <td>verbose</td>\n" 1584 " <td>optional</td>\n" 1586 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1587 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1588 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1593 " <td>exclude</td>\n" 1594 " <td>optional</td>\n" 1595 " <td>String</td>\n" 1596 " <td class=\"description\">A name of a check which should not be performed. The parameter can be repeated as\n" 1597 " many times as needed.</td>\n" 1598 " <td>A string</td>\n" 1603 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n" 1604 " status is set to 500. If verbose flag is provided then the HTTP body contains a JSON\n" 1605 " dictionary with detailed information.</p>\n" 1606 " <hr><br><br><a id=\"_readyz_cassandra\"></a><h2>/readyz/cassandra</h2>\n" 1607 " <p>Performs a cassandra retrieval check. It can be used by monitoring facilities.</p>\n" 1608 " <table class=\"first-column\">\n" 1610 " <th>Parameter</th>\n" 1611 " <th>Optional</th>\n" 1613 " <th>Description</th>\n" 1614 " <th>Allowed Values</th>\n" 1615 " <th>Default</th>\n" 1618 " <td>verbose</td>\n" 1619 " <td>optional</td>\n" 1621 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1622 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1623 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1629 " <p>HTTP status is set to 200 if cassandra retrieval is ok. Otherwise the HTTP status\n" 1630 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n" 1631 " with detailed information.</p>\n" 1632 " <hr><br><br><a id=\"_readyz_connections\"></a><h2>/readyz/connections</h2>\n" 1633 " <p>Checks that the current number of the client connections is within the soft limit.\n" 1634 " It can be used by monitoring facilities.</p>\n" 1635 " <table class=\"first-column\">\n" 1637 " <th>Parameter</th>\n" 1638 " <th>Optional</th>\n" 1640 " <th>Description</th>\n" 1641 " <th>Allowed Values</th>\n" 1642 " <th>Default</th>\n" 1645 " <td>verbose</td>\n" 1646 " <td>optional</td>\n" 1648 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1649 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1650 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1656 " <p>HTTP status is set to 200 if the current number of the client connections is within\n" 1657 " the soft limit. Otherwise the HTTP status is set to 503. If verbose flag is provided\n" 1658 " then the HTTP body contains a JSON dictionary with detailed information.</p>\n" 1659 " <hr><br><br><a id=\"_readyz_lmdb\"></a><h2>/readyz/lmdb</h2>\n" 1660 " <p>Performs an LMDB retrieval check. It can be used by monitoring facilities.</p>\n" 1661 " <table class=\"first-column\">\n" 1663 " <th>Parameter</th>\n" 1664 " <th>Optional</th>\n" 1666 " <th>Description</th>\n" 1667 " <th>Allowed Values</th>\n" 1668 " <th>Default</th>\n" 1671 " <td>verbose</td>\n" 1672 " <td>optional</td>\n" 1674 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1675 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1676 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1682 " <p>HTTP status is set to 200 if LMDB retrieval check succeeded. Otherwise the HTTP status\n" 1683 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n" 1684 " with detailed information.</p>\n" 1685 " <hr><br><br><a id=\"_readyz_wgs\"></a><h2>/readyz/wgs</h2>\n" 1686 " <p>Performs a WGS retrieval check. It can be used by monitoring facilities.</p>\n" 1687 " <table class=\"first-column\">\n" 1689 " <th>Parameter</th>\n" 1690 " <th>Optional</th>\n" 1692 " <th>Description</th>\n" 1693 " <th>Allowed Values</th>\n" 1694 " <th>Default</th>\n" 1697 " <td>verbose</td>\n" 1698 " <td>optional</td>\n" 1700 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1701 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1702 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1708 " <p>HTTP status is set to 200 if WGS retrieval check succeeded. Otherwise the HTTP status\n" 1709 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n" 1710 " with detailed information.</p>\n" 1711 " <hr><br><br><a id=\"_readyz_cdd\"></a><h2>/readyz/cdd</h2>\n" 1712 " <p>Performs a CDD retrieval check. It can be used by monitoring facilities.</p>\n" 1713 " <table class=\"first-column\">\n" 1715 " <th>Parameter</th>\n" 1716 " <th>Optional</th>\n" 1718 " <th>Description</th>\n" 1719 " <th>Allowed Values</th>\n" 1720 " <th>Default</th>\n" 1723 " <td>verbose</td>\n" 1724 " <td>optional</td>\n" 1726 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1727 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1728 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1734 " <p>HTTP status is set to 200 if CDD retrieval check succeeded. Otherwise the HTTP status\n" 1735 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n" 1736 " with detailed information.</p>\n" 1737 " <hr><br><br><a id=\"_readyz_snp\"></a><h2>/readyz/snp</h2>\n" 1738 " <p>Performs a SNP retrieval check. It can be used by monitoring facilities.</p>\n" 1739 " <table class=\"first-column\">\n" 1741 " <th>Parameter</th>\n" 1742 " <th>Optional</th>\n" 1744 " <th>Description</th>\n" 1745 " <th>Allowed Values</th>\n" 1746 " <th>Default</th>\n" 1749 " <td>verbose</td>\n" 1750 " <td>optional</td>\n" 1752 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n" 1753 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n" 1754 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n" 1760 " <p>HTTP status is set to 200 if SNP retrieval check succeeded. Otherwise the HTTP status\n" 1761 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n" 1762 " with detailed information.</p>\n" 1763 " <hr><br><br><a id=\"TEST_io\"></a><h2>TEST/io</h2>\n" 1764 " <p>Sends back random binary data to test the I/O performance. It works only if the server\n" 1765 " configuration file has the [DEBUG]/psg_allow_io_test value set to true</p>\n" 1766 " <table class=\"first-column\">\n" 1768 " <th>Parameter</th>\n" 1769 " <th>Optional</th>\n" 1771 " <th>Description</th>\n" 1772 " <th>Allowed Values</th>\n" 1773 " <th>Default</th>\n" 1776 " <td>return_data_size</td>\n" 1777 " <td>mandatory</td>\n" 1778 " <td>Integer</td>\n" 1779 " <td class=\"description\">Size in bytes (positive integer up to 1000000000) which should be sent to the client.\n" 1780 " The data are random.</td>\n" 1781 " <td>An integer in the range 0 ... 1000000000</td>\n" 1786 " <td>optional</td>\n" 1787 " <td>String</td>\n" 1788 " <td class=\"description\">It tells if the logging of the request should be done or not</td>\n" 1789 " <td>yes and no</td>\n" 1794 " <p>The HTTP body is a random data of the requested length</p>\n" 1795 " <hr><br><br><a id=\"health\"></a><h2>health</h2>\n" 1796 " <p>Performs a basic functionality check. It can be used by monitoring facilities.</p>\n" 1798 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n" 1799 " status is set to 500 and the HTTP body may have a detailed message.</p>\n" 1800 " <hr><br><br><a id=\"deep-health\"></a><h2>deep-health</h2>\n" 1801 " <p>At the moment the implementation matches the 'health' command.</p>\n" 1803 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n" 1804 " status is set to 500 and the HTTP body may have a detailed message.</p>\n" 1805 " <hr><br><br><a id=\"favicon.ico\"></a><h2>favicon.ico</h2>\n" 1806 " <p>Always replies 'not found'</p>\n" 1808 " <p>The standard HTTP protocol is used</p>\n" 1809 " <hr><br><br><a id=\"unknown\"></a><h2>unknown</h2>\n" 1810 " <p>Always replies 'ok' in terms of http. The nested PSG protocol always tells 'bad request'</p>\n" 1812 " <p>The HTTP body uses PSG protocol for a 'bad request' message</p>\n" 1813 " <hr><br><br><h2>References</h2>\n" 1815 " <li><a href=\"https://github.com/ncbi/cxx-toolkit/blob/gh-pages/misc/PSG%20Server.docx\">PubSeq Gateway Server Overview and the Protocol Specification</a></li>\n"

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