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1 "<!DOCTYPE HTML><html>\n"
3 " <title>PubSeq Gateway - Help Page</title>\n"
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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>Aug 20 2024 16:05:56</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=\"#IPG_resolve\">IPG/resolve</a></li>\n"
49 " <li><a href=\"#ADMIN_config\">ADMIN/config</a></li>\n"
50 " <li><a href=\"#ADMIN_info\">ADMIN/info</a></li>\n"
51 " <li><a href=\"#ADMIN_status\">ADMIN/status</a></li>\n"
52 " <li><a href=\"#ADMIN_shutdown\">ADMIN/shutdown</a></li>\n"
53 " <li><a href=\"#ADMIN_get_alerts\">ADMIN/get_alerts</a></li>\n"
54 " <li><a href=\"#ADMIN_ack_alerts\">ADMIN/ack_alerts</a></li>\n"
55 " <li><a href=\"#ADMIN_statistics\">ADMIN/statistics</a></li>\n"
56 " <li><a href=\"#healthz\">healthz</a></li>\n"
57 " <li><a href=\"#livez\">livez</a></li>\n"
58 " <li><a href=\"#readyz\">readyz</a></li>\n"
59 " <li><a href=\"#_readyz_cassandra\">/readyz/cassandra</a></li>\n"
60 " <li><a href=\"#_readyz_lmdb\">/readyz/lmdb</a></li>\n"
61 " <li><a href=\"#_readyz_wgs\">/readyz/wgs</a></li>\n"
62 " <li><a href=\"#_readyz_cdd\">/readyz/cdd</a></li>\n"
63 " <li><a href=\"#_readyz_snp\">/readyz/snp</a></li>\n"
64 " <li><a href=\"#TEST_io\">TEST/io</a></li>\n"
65 " <li><a href=\"#health\">health</a></li>\n"
66 " <li><a href=\"#deep-health\">deep-health</a></li>\n"
67 " <li><a href=\"#favicon.ico\">favicon.ico</a></li>\n"
68 " <li><a href=\"#unknown\">unknown</a></li>\n"
69 " </ul><a id=\"ID_getblob\"></a><h2>ID/getblob</h2>\n"
70 " <p>Retrieves blob chunks basing on the blob identifier</p>\n"
71 " <table class=\"first-column\">\n"
73 " <th>Parameter</th>\n"
74 " <th>Optional</th>\n"
76 " <th>Description</th>\n"
77 " <th>Allowed Values</th>\n"
82 " <td>mandatory</td>\n"
84 " <td class=\"description\"><sat>.<sat_key>. The blob sat and sat key. Both must be positive integers.</td>\n"
85 " <td>Non empty string. The interpretation of the blob id depends on a processor. Cassandra\n"
86 " processor expects the following format: <sat>.<sat key> where boath are integers</td>\n"
91 " <td>optional</td>\n"
93 " <td class=\"description\">TSE option controls what blob is provided:<br><br><table class=\"nested\">\n"
96 " <td>ID2 split available</td>\n"
97 " <td>ID2 split not available</td>\n"
101 " <td>Nothing</td>\n"
102 " <td>Nothing</td>\n"
106 " <td>Split INFO blob only</td>\n"
107 " <td>Nothing</td>\n"
111 " <td>Split INFO blob only</td>\n"
112 " <td>All Cassandra data chunks of the blob itself</td>\n"
116 " <td>All split blobs</td>\n"
117 " <td>All Cassandra data chunks of the blob itself</td>\n"
121 " <td>All Cassandra data chunks of the blob itself</td>\n"
122 " <td>All Cassandra data chunks of the blob itself</td>\n"
126 " <td>none, whole, orig, smart and slim</td>\n"
130 " <td>last_modified</td>\n"
131 " <td>optional</td>\n"
132 " <td>Integer</td>\n"
133 " <td class=\"description\">The blob last modification. If provided then the exact match will be requested with\n"
134 " the Cassandra storage corresponding field value.</td>\n"
135 " <td>Positive integer. Not provided means that the most recent match will be selected.</td>\n"
139 " <td>use_cache</td>\n"
140 " <td>optional</td>\n"
142 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
143 " affects the seq id resolution step and the blob properties lookup step. The following\n"
144 " options are available:<br><br><table class=\"nested\">\n"
147 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
148 " Cassandra database for the lookups.</td>\n"
152 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
153 " only the LMDB cache.</td>\n"
157 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
161 " <td>yes, no and not provided</td>\n"
165 " <td>include_hup</td>\n"
166 " <td>optional</td>\n"
168 " <td class=\"description\">Explicitly tells the server if it should try to retrieve data from HUP keyspaces.\n"
169 " If data are coming from a secure keyspace then the following logic is used. If the\n"
170 " include_hup option is provided then the decision is made basing on the provided value.\n"
171 " Otherwise a decision is made basing on the presence of the WebCubbyUser cookie. If\n"
172 " it was decided that HUP data needs to be provided then the server uses the WebCubbyUser\n"
173 " cookie value to perform an authorization check.</td>\n"
174 " <td>yes and no</td>\n"
178 " <td>client_id</td>\n"
179 " <td>optional</td>\n"
181 " <td class=\"description\">The client identifier. If provided then the exclude blob feature takes place.</td>\n"
182 " <td>A string identifier</td>\n"
186 " <td>send_blob_if_small</td>\n"
187 " <td>optional</td>\n"
188 " <td>Integer</td>\n"
189 " <td class=\"description\"></td>\n"
190 " <td>An integer greater or equal 0</td>\n"
195 " <td>optional</td>\n"
197 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
198 " <td>yes and no</td>\n"
203 " <td>optional</td>\n"
204 " <td>Integer</td>\n"
205 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n"
206 " <td>An integer greater or equal 0</td>\n"
210 " <td>enable_processor</td>\n"
211 " <td>optional</td>\n"
213 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
214 " repeated as many times as needed.</td>\n"
215 " <td>A string</td>\n"
219 " <td>disable_processor</td>\n"
220 " <td>optional</td>\n"
222 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
223 " be repeated as many times as needed.</td>\n"
224 " <td>A string</td>\n"
228 " <td>processor_events</td>\n"
229 " <td>optional</td>\n"
231 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
232 " <td>yes and no</td>\n"
237 " <p>The PSG protocol is used in the HTTP body. The blob properties and chunks are provided.</p>\n"
238 " <hr><br><br><a id=\"ID_get\"></a><h2>ID/get</h2>\n"
239 " <p>Retrieves blob chunks basing on the seq_id and seq_id_type</p>\n"
240 " <table class=\"first-column\">\n"
242 " <th>Parameter</th>\n"
243 " <th>Optional</th>\n"
245 " <th>Description</th>\n"
246 " <th>Allowed Values</th>\n"
247 " <th>Default</th>\n"
251 " <td>mandatory</td>\n"
253 " <td class=\"description\">Sequence identifier</td>\n"
254 " <td>A string identifier</td>\n"
258 " <td>seq_id_type</td>\n"
259 " <td>optional</td>\n"
260 " <td>Integer</td>\n"
261 " <td class=\"description\">Sequence identifier type</td>\n"
262 " <td>Integer type greater than 0</td>\n"
266 " <td>use_cache</td>\n"
267 " <td>optional</td>\n"
269 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
270 " affects the seq id resolution step and the blob properties lookup step. The following\n"
271 " options are available:<br><br><table class=\"nested\">\n"
274 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
275 " Cassandra database for the lookups.</td>\n"
279 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
280 " only the LMDB cache.</td>\n"
284 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
288 " <td>yes, no and not provided</td>\n"
293 " <td>optional</td>\n"
295 " <td class=\"description\">TSE option controls what blob is provided:<br><br><table class=\"nested\">\n"
298 " <td>ID2 split available</td>\n"
299 " <td>ID2 split not available</td>\n"
303 " <td>Nothing</td>\n"
304 " <td>Nothing</td>\n"
308 " <td>Split INFO blob only</td>\n"
309 " <td>Nothing</td>\n"
313 " <td>Split INFO blob only</td>\n"
314 " <td>All Cassandra data chunks of the blob itself</td>\n"
318 " <td>All split blobs</td>\n"
319 " <td>All Cassandra data chunks of the blob itself</td>\n"
323 " <td>All Cassandra data chunks of the blob itself</td>\n"
324 " <td>All Cassandra data chunks of the blob itself</td>\n"
328 " <td>none, whole, orig, smart and slim</td>\n"
332 " <td>exclude_blobs</td>\n"
333 " <td>optional</td>\n"
335 " <td class=\"description\">A comma separated list of blob identifiers which client already has. If provided then\n"
336 " if the resolution of sequence identifier/sequence identifier type matches one of the\n"
337 " blob identifiers in the list then the blob will not be sent. The format of the blob\n"
338 " identifier depends on a processor. For example, a Cassandra processor expects the\n"
339 " format as <sat>.<sat key> where both of them are integers. Note: it works in conjunction\n"
340 " with the client_id parameter.</td>\n"
341 " <td>A list of blob indentifiers</td>\n"
345 " <td>client_id</td>\n"
346 " <td>optional</td>\n"
348 " <td class=\"description\">The client identifier. If provided then the exclude blob feature takes place.</td>\n"
349 " <td>A string identifier</td>\n"
353 " <td>acc_substitution</td>\n"
354 " <td>optional</td>\n"
356 " <td class=\"description\">The option controls how the bioseq info accession substitution is done. If the substitution\n"
357 " is needed then the seq_ids list is analyzed. If there is one with Gi then it is taken\n"
358 " for substitution. Otherwise an arbitrary one is picked. The supported policy values\n"
359 " are:<br><br><table class=\"nested\">\n"
361 " <td>default</td>\n"
362 " <td>substitute if version value (version <= 0) or seq_id_type is Gi(12)</td>\n"
365 " <td>limited</td>\n"
366 " <td>substitute only if the resolved record's seq_id_type is GI(12)</td>\n"
370 " <td>the accession substitution is never done</td>\n"
374 " <td>limited, never or default</td>\n"
375 " <td>default</td>\n"
378 " <td>send_blob_if_small</td>\n"
379 " <td>optional</td>\n"
380 " <td>Integer</td>\n"
381 " <td class=\"description\"></td>\n"
382 " <td>An integer greater or equal 0</td>\n"
386 " <td>resend_timeout</td>\n"
387 " <td>optional</td>\n"
389 " <td class=\"description\">If the blob has already been sent to the client more than this time ago then the blob\n"
390 " will be sent anyway. If less then the 'already sent' reply will have an additional\n"
391 " field 'sent_seconds_ago' with the corresponding value. The special value 0 means that\n"
392 " the blob will be sent regardless when it was already sent.</td>\n"
393 " <td>Floating point value greater or equal 0.0</td>\n"
394 " <td>Taken from [SERVER]/resend_timeout configuration setting</td>\n"
397 " <td>seq_id_resolve</td>\n"
398 " <td>optional</td>\n"
400 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n"
401 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n"
402 " <td>yes and no</td>\n"
406 " <td>include_hup</td>\n"
407 " <td>optional</td>\n"
409 " <td class=\"description\">Explicitly tells the server if it should try to retrieve data from HUP keyspaces.\n"
410 " If data are coming from a secure keyspace then the following logic is used. If the\n"
411 " include_hup option is provided then the decision is made basing on the provided value.\n"
412 " Otherwise a decision is made basing on the presence of the WebCubbyUser cookie. If\n"
413 " it was decided that HUP data needs to be provided then the server uses the WebCubbyUser\n"
414 " cookie value to perform an authorization check.</td>\n"
415 " <td>yes and no</td>\n"
420 " <td>optional</td>\n"
422 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
423 " <td>yes and no</td>\n"
428 " <td>optional</td>\n"
429 " <td>Integer</td>\n"
430 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n"
431 " <td>An integer greater or equal 0</td>\n"
435 " <td>enable_processor</td>\n"
436 " <td>optional</td>\n"
438 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
439 " repeated as many times as needed.</td>\n"
440 " <td>A string</td>\n"
444 " <td>disable_processor</td>\n"
445 " <td>optional</td>\n"
447 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
448 " be repeated as many times as needed.</td>\n"
449 " <td>A string</td>\n"
453 " <td>processor_events</td>\n"
454 " <td>optional</td>\n"
456 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
457 " <td>yes and no</td>\n"
462 " <p>The PSG protocol is used in the HTTP body. The bioseq info, blob properties and chunks\n"
463 " are provided.</p>\n"
464 " <hr><br><br><a id=\"ID_get_tse_chunk\"></a><h2>ID/get_tse_chunk</h2>\n"
465 " <p>Retrieves a TSE blob chunk</p>\n"
466 " <table class=\"first-column\">\n"
468 " <th>Parameter</th>\n"
469 " <th>Optional</th>\n"
471 " <th>Description</th>\n"
472 " <th>Allowed Values</th>\n"
473 " <th>Default</th>\n"
476 " <td>id2_chunk</td>\n"
477 " <td>mandatory</td>\n"
478 " <td>Integer</td>\n"
479 " <td class=\"description\">The tse blob chunk number. The Cassandra processor recognizes a special value of 999999999\n"
480 " for the parameter. In this case the effective chunk number will be taken from the\n"
481 " id2_info parameter</td>\n"
482 " <td>Integer greater or equal 0. Some processors may introduce more strict rules. For example,\n"
483 " Cassandra processor requires the chunk number to be greater than 0.</td>\n"
487 " <td>id2_info</td>\n"
488 " <td>mandatory</td>\n"
490 " <td class=\"description\">The following formats are recognized:<br><br><table class=\"nested\">\n"
492 " <td>Cassandra processor, option 1</td>\n"
493 " <td>3 or 4 integers separated by '.': <sat>.<info>.<chunks>[.<split version>]</td>\n"
496 " <td>Cassandra processor, option 2</td>\n"
497 " <td>psg~~tse_id-<sat>.<sat key>[~~tse_last_modified-<int>[~~tse_split_version-<int>]</td>\n"
500 " <td>Other processors</td>\n"
501 " <td>id2~~tse_id-<string>~~tse_last_modified-<int>~~tse_split_version-<int></td>\n"
505 " <td>A string in a format recognisable by one of the processors</td>\n"
509 " <td>use_cache</td>\n"
510 " <td>optional</td>\n"
512 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
513 " affects the seq id resolution step and the blob properties lookup step. The following\n"
514 " options are available:<br><br><table class=\"nested\">\n"
517 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
518 " Cassandra database for the lookups.</td>\n"
522 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
523 " only the LMDB cache.</td>\n"
527 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
531 " <td>yes, no and not provided</td>\n"
535 " <td>include_hup</td>\n"
536 " <td>optional</td>\n"
538 " <td class=\"description\">Explicitly tells the server if it should try to retrieve data from HUP keyspaces.\n"
539 " If data are coming from a secure keyspace then the following logic is used. If the\n"
540 " include_hup option is provided then the decision is made basing on the provided value.\n"
541 " Otherwise a decision is made basing on the presence of the WebCubbyUser cookie. If\n"
542 " it was decided that HUP data needs to be provided then the server uses the WebCubbyUser\n"
543 " cookie value to perform an authorization check.</td>\n"
544 " <td>yes and no</td>\n"
549 " <td>optional</td>\n"
551 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
552 " <td>yes and no</td>\n"
557 " <td>optional</td>\n"
558 " <td>Integer</td>\n"
559 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n"
560 " <td>An integer greater or equal 0</td>\n"
564 " <td>enable_processor</td>\n"
565 " <td>optional</td>\n"
567 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
568 " repeated as many times as needed.</td>\n"
569 " <td>A string</td>\n"
573 " <td>disable_processor</td>\n"
574 " <td>optional</td>\n"
576 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
577 " be repeated as many times as needed.</td>\n"
578 " <td>A string</td>\n"
582 " <td>processor_events</td>\n"
583 " <td>optional</td>\n"
585 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
586 " <td>yes and no</td>\n"
591 " <p>The PSG protocol is used in the HTTP body. The blob properties and chunks are provided.</p>\n"
592 " <hr><br><br><a id=\"ID_resolve\"></a><h2>ID/resolve</h2>\n"
593 " <p>Resolve seq_id and provide bioseq info</p>\n"
594 " <table class=\"first-column\">\n"
596 " <th>Parameter</th>\n"
597 " <th>Optional</th>\n"
599 " <th>Description</th>\n"
600 " <th>Allowed Values</th>\n"
601 " <th>Default</th>\n"
605 " <td>mandatory</td>\n"
607 " <td class=\"description\">Sequence identifier</td>\n"
608 " <td>A string identifier</td>\n"
612 " <td>seq_id_type</td>\n"
613 " <td>optional</td>\n"
614 " <td>Integer</td>\n"
615 " <td class=\"description\">Sequence identifier type</td>\n"
616 " <td>Integer type greater than 0</td>\n"
620 " <td>use_cache</td>\n"
621 " <td>optional</td>\n"
623 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
624 " affects the seq id resolution step and the blob properties lookup step. The following\n"
625 " options are available:<br><br><table class=\"nested\">\n"
628 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
629 " Cassandra database for the lookups.</td>\n"
633 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
634 " only the LMDB cache.</td>\n"
638 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
642 " <td>yes, no and not provided</td>\n"
647 " <td>optional</td>\n"
649 " <td class=\"description\">The format of the data sent to the client. Available options:<br><br><table class=\"nested\">\n"
651 " <td>protobuf</td>\n"
652 " <td>bioseq info will be sent as a protobuf binary data</td>\n"
656 " <td>bioseq info will be sent as a serialized JSON dictionary</td>\n"
660 " <td>the server decides what format to use: protobuf or json</td>\n"
664 " <td>protobuf, json or native</td>\n"
668 " <td>all_info</td>\n"
669 " <td>optional</td>\n"
671 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
673 " <td>yes and no</td>\n"
677 " <td>canon_id</td>\n"
678 " <td>optional</td>\n"
680 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
682 " <td>yes and no</td>\n"
686 " <td>seq_ids</td>\n"
687 " <td>optional</td>\n"
689 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
691 " <td>yes and no</td>\n"
695 " <td>mol_type</td>\n"
696 " <td>optional</td>\n"
698 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
700 " <td>yes and no</td>\n"
705 " <td>optional</td>\n"
707 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
709 " <td>yes and no</td>\n"
714 " <td>optional</td>\n"
716 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
718 " <td>yes and no</td>\n"
722 " <td>blob_id</td>\n"
723 " <td>optional</td>\n"
725 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
727 " <td>yes and no</td>\n"
732 " <td>optional</td>\n"
734 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
736 " <td>yes and no</td>\n"
741 " <td>optional</td>\n"
743 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
745 " <td>yes and no</td>\n"
749 " <td>date_changed</td>\n"
750 " <td>optional</td>\n"
752 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
754 " <td>yes and no</td>\n"
759 " <td>optional</td>\n"
761 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
763 " <td>yes and no</td>\n"
768 " <td>optional</td>\n"
770 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
772 " <td>yes and no</td>\n"
776 " <td>seq_state</td>\n"
777 " <td>optional</td>\n"
779 " <td class=\"description\">A flag to specify explicitly what values to include/exclude from the provided bioseq\n"
781 " <td>yes and no</td>\n"
785 " <td>acc_substitution</td>\n"
786 " <td>optional</td>\n"
788 " <td class=\"description\">The option controls how the bioseq info accession substitution is done. If the substitution\n"
789 " is needed then the seq_ids list is analyzed. If there is one with Gi then it is taken\n"
790 " for substitution. Otherwise an arbitrary one is picked. The supported policy values\n"
791 " are:<br><br><table class=\"nested\">\n"
793 " <td>default</td>\n"
794 " <td>substitute if version value (version <= 0) or seq_id_type is Gi(12)</td>\n"
797 " <td>limited</td>\n"
798 " <td>substitute only if the resolved record's seq_id_type is GI(12)</td>\n"
802 " <td>the accession substitution is never done</td>\n"
806 " <td>limited, never or default</td>\n"
807 " <td>default</td>\n"
810 " <td>seq_id_resolve</td>\n"
811 " <td>optional</td>\n"
813 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n"
814 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n"
815 " <td>yes and no</td>\n"
820 " <td>optional</td>\n"
822 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
823 " <td>yes and no</td>\n"
828 " <td>optional</td>\n"
829 " <td>Integer</td>\n"
830 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n"
831 " <td>An integer greater or equal 0</td>\n"
835 " <td>enable_processor</td>\n"
836 " <td>optional</td>\n"
838 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
839 " repeated as many times as needed.</td>\n"
840 " <td>A string</td>\n"
844 " <td>disable_processor</td>\n"
845 " <td>optional</td>\n"
847 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
848 " be repeated as many times as needed.</td>\n"
849 " <td>A string</td>\n"
853 " <td>processor_events</td>\n"
854 " <td>optional</td>\n"
856 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
857 " <td>yes and no</td>\n"
862 " <p>The bioseq info is sent back in the HTTP body as binary protobuf or as PSG protocol\n"
863 " chunks depending on the protocol choice</p>\n"
864 " <hr><br><br><a id=\"ID_get_na\"></a><h2>ID/get_na</h2>\n"
865 " <p>Retrieves named annotations</p>\n"
866 " <table class=\"first-column\">\n"
868 " <th>Parameter</th>\n"
869 " <th>Optional</th>\n"
871 " <th>Description</th>\n"
872 " <th>Allowed Values</th>\n"
873 " <th>Default</th>\n"
877 " <td>optional</td>\n"
879 " <td class=\"description\">Sequence identifier. This or seq_ids parameter value must be provided for the request.</td>\n"
880 " <td>A string identifier</td>\n"
884 " <td>seq_ids</td>\n"
885 " <td>optional</td>\n"
887 " <td class=\"description\">A space separated list of the sequence identifier synonims. This or seq_id parameter\n"
888 " value must be provided for the request.</td>\n"
889 " <td>A list of space separated string identifiers</td>\n"
893 " <td>seq_id_type</td>\n"
894 " <td>optional</td>\n"
895 " <td>Integer</td>\n"
896 " <td class=\"description\">Sequence identifier type</td>\n"
897 " <td>Integer type greater than 0</td>\n"
902 " <td>mandatory</td>\n"
904 " <td class=\"description\">A comma separated list of named annotations to be retrieved.</td>\n"
905 " <td>A string</td>\n"
909 " <td>use_cache</td>\n"
910 " <td>optional</td>\n"
912 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
913 " affects the seq id resolution step and the blob properties lookup step. The following\n"
914 " options are available:<br><br><table class=\"nested\">\n"
917 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
918 " Cassandra database for the lookups.</td>\n"
922 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
923 " only the LMDB cache.</td>\n"
927 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
931 " <td>yes, no and not provided</td>\n"
936 " <td>optional</td>\n"
938 " <td class=\"description\">The format of the data sent to the client. Available options:<br><br><table class=\"nested\">\n"
940 " <td>protobuf</td>\n"
941 " <td>bioseq info will be sent as a protobuf binary data</td>\n"
945 " <td>bioseq info will be sent as a serialized JSON dictionary</td>\n"
949 " <td>the server decides what format to use: protobuf or json</td>\n"
953 " <td>protobuf, json or native</td>\n"
958 " <td>optional</td>\n"
960 " <td class=\"description\">TSE option controls what blob is provided:<br><br><table class=\"nested\">\n"
963 " <td>ID2 split available</td>\n"
964 " <td>ID2 split not available</td>\n"
968 " <td>Nothing</td>\n"
969 " <td>Nothing</td>\n"
973 " <td>Split INFO blob only</td>\n"
974 " <td>Nothing</td>\n"
978 " <td>Split INFO blob only</td>\n"
979 " <td>All Cassandra data chunks of the blob itself</td>\n"
983 " <td>All split blobs</td>\n"
984 " <td>All Cassandra data chunks of the blob itself</td>\n"
988 " <td>All Cassandra data chunks of the blob itself</td>\n"
989 " <td>All Cassandra data chunks of the blob itself</td>\n"
993 " <td>none, whole, orig, smart and slim</td>\n"
997 " <td>client_id</td>\n"
998 " <td>optional</td>\n"
1000 " <td class=\"description\">The client identifier. If provided then the exclude blob feature takes place.</td>\n"
1001 " <td>A string identifier</td>\n"
1005 " <td>send_blob_if_small</td>\n"
1006 " <td>optional</td>\n"
1007 " <td>Integer</td>\n"
1008 " <td class=\"description\"></td>\n"
1009 " <td>An integer greater or equal 0</td>\n"
1013 " <td>seq_id_resolve</td>\n"
1014 " <td>optional</td>\n"
1015 " <td>String</td>\n"
1016 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n"
1017 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n"
1018 " <td>yes and no</td>\n"
1022 " <td>resend_timeout</td>\n"
1023 " <td>optional</td>\n"
1025 " <td class=\"description\">If the blob has already been sent to the client more than this time ago then the blob\n"
1026 " will be sent anyway. If less then the 'already sent' reply will have an additional\n"
1027 " field 'sent_seconds_ago' with the corresponding value. The special value 0 means that\n"
1028 " the blob will be sent regardless when it was already sent.</td>\n"
1029 " <td>Floating point value greater or equal 0.0</td>\n"
1030 " <td>Taken from [SERVER]/resend_timeout configuration setting</td>\n"
1033 " <td>snp_scale_limit</td>\n"
1034 " <td>optional</td>\n"
1035 " <td>String</td>\n"
1036 " <td class=\"description\">GenBank ID2 SNP reader parameter</td>\n"
1037 " <td>chromosome, contig, supercontig, unit and not provided</td>\n"
1042 " <td>optional</td>\n"
1043 " <td>String</td>\n"
1044 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
1045 " <td>yes and no</td>\n"
1050 " <td>optional</td>\n"
1051 " <td>Integer</td>\n"
1052 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n"
1053 " <td>An integer greater or equal 0</td>\n"
1057 " <td>enable_processor</td>\n"
1058 " <td>optional</td>\n"
1059 " <td>String</td>\n"
1060 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
1061 " repeated as many times as needed.</td>\n"
1062 " <td>A string</td>\n"
1066 " <td>disable_processor</td>\n"
1067 " <td>optional</td>\n"
1068 " <td>String</td>\n"
1069 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
1070 " be repeated as many times as needed.</td>\n"
1071 " <td>A string</td>\n"
1075 " <td>processor_events</td>\n"
1076 " <td>optional</td>\n"
1077 " <td>String</td>\n"
1078 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
1079 " <td>yes and no</td>\n"
1084 " <p>The PSG protocol is used in the HTTP body. The bioseq info and named annotation chunks\n"
1085 " are provided.</p>\n"
1086 " <hr><br><br><a id=\"ID_get_acc_ver_history\"></a><h2>ID/get_acc_ver_history</h2>\n"
1087 " <p>Retrieves accession version history</p>\n"
1088 " <table class=\"first-column\">\n"
1090 " <th>Parameter</th>\n"
1091 " <th>Optional</th>\n"
1093 " <th>Description</th>\n"
1094 " <th>Allowed Values</th>\n"
1095 " <th>Default</th>\n"
1098 " <td>seq_id</td>\n"
1099 " <td>mandatory</td>\n"
1100 " <td>String</td>\n"
1101 " <td class=\"description\">Sequence identifier</td>\n"
1102 " <td>A string identifier</td>\n"
1106 " <td>seq_id_type</td>\n"
1107 " <td>optional</td>\n"
1108 " <td>Integer</td>\n"
1109 " <td class=\"description\">Sequence identifier type</td>\n"
1110 " <td>Integer type greater than 0</td>\n"
1114 " <td>use_cache</td>\n"
1115 " <td>optional</td>\n"
1116 " <td>String</td>\n"
1117 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
1118 " affects the seq id resolution step and the blob properties lookup step. The following\n"
1119 " options are available:<br><br><table class=\"nested\">\n"
1122 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
1123 " Cassandra database for the lookups.</td>\n"
1127 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
1128 " only the LMDB cache.</td>\n"
1132 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
1136 " <td>yes, no and not provided</td>\n"
1141 " <td>optional</td>\n"
1142 " <td>String</td>\n"
1143 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
1144 " <td>yes and no</td>\n"
1149 " <td>optional</td>\n"
1150 " <td>Integer</td>\n"
1151 " <td class=\"description\">A numbers of hops before the request reached the server</td>\n"
1152 " <td>An integer greater or equal 0</td>\n"
1156 " <td>enable_processor</td>\n"
1157 " <td>optional</td>\n"
1158 " <td>String</td>\n"
1159 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
1160 " repeated as many times as needed.</td>\n"
1161 " <td>A string</td>\n"
1165 " <td>disable_processor</td>\n"
1166 " <td>optional</td>\n"
1167 " <td>String</td>\n"
1168 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
1169 " be repeated as many times as needed.</td>\n"
1170 " <td>A string</td>\n"
1174 " <td>processor_events</td>\n"
1175 " <td>optional</td>\n"
1176 " <td>String</td>\n"
1177 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
1178 " <td>yes and no</td>\n"
1183 " <p>The PSG protocol is used in the HTTP body. The bioseq info and accession version history\n"
1184 " chunks are provided.</p>\n"
1185 " <hr><br><br><a id=\"IPG_resolve\"></a><h2>IPG/resolve</h2>\n"
1186 " <p>Resolve nucleotide/protein/ipg and provide ipg info</p>\n"
1187 " <table class=\"first-column\">\n"
1189 " <th>Parameter</th>\n"
1190 " <th>Optional</th>\n"
1192 " <th>Description</th>\n"
1193 " <th>Allowed Values</th>\n"
1194 " <th>Default</th>\n"
1197 " <td>protein</td>\n"
1198 " <td>mandatory</td>\n"
1199 " <td>String</td>\n"
1200 " <td class=\"description\">The protein to be resolved. It may be ommitted if ipg is provided.</td>\n"
1201 " <td>A string identifier</td>\n"
1205 " <td>nucleotide</td>\n"
1206 " <td>optional</td>\n"
1207 " <td>String</td>\n"
1208 " <td class=\"description\">The nucleotide to be resolved.</td>\n"
1209 " <td>A string identifier</td>\n"
1214 " <td>mandatory</td>\n"
1215 " <td>Integer</td>\n"
1216 " <td class=\"description\">The ipg to be resolved. It may be ommitted if protein is provided.</td>\n"
1217 " <td>An integer greater than 0</td>\n"
1221 " <td>use_cache</td>\n"
1222 " <td>optional</td>\n"
1223 " <td>String</td>\n"
1224 " <td class=\"description\">The option controls if the Cassandra LMDB cache and/or database should be used. It\n"
1225 " affects the seq id resolution step and the blob properties lookup step. The following\n"
1226 " options are available:<br><br><table class=\"nested\">\n"
1229 " <td>do not use LMDB cache (tables SI2CSI, BIOSEQ_INFO and BLOB_PROP) at all; use only\n"
1230 " Cassandra database for the lookups.</td>\n"
1234 " <td>do not use tables SI2CSI, BIOSEQ_INFO and BLOB_PROP in the Cassandra database; use\n"
1235 " only the LMDB cache.</td>\n"
1239 " <td>use the LMDB cache if at all possible; then, fallback to Cassandra storage.</td>\n"
1243 " <td>yes, no and not provided</td>\n"
1247 " <td>seq_id_resolve</td>\n"
1248 " <td>optional</td>\n"
1249 " <td>String</td>\n"
1250 " <td class=\"description\">If yes then use the full resolution procedure using all provided sequence identifiers.\n"
1251 " Otherwise use only bioseq info table and GI sequence identifiers.</td>\n"
1252 " <td>yes and no</td>\n"
1257 " <td>optional</td>\n"
1258 " <td>String</td>\n"
1259 " <td class=\"description\">The option to include trace messages to the server output</td>\n"
1260 " <td>yes and no</td>\n"
1264 " <td>enable_processor</td>\n"
1265 " <td>optional</td>\n"
1266 " <td>String</td>\n"
1267 " <td class=\"description\">A name of a processor which is allowed to process a request. The parameter can be\n"
1268 " repeated as many times as needed.</td>\n"
1269 " <td>A string</td>\n"
1273 " <td>disable_processor</td>\n"
1274 " <td>optional</td>\n"
1275 " <td>String</td>\n"
1276 " <td class=\"description\">A name of a processor which is disallowed to process a request. The parameter can\n"
1277 " be repeated as many times as needed.</td>\n"
1278 " <td>A string</td>\n"
1282 " <td>processor_events</td>\n"
1283 " <td>optional</td>\n"
1284 " <td>String</td>\n"
1285 " <td class=\"description\">Switch on/off additional reply chunks which tell about the processor</td>\n"
1286 " <td>yes and no</td>\n"
1291 " <p>The ipg record(s) is sent baback in the HTTP body as PSG protocol chunks</p>\n"
1292 " <hr><br><br><a id=\"ADMIN_config\"></a><h2>ADMIN/config</h2>\n"
1293 " <p>Provides the server configuration information</p>\n"
1295 " <p>The HTTP body is a JSON dictionary with the configuration information. The request\n"
1296 " may be configured as protected in the server settings. If so then the server will\n"
1297 " use the value of the AdminAuthToken cookie to check permissions.</p>\n"
1298 " <hr><br><br><a id=\"ADMIN_info\"></a><h2>ADMIN/info</h2>\n"
1299 " <p>Provides the server run-time information</p>\n"
1301 " <p>The HTTP body is a JSON dictionary with the run-time information like resource consumption.\n"
1302 " The request may be configured as protected in the server settings. If so then the\n"
1303 " server will use the value of the AdminAuthToken cookie to check permissions.</p>\n"
1304 " <hr><br><br><a id=\"ADMIN_status\"></a><h2>ADMIN/status</h2>\n"
1305 " <p>Provides the server event counters</p>\n"
1307 " <p>The HTTP body is a JSON dictionary with various event counters. The request may be\n"
1308 " configured as protected in the server settings. If so then the server will use the\n"
1309 " value of the AdminAuthToken cookie to check permissions.</p>\n"
1310 " <hr><br><br><a id=\"ADMIN_shutdown\"></a><h2>ADMIN/shutdown</h2>\n"
1311 " <p>Performs the server shutdown</p>\n"
1312 " <table class=\"first-column\">\n"
1314 " <th>Parameter</th>\n"
1315 " <th>Optional</th>\n"
1317 " <th>Description</th>\n"
1318 " <th>Allowed Values</th>\n"
1319 " <th>Default</th>\n"
1322 " <td>username</td>\n"
1323 " <td>optional</td>\n"
1324 " <td>String</td>\n"
1325 " <td class=\"description\">The user name who requested the shutdown</td>\n"
1326 " <td>A string identifier</td>\n"
1330 " <td>auth_token</td>\n"
1331 " <td>optional</td>\n"
1332 " <td>String</td>\n"
1333 " <td class=\"description\">Authorization token. If the configuration [ADMIN]/auth_token value is configured then\n"
1334 " the request must have the token value matching the configured to be granted.</td>\n"
1335 " <td>A string identifier</td>\n"
1339 " <td>timeout</td>\n"
1340 " <td>optional</td>\n"
1341 " <td>Integer</td>\n"
1342 " <td class=\"description\">The timeout in seconds within which the shutdown must be performed. If 0 then it leads\n"
1343 " to an immediate shutdown. If 1 or more seconds then the server will reject all new\n"
1344 " requests and wait till the timeout is over or all the pending requests are completed\n"
1345 " and then do the shutdown.</td>\n"
1346 " <td>An integer greater or equal 0</td>\n"
1351 " <p>The standard HTTP protocol is used. The request may be configured as protected in\n"
1352 " the server settings. If so then the server will use the value of the AdminAuthToken\n"
1353 " cookie to check permissions.</p>\n"
1354 " <hr><br><br><a id=\"ADMIN_get_alerts\"></a><h2>ADMIN/get_alerts</h2>\n"
1355 " <p>Provides the server alerts</p>\n"
1357 " <p>The HTTP body is a JSON dictionary with the current server alerts. The request may\n"
1358 " be configured as protected in the server settings. If so then the server will use\n"
1359 " the value of the AdminAuthToken cookie to check permissions.</p>\n"
1360 " <hr><br><br><a id=\"ADMIN_ack_alerts\"></a><h2>ADMIN/ack_alerts</h2>\n"
1361 " <p>Acknowledge an alert</p>\n"
1362 " <table class=\"first-column\">\n"
1364 " <th>Parameter</th>\n"
1365 " <th>Optional</th>\n"
1367 " <th>Description</th>\n"
1368 " <th>Allowed Values</th>\n"
1369 " <th>Default</th>\n"
1373 " <td>mandatory</td>\n"
1374 " <td>String</td>\n"
1375 " <td class=\"description\">The alert identifier to acknowledge</td>\n"
1376 " <td>A string identifier</td>\n"
1380 " <td>username</td>\n"
1381 " <td>mandatory</td>\n"
1382 " <td>String</td>\n"
1383 " <td class=\"description\">The user name who acknowledges the alert</td>\n"
1384 " <td>A string identifier</td>\n"
1389 " <p>The standard HTTP protocol is used. The request may be configured as protected in\n"
1390 " the server settings. If so then the server will use the value of the AdminAuthToken\n"
1391 " cookie to check permissions.</p>\n"
1392 " <hr><br><br><a id=\"ADMIN_statistics\"></a><h2>ADMIN/statistics</h2>\n"
1393 " <p>Provides the server collected statistics</p>\n"
1394 " <table class=\"first-column\">\n"
1396 " <th>Parameter</th>\n"
1397 " <th>Optional</th>\n"
1399 " <th>Description</th>\n"
1400 " <th>Allowed Values</th>\n"
1401 " <th>Default</th>\n"
1405 " <td>optional</td>\n"
1406 " <td>String</td>\n"
1407 " <td class=\"description\">If provided then the collected statistics is rest. Otherwise the collected statistics\n"
1408 " is sent to the client.</td>\n"
1409 " <td>yes and no</td>\n"
1413 " <td>most_recent_time</td>\n"
1414 " <td>optional</td>\n"
1415 " <td>Integer</td>\n"
1416 " <td class=\"description\">Number of seconds in the past for the most recent time range limit</td>\n"
1417 " <td>An integer greater or equal 0</td>\n"
1421 " <td>most_ancient_time</td>\n"
1422 " <td>optional</td>\n"
1423 " <td>Integer</td>\n"
1424 " <td class=\"description\">Number of seconds in the past for the most ancient time range limit</td>\n"
1425 " <td>An integer greater or equal 0</td>\n"
1426 " <td>Effectively infinity, max integer</td>\n"
1429 " <td>histogram_names</td>\n"
1430 " <td>optional</td>\n"
1431 " <td>String</td>\n"
1432 " <td class=\"description\">Comma separated list of the histogram names. If provided then the server returns all\n"
1433 " existing histograms (listed in histogram_names) which intersect with the specified\n"
1434 " time period.</td>\n"
1435 " <td>A comma separated list of string identifiers</td>\n"
1439 " <td>time_series</td>\n"
1440 " <td>optional</td>\n"
1441 " <td>String</td>\n"
1442 " <td class=\"description\">Describes the aggregation of the per-minute data collected by the server. Format:\n"
1443 " <int>:<int>[ <int:<int>]* <int>:\n"
1444 " There are pairs of integers divided by ':'. The pairs are divided by spaces. The first\n"
1445 " integer is how many minutes to be aggregated, the second integer is the last index\n"
1446 " of the data sequence to be aggregated. For each aggregation the server calculates\n"
1447 " the average number of requests per second. The last pair must not have the second\n"
1448 " integer - this is an item which describes the aggregation till the end of the available\n"
1449 " data. A special value is also supported: no. This value means that the server will\n"
1450 " not send time series data at all.</td>\n"
1451 " <td>no or aggregation description string</td>\n"
1452 " <td>1:59 5:1439 60:</td>\n"
1456 " <p>The HTTP body is a JSON dictionary with the collected statistics information. The\n"
1457 " request may be configured as protected in the server settings. If so then the server\n"
1458 " will use the value of the AdminAuthToken cookie to check permissions.</p>\n"
1459 " <hr><br><br><a id=\"healthz\"></a><h2>healthz</h2>\n"
1460 " <p>Performs a functionality check. It can be used by monitoring facilities.</p>\n"
1461 " <table class=\"first-column\">\n"
1463 " <th>Parameter</th>\n"
1464 " <th>Optional</th>\n"
1466 " <th>Description</th>\n"
1467 " <th>Allowed Values</th>\n"
1468 " <th>Default</th>\n"
1471 " <td>verbose</td>\n"
1472 " <td>optional</td>\n"
1474 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n"
1475 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n"
1476 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n"
1481 " <td>exclude</td>\n"
1482 " <td>optional</td>\n"
1483 " <td>String</td>\n"
1484 " <td class=\"description\">A name of a check which should not be performed. The parameter can be repeated as\n"
1485 " many times as needed.</td>\n"
1486 " <td>A string</td>\n"
1491 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n"
1492 " status is set to 500. If verbose flag is provided then the HTTP body contains a JSON\n"
1493 " dictionary with detailed information.</p>\n"
1494 " <hr><br><br><a id=\"livez\"></a><h2>livez</h2>\n"
1495 " <p>Performs a live check. It can be used by monitoring facilities.</p>\n"
1496 " <table class=\"first-column\">\n"
1498 " <th>Parameter</th>\n"
1499 " <th>Optional</th>\n"
1501 " <th>Description</th>\n"
1502 " <th>Allowed Values</th>\n"
1503 " <th>Default</th>\n"
1506 " <td>verbose</td>\n"
1507 " <td>optional</td>\n"
1509 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n"
1510 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n"
1511 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n"
1517 " <p>HTTP status is set to 200 if the live check succeeded. Otherwise the HTTP status is\n"
1518 " set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n"
1519 " with detailed information.</p>\n"
1520 " <hr><br><br><a id=\"readyz\"></a><h2>readyz</h2>\n"
1521 " <p>Performs a functionality check. It can be used by monitoring facilities.</p>\n"
1522 " <table class=\"first-column\">\n"
1524 " <th>Parameter</th>\n"
1525 " <th>Optional</th>\n"
1527 " <th>Description</th>\n"
1528 " <th>Allowed Values</th>\n"
1529 " <th>Default</th>\n"
1532 " <td>verbose</td>\n"
1533 " <td>optional</td>\n"
1535 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n"
1536 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n"
1537 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n"
1542 " <td>exclude</td>\n"
1543 " <td>optional</td>\n"
1544 " <td>String</td>\n"
1545 " <td class=\"description\">A name of a check which should not be performed. The parameter can be repeated as\n"
1546 " many times as needed.</td>\n"
1547 " <td>A string</td>\n"
1552 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n"
1553 " status is set to 500. If verbose flag is provided then the HTTP body contains a JSON\n"
1554 " dictionary with detailed information.</p>\n"
1555 " <hr><br><br><a id=\"_readyz_cassandra\"></a><h2>/readyz/cassandra</h2>\n"
1556 " <p>Performs a cassandra retrieval check. It can be used by monitoring facilities.</p>\n"
1557 " <table class=\"first-column\">\n"
1559 " <th>Parameter</th>\n"
1560 " <th>Optional</th>\n"
1562 " <th>Description</th>\n"
1563 " <th>Allowed Values</th>\n"
1564 " <th>Default</th>\n"
1567 " <td>verbose</td>\n"
1568 " <td>optional</td>\n"
1570 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n"
1571 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n"
1572 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n"
1578 " <p>HTTP status is set to 200 if cassandra retrieval is ok. Otherwise the HTTP status\n"
1579 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n"
1580 " with detailed information.</p>\n"
1581 " <hr><br><br><a id=\"_readyz_lmdb\"></a><h2>/readyz/lmdb</h2>\n"
1582 " <p>Performs an LMDB retrieval check. It can be used by monitoring facilities.</p>\n"
1583 " <table class=\"first-column\">\n"
1585 " <th>Parameter</th>\n"
1586 " <th>Optional</th>\n"
1588 " <th>Description</th>\n"
1589 " <th>Allowed Values</th>\n"
1590 " <th>Default</th>\n"
1593 " <td>verbose</td>\n"
1594 " <td>optional</td>\n"
1596 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n"
1597 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n"
1598 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n"
1604 " <p>HTTP status is set to 200 if LMDB retrieval check succeeded. Otherwise the HTTP status\n"
1605 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n"
1606 " with detailed information.</p>\n"
1607 " <hr><br><br><a id=\"_readyz_wgs\"></a><h2>/readyz/wgs</h2>\n"
1608 " <p>Performs a WGS retrieval check. It can be used by monitoring facilities.</p>\n"
1609 " <table class=\"first-column\">\n"
1611 " <th>Parameter</th>\n"
1612 " <th>Optional</th>\n"
1614 " <th>Description</th>\n"
1615 " <th>Allowed Values</th>\n"
1616 " <th>Default</th>\n"
1619 " <td>verbose</td>\n"
1620 " <td>optional</td>\n"
1622 " <td class=\"description\">This is a flag parameter, no value is needed (if value is provided then it will be\n"
1623 " silently ignored). If the flag is provided then the reply HTTP body will contain a\n"
1624 " JSON dictionary, Otherwise the reply HTTP body will be empty</td>\n"
1630 " <p>HTTP status is set to 200 if WGS retrieval check succeeded. Otherwise the HTTP status\n"
1631 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n"
1632 " with detailed information.</p>\n"
1633 " <hr><br><br><a id=\"_readyz_cdd\"></a><h2>/readyz/cdd</h2>\n"
1634 " <p>Performs a CDD retrieval check. 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 CDD retrieval check succeeded. Otherwise the HTTP status\n"
1657 " is set to 500. If verbose flag is provided then the HTTP body contains a JSON dictionary\n"
1658 " with detailed information.</p>\n"
1659 " <hr><br><br><a id=\"_readyz_snp\"></a><h2>/readyz/snp</h2>\n"
1660 " <p>Performs a SNP 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 SNP 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=\"TEST_io\"></a><h2>TEST/io</h2>\n"
1686 " <p>Sends back random binary data to test the I/O performance. It works only if the server\n"
1687 " configuration file has the [DEBUG]/psg_allow_io_test value set to true</p>\n"
1688 " <table class=\"first-column\">\n"
1690 " <th>Parameter</th>\n"
1691 " <th>Optional</th>\n"
1693 " <th>Description</th>\n"
1694 " <th>Allowed Values</th>\n"
1695 " <th>Default</th>\n"
1698 " <td>return_data_size</td>\n"
1699 " <td>mandatory</td>\n"
1700 " <td>Integer</td>\n"
1701 " <td class=\"description\">Size in bytes (positive integer up to 1000000000) which should be sent to the client.\n"
1702 " The data are random.</td>\n"
1703 " <td>An integer in the range 0 ... 1000000000</td>\n"
1708 " <td>optional</td>\n"
1709 " <td>String</td>\n"
1710 " <td class=\"description\">It tells if the logging of the request should be done or not</td>\n"
1711 " <td>yes and no</td>\n"
1716 " <p>The HTTP body is a random data of the requested length</p>\n"
1717 " <hr><br><br><a id=\"health\"></a><h2>health</h2>\n"
1718 " <p>Performs a basic functionality check. It can be used by monitoring facilities.</p>\n"
1720 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n"
1721 " status is set to 500 and the HTTP body may have a detailed message.</p>\n"
1722 " <hr><br><br><a id=\"deep-health\"></a><h2>deep-health</h2>\n"
1723 " <p>At the moment the implementation matches the 'health' command.</p>\n"
1725 " <p>HTTP status is set to 200 if the functionality check succeeded. Otherwise the HTTP\n"
1726 " status is set to 500 and the HTTP body may have a detailed message.</p>\n"
1727 " <hr><br><br><a id=\"favicon.ico\"></a><h2>favicon.ico</h2>\n"
1728 " <p>Always replies 'not found'</p>\n"
1730 " <p>The standard HTTP protocol is used</p>\n"
1731 " <hr><br><br><a id=\"unknown\"></a><h2>unknown</h2>\n"
1732 " <p>Always replies 'ok' in terms of http. The nested PSG protocol always tells 'bad request'</p>\n"
1734 " <p>The HTTP body uses PSG protocol for a 'bad request' message</p>\n"
1735 " <hr><br><br><h2>References</h2>\n"
1737 " <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"
