Retrieves the classification results for a given query.
+ + + +Retrieves the classification results for a given sequence.
+the ID of the query.
+the InChIKey of the entity.
Retrieves the classification results for a given sequence.
+ + +
+ + + +87 +88 +89 +90 +91 +92 +93 +94 +95 +96 +97 +98 +99 +100 +101+ |
+
+ # File 'lib/classyfire_api.rb', line 87 + +def ClassyFireAPI.get_sequence_classification(fingerprint,format="json") + begin + if format == "json" + RestClient.get "#{URL}/entities/#{fingerprint}.#{format}", :accept => :json + end + rescue RestClient::ResourceNotFound => e + e.response + rescue RestClient::InternalServerError => e + e.response + rescue RestClient::GatewayTimeout => e + e.response + rescue RestClient::RequestTimeout => e + e.response + end +end+ |
+
-85 -86 -87 -88 -89 -90 -91 -92+128 +129 +130 +131 +132 +133 +134 +135
# File 'lib/classyfire_api.rb', line 85 +# File 'lib/classyfire_api.rb', line 128 def ClassyFireAPI.query_status(query_id) begin @@ -785,49 +932,6 @@ retrieve the strutcure's classification from ClassyFire.-266 -267 -268 -269 -270 -271 -272 -273 -274 -275 -276 -277 -278 -279 -280 -281 -282 -283 -284 -285 -286 -287 -288 -289 -290 -291 -292 -293 -294 -295 -296 -297 -298 -299 -300 -301 -302 -303 -304 -305 -306 -307 -308 309 310 311 @@ -847,10 +951,53 @@ retrieve the strutcure's classification from ClassyFire. 325 326 327 -328+328 +329 +330 +331 +332 +333 +334 +335 +336 +337 +338 +339 +340 +341 +342 +343 +344 +345 +346 +347 +348 +349 +350 +351 +352 +353 +354 +355 +356 +357 +358 +359 +360 +361 +362 +363 +364 +365 +366 +367 +368 +369 +370 +371
# File 'lib/classyfire_api.rb', line 266 +# File 'lib/classyfire_api.rb', line 309 def ClassyFireAPI.retrieve_classification(input,output) absolute_path = File.(input) @@ -986,49 +1133,6 @@ format.-335 -336 -337 -338 -339 -340 -341 -342 -343 -344 -345 -346 -347 -348 -349 -350 -351 -352 -353 -354 -355 -356 -357 -358 -359 -360 -361 -362 -363 -364 -365 -366 -367 -368 -369 -370 -371 -372 -373 -374 -375 -376 -377 378 379 380 @@ -1039,10 +1143,53 @@ format. 385 386 387 -388+388 +389 +390 +391 +392 +393 +394 +395 +396 +397 +398 +399 +400 +401 +402 +403 +404 +405 +406 +407 +408 +409 +410 +411 +412 +413 +414 +415 +416 +417 +418 +419 +420 +421 +422 +423 +424 +425 +426 +427 +428 +429 +430 +431
# File 'lib/classyfire_api.rb', line 335 +# File 'lib/classyfire_api.rb', line 378 def ClassyFireAPI.retrieve_entities_json(input,output) absolute_path = File.(input) @@ -1169,49 +1316,6 @@ format.-397 -398 -399 -400 -401 -402 -403 -404 -405 -406 -407 -408 -409 -410 -411 -412 -413 -414 -415 -416 -417 -418 -419 -420 -421 -422 -423 -424 -425 -426 -427 -428 -429 -430 -431 -432 -433 -434 -435 -436 -437 -438 -439 440 441 442 @@ -1228,10 +1332,53 @@ format. 453 454 455 -456+456 +457 +458 +459 +460 +461 +462 +463 +464 +465 +466 +467 +468 +469 +470 +471 +472 +473 +474 +475 +476 +477 +478 +479 +480 +481 +482 +483 +484 +485 +486 +487 +488 +489 +490 +491 +492 +493 +494 +495 +496 +497 +498 +499
# File 'lib/classyfire_api.rb', line 397 +# File 'lib/classyfire_api.rb', line 440 def ClassyFireAPI.retrieve_entities_sdf(input,output) absolute_path = File.(input) @@ -1362,19 +1509,19 @@ slice_length [Integer] The maximum number of entries for each query input-184 -185 -186 -187 -188 -189 -190 -191 -192 -193+227 +228 +229 +230 +231 +232 +233 +234 +235 +236
# File 'lib/classyfire_api.rb', line 184 +# File 'lib/classyfire_api.rb', line 227 def ClassyFireAPI.submit_queries_from_directory(folder,slice_length,type="STRUCTURE") if File.directory?(folder) @@ -1575,49 +1722,6 @@ framgments from the index 'start'.-107 -108 -109 -110 -111 -112 -113 -114 -115 -116 -117 -118 -119 -120 -121 -122 -123 -124 -125 -126 -127 -128 -129 -130 -131 -132 -133 -134 -135 -136 -137 -138 -139 -140 -141 -142 -143 -144 -145 -146 -147 -148 -149 150 151 152 @@ -1637,10 +1741,53 @@ framgments from the index 'start'. 166 167 168 -169+169 +170 +171 +172 +173 +174 +175 +176 +177 +178 +179 +180 +181 +182 +183 +184 +185 +186 +187 +188 +189 +190 +191 +192 +193 +194 +195 +196 +197 +198 +199 +200 +201 +202 +203 +204 +205 +206 +207 +208 +209 +210 +211 +212
# File 'lib/classyfire_api.rb', line 107 +# File 'lib/classyfire_api.rb', line 150 def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length, start, type='STRUCTURE') @start_time = Time.now @@ -1803,49 +1950,6 @@ text. is fragmented into n part of #slice_length entries each).-209 -210 -211 -212 -213 -214 -215 -216 -217 -218 -219 -220 -221 -222 -223 -224 -225 -226 -227 -228 -229 -230 -231 -232 -233 -234 -235 -236 -237 -238 -239 -240 -241 -242 -243 -244 -245 -246 -247 -248 -249 -250 -251 252 253 254 @@ -1853,10 +1957,53 @@ text. is fragmented into n part of #slice_length entries each). 256 257 258 -259+259 +260 +261 +262 +263 +264 +265 +266 +267 +268 +269 +270 +271 +272 +273 +274 +275 +276 +277 +278 +279 +280 +281 +282 +283 +284 +285 +286 +287 +288 +289 +290 +291 +292 +293 +294 +295 +296 +297 +298 +299 +300 +301 +302
# File 'lib/classyfire_api.rb', line 209 +# File 'lib/classyfire_api.rb', line 252 def ClassyFireAPI.submit_random_subset_of_query_input_in_chunks(tab_separated_input_file,size, type='STRUCTURE') @start_time = Time.now @@ -1919,7 +2066,7 @@ text. is fragmented into n part of #slice_length entries each). diff --git a/doc/EntityResource.html b/doc/EntityResource.html index 5fe5906..e6521d8 100644 --- a/doc/EntityResource.html +++ b/doc/EntityResource.html @@ -114,7 +114,7 @@ diff --git a/doc/QueryResource.html b/doc/QueryResource.html index 2611f26..87f20f1 100644 --- a/doc/QueryResource.html +++ b/doc/QueryResource.html @@ -183,7 +183,7 @@ diff --git a/doc/SequenceResource.html b/doc/SequenceResource.html new file mode 100644 index 0000000..4bffc57 --- /dev/null +++ b/doc/SequenceResource.html @@ -0,0 +1,123 @@ + + + + ++ Class: SequenceResource + + — Documentation by YARD 0.8.7.6 + + + + + + + + + + + + + + + + + ++ + + + ++ + + ++ + + + + \ No newline at end of file diff --git a/doc/_index.html b/doc/_index.html index f8f7858..19d7247 100644 --- a/doc/_index.html +++ b/doc/_index.html @@ -118,6 +118,19 @@ + +Class: SequenceResource + + + +
+ ++ +
+ + + + + + + + + + + + +- Inherits:
+- + ActiveResource::Base + +
+ + + + + + + + + ++
+ show all + +- Object
+ +- ActiveResource::Base
+ +- SequenceResource
+ +- Defined in:
+- lib/sequence_resource.rb
+ +
++ +Sequences are represented by the Sequence model, through which one can +access the compound's structure-based classification.
+ +GET
+ +/sequence/fingerprint
+ +A (FASTA) sequence's classification can be retrieved in the JSON. In +this example, the sequence has the fingerprint = +“8bf70c23ac100cd2c3955081d8613325”
+ +++ +ClassyFireAPI.get_sequence_classification(“8bf70c23ac100cd2c3955081d8613325”,“json”)
+Where:
+ +++The sequence's fingerprint is “8bf70c23ac100cd2c3955081d8613325”,
+ +The output format is “json” (JSON).
+
The Query model represents the chemical structure to be classified. Its @@ -141,12 +168,13 @@ attributes are the query label and the query input.
The query label is an identifier
The query input contains the compound's identifier (optional) and its -structural representation, separated by a comma. The chemical structure is +structural representation, separated by a tab. The chemical structure is represented either in the Daylight -SMILES or the format, the InChI -format.
+format. Moreover, the compound can be represented with its IUPAC name.
-+ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)
-
ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”) +where the parameters are:
-where the parameters are:
- --The query label: curl_test,
The entity identifiers: MOL1,MOL2
@@ -197,14 +222,14 @@ XML format.Who do I talk to?
diff --git a/doc/index.html b/doc/index.html index 30215ef..5b8643f 100644 --- a/doc/index.html +++ b/doc/index.html @@ -131,7 +131,34 @@ InChIKey=LABTWGUMFABVFG-ONEGZZNKSA-N.
- -
Repo owner or admin
+Yannick Djoumbou Feunang: djoumbou@ualberta.ca
Other community or team contact
++ +Sequences are represented by the Sequence model, through which one can +access the compound's structure-based classification.
+ +GET
+ +/sequence/fingerprint
+ +A (FASTA) sequence's classification can be retrieved in the JSON. In +this example, the sequence has the fingerprint = +“8bf70c23ac100cd2c3955081d8613325”
+ +++ +ClassyFireAPI.get_sequence_classification(“8bf70c23ac100cd2c3955081d8613325”,“json”)
+Where:
+ +++The sequence's fingerprint is “8bf70c23ac100cd2c3955081d8613325”,
+ +The output format is “json” (JSON).
+
The Query model represents the chemical structure to be classified. Its @@ -141,12 +168,13 @@ attributes are the query label and the query input.
The query label is an identifier
The query input contains the compound's identifier (optional) and its -structural representation, separated by a comma. The chemical structure is +structural representation, separated by a tab. The chemical structure is represented either in the Daylight -SMILES or the format, the InChI -format.
+format. Moreover, the compound can be represented with its IUPAC name.
-+ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”)
-
ClassyFireAPI.submit_query(“curl_test”,“MOL1tCCCOCCnMOL2tCOCC=CCCC”,“STRUCTURE”) +where the parameters are:
-where the parameters are:
- -The query label: curl_test,
The entity identifiers: MOL1,MOL2
@@ -197,14 +222,14 @@ XML format.Who do I talk to?
diff --git a/doc/method_list.html b/doc/method_list.html index 324e0cb..8a94711 100644 --- a/doc/method_list.html +++ b/doc/method_list.html @@ -64,54 +64,60 @@
- -
Repo owner or admin
+Yannick Djoumbou Feunang: djoumbou@ualberta.ca
Other community or team contact
+ get_sequence_classification + ClassyFireAPI + + + +query_status ClassyFireAPI -+ retrieve_classification ClassyFireAPI -+ retrieve_entities_json ClassyFireAPI -+ retrieve_entities_sdf ClassyFireAPI -+ submit_queries_from_directory ClassyFireAPI -+ submit_query ClassyFireAPI -+ submit_query_input_in_chunks ClassyFireAPI -+ submit_random_subset_of_query_input_in_chunks ClassyFireAPI -+ #to_param QueryResource diff --git a/doc/top-level-namespace.html b/doc/top-level-namespace.html index 5c5e989..e36a234 100644 --- a/doc/top-level-namespace.html +++ b/doc/top-level-namespace.html @@ -89,7 +89,7 @@ - Classes: EntityResource, QueryResource + Classes: EntityResource, QueryResource, SequenceResource @@ -105,7 +105,7 @@ diff --git a/lib/classyfire_api.rb b/lib/classyfire_api.rb index 82bf645..dffe982 100644 --- a/lib/classyfire_api.rb +++ b/lib/classyfire_api.rb @@ -55,7 +55,7 @@ module ClassyFireAPI # Retrieves the classification results for a given entity. # - # @param inchikey [String] the ID of the query. + # @param inchikey [String] the InChIKey of the entity. # @param format [String] the format of the query, 'text' (either JSON, CSV, or SDF) # @return [Text] A text file displaying the classification results for the entity in the specified format. def ClassyFireAPI.get_entity_classification(inchikey,format="json") @@ -79,6 +79,49 @@ module ClassyFireAPI end end + # Retrieves the classification results for a given sequence. + # + # @param the fingerprint [String] the fingerprint (generated from the sequence using Digest::MD5). + # @param format [String] the format of the query (Only JSON) + # @return [Text] A text file displaying the classification results for the entity in the specified format. + def ClassyFireAPI.get_sequence_classification(fingerprint,format="json") + begin + if format == "json" + RestClient.get "#{URL}/entities/#{fingerprint}.#{format}", :accept => :json + end + rescue RestClient::ResourceNotFound => e + e.response + rescue RestClient::InternalServerError => e + e.response + rescue RestClient::GatewayTimeout => e + e.response + rescue RestClient::RequestTimeout => e + e.response + end + end + + def ClassyFireAPI.get_entity_classification(inchikey,format="json") + inchikey_id = inchikey.to_s.gsub('InChIKey=','') + begin + if format == "json" + RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :json + elsif format == "sdf" + RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :sdf + elsif format == "csv" + RestClient.get "#{URL}/entities/#{inchikey_id}.#{format}", :accept => :csv + end + rescue RestClient::ResourceNotFound => e + e.response + rescue RestClient::InternalServerError => e + e.response + rescue RestClient::GatewayTimeout => e + e.response + rescue RestClient::RequestTimeout => e + e.response + end + end + + # Retrieves the status of a query # @param query_id [Integer] the ID of the query # @return [String] the query status, 'Done' or 'In progress', 'string' diff --git a/lib/sequence_resource.rb b/lib/sequence_resource.rb new file mode 100644 index 0000000..8473d75 --- /dev/null +++ b/lib/sequence_resource.rb @@ -0,0 +1,6 @@ +require 'active_resource' + +class SequenceResource < ActiveResource::Base + self.site ='http://classyfire.wishartlab.com' + self.element_name = "sequence" +end \ No newline at end of file