Incorporate remote clinical pipeline and stave #793
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@@ Coverage Diff @@
## master #793 +/- ##
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Coverage 80.75% 80.75%
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Hits 15637 15637
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…sh13y/forte into 745_clinical_pipeline_stave
…sh13y/forte into 745_clinical_pipeline_stave
| @@ -0,0 +1,3 @@ | |||
| { | |||
| "index.mapping.coerce": false | |||
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Is this file used here? Couldn't find a reference in code.
Btw, this file is also quite small, if it is used in code, maybe using it directly in the code is easier (for example purposes)
| { | ||
| "name": "query_chatbot.json", | ||
| "project_id": 99, | ||
| "textPack": "{\n \"py/object\": \"forte.data.data_pack.DataPack\",\n \"py/state\": {\n \"creation_records\": {},\n \"field_records\": {},\n \"links\": [],\n \"groups\": [],\n \"meta\": {\n \"py/object\": \"forte.data.data_pack.Meta\",\n \"py/state\": {\n \"pack_name\": \"query_chatbot\",\n \"_pack_id\": 3,\n \"language\": \"eng\",\n \"span_unit\": \"character\"\n }\n },\n \"_text\": \"Welcome! Please type in a query to retrieve relevant clinical reports.\",\n \"annotations\": [\n {\n \"py/object\": \"ft.onto.base_ontology.Utterance\",\n \"py/state\": {\n \"_span\": {\n \"py/object\": \"forte.data.span.Span\",\n \"begin\": 0,\n \"end\": 70\n },\n \"_tid\": 0,\n \"speaker\": \"ai\"\n }\n }\n ],\n \"generics\": [],\n \"replace_back_operations\": [],\n \"processed_original_spans\": [],\n \"orig_text_len\": 70,\n \"serialization\": {\n \"next_id\": 1\n }\n }\n}" |
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These files don't look like JSON to me, there are these \ escapes here and there. I guess these are serialized in the wrong way.
| { | ||
| "name": "clinical_pipeline_base", | ||
| "project_type": "single_pack", | ||
| "ontology": "{\n \"name\": \"base_ontology\",\n \"definitions\": [\n {\n \"entry_name\": \"ft.onto.base_ontology.Token\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation :class:`Token`, used to represent a token or a word.\",\n \"attributes\": [\n {\n \"name\": \"pos\",\n \"type\": \"str\"\n },\n {\n \"name\": \"ud_xpos\",\n \"type\": \"str\",\n \"description\": \"Language specific pos tag. Used in CoNLL-U Format. Refer to https://universaldependencies.org/format.html\"\n },\n {\n \"name\": \"lemma\",\n \"type\": \"str\",\n \"description\": \"Lemma or stem of word form.\"\n },\n {\n \"name\": \"chunk\",\n \"type\": \"str\"\n },\n {\n \"name\": \"ner\",\n \"type\": \"str\"\n },\n {\n \"name\": \"sense\",\n \"type\": \"str\"\n },\n {\n \"name\": \"is_root\",\n \"type\": \"bool\"\n },\n {\n \"name\": \"ud_features\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"str\"\n },\n {\n \"name\": \"ud_misc\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"str\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Subword\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"Used to represent subword tokenization results.\",\n \"attributes\": [\n {\n \"name\": \"is_first_segment\",\n \"type\": \"bool\"\n },\n {\n \"name\": \"is_unk\",\n \"type\": \"bool\"\n },\n {\n \"name\": \"vocab_id\",\n \"type\": \"int\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Classification\",\n \"parent_entry\": \"forte.data.ontology.top.Generics\",\n \"description\": \"Used to store values for classification prediction\",\n \"attributes\": [\n {\n \"name\": \"classification_result\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"float\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Document\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `Document`, normally used to represent a document.\",\n \"attributes\": [\n {\n \"name\": \"document_class\",\n \"type\": \"List\",\n \"item_type\": \"str\",\n \"description\": \"A list of class names that the document belongs to.\"\n },\n {\n \"name\": \"sentiment\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"float\"\n },\n {\n \"name\": \"classifications\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"ft.onto.base_ontology.Classification\",\n \"description\": \"Stores the classification results for this document. The key is the name/task of the classification, the value is an classification object storing the results.\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Sentence\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `Sentence`, normally used to represent a sentence.\",\n \"attributes\": [\n {\n \"name\": \"speaker\",\n \"type\": \"str\"\n },\n {\n \"name\": \"part_id\",\n \"type\": \"int\"\n },\n {\n \"name\": \"sentiment\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"float\"\n },\n {\n \"name\": \"classification\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"float\"\n },\n {\n \"name\": \"classifications\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"ft.onto.base_ontology.Classification\",\n \"description\": \"Stores the classification results for this sentence. The key is the name/task of the classification, the value is an classification object storing the results.\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Phrase\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `Phrase`.\",\n \"attributes\": [\n {\n \"name\": \"phrase_type\",\n \"type\": \"str\"\n },\n {\n \"name\": \"headword\",\n \"type\": \"ft.onto.base_ontology.Token\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.UtteranceContext\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"`UtteranceContext` represents the context part in dialogue.\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Utterance\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `Utterance`, normally used to represent an utterance in dialogue.\",\n \"attributes\": [\n {\n \"name\": \"speaker\",\n \"type\": \"str\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.PredicateArgument\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `PredicateArgument`, normally used to represent an argument of a predicate, can be linked to the predicate via the predicate link.\",\n \"attributes\": [\n {\n \"name\": \"ner_type\",\n \"type\": \"str\"\n },\n {\n \"name\": \"predicate_lemma\",\n \"type\": \"str\"\n },\n {\n \"name\": \"is_verb\",\n \"type\": \"bool\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.EntityMention\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `EntityMention`, normally used to represent an Entity Mention in a piece of text.\",\n \"attributes\": [\n {\n \"name\": \"ner_type\",\n \"type\": \"str\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.EventMention\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `EventMention`, used to refer to a mention of an event.\",\n \"attributes\": [\n {\n \"name\": \"event_type\",\n \"type\": \"str\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.PredicateMention\",\n \"parent_entry\": \"ft.onto.base_ontology.Phrase\",\n \"description\": \"A span based annotation `PredicateMention`, normally used to represent a predicate (normally verbs) in a piece of text.\",\n \"attributes\": [\n {\n \"name\": \"predicate_lemma\",\n \"type\": \"str\"\n },\n {\n \"name\": \"framenet_id\",\n \"type\": \"str\"\n },\n {\n \"name\": \"is_verb\",\n \"type\": \"bool\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.PredicateLink\",\n \"parent_entry\": \"forte.data.ontology.top.Link\",\n \"description\": \"A `Link` type entry which represent a semantic role link between a predicate and its argument.\",\n \"attributes\": [\n {\n \"name\": \"arg_type\",\n \"type\": \"str\",\n \"description\": \"The predicate link type.\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.PredicateMention\",\n \"child_type\": \"ft.onto.base_ontology.PredicateArgument\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Dependency\",\n \"parent_entry\": \"forte.data.ontology.top.Link\",\n \"description\": \"A `Link` type entry which represent a syntactic dependency.\",\n \"attributes\": [\n {\n \"name\": \"dep_label\",\n \"type\": \"str\",\n \"description\": \"The dependency label.\"\n },\n {\n \"name\": \"rel_type\",\n \"type\": \"str\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.Token\",\n \"child_type\": \"ft.onto.base_ontology.Token\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.EnhancedDependency\",\n \"parent_entry\": \"forte.data.ontology.top.Link\",\n \"description\": \"A `Link` type entry which represent a enhanced dependency: \\n https://universaldependencies.org/u/overview/enhanced-syntax.html\",\n \"attributes\": [\n {\n \"name\": \"dep_label\",\n \"type\": \"str\",\n \"description\": \"The enhanced dependency label in Universal Dependency.\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.Token\",\n \"child_type\": \"ft.onto.base_ontology.Token\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.RelationLink\",\n \"parent_entry\": \"forte.data.ontology.top.Link\",\n \"description\": \"A `Link` type entry which represent a relation between two entity mentions\",\n \"attributes\": [\n {\n \"name\": \"rel_type\",\n \"type\": \"str\",\n \"description\": \"The type of the relation.\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.EntityMention\",\n \"child_type\": \"ft.onto.base_ontology.EntityMention\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.CrossDocEntityRelation\",\n \"parent_entry\": \"forte.data.ontology.top.MultiPackLink\",\n \"description\": \"A `Link` type entry which represent a relation between two entity mentions across the packs.\",\n \"attributes\": [\n {\n \"name\": \"rel_type\",\n \"type\": \"str\",\n \"description\": \"The type of the relation.\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.EntityMention\",\n \"child_type\": \"ft.onto.base_ontology.EntityMention\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.CoreferenceGroup\",\n \"parent_entry\": \"forte.data.ontology.top.Group\",\n \"description\": \"A group type entry that take `EntityMention`, as members, used to represent coreferent group of entities.\",\n \"member_type\": \"ft.onto.base_ontology.EntityMention\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.EventRelation\",\n \"parent_entry\": \"forte.data.ontology.top.Link\",\n \"description\": \"A `Link` type entry which represent a relation between two event mentions.\",\n \"attributes\": [\n {\n \"name\": \"rel_type\",\n \"type\": \"str\",\n \"description\": \"The type of the relation.\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.EventMention\",\n \"child_type\": \"ft.onto.base_ontology.EventMention\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.CrossDocEventRelation\",\n \"parent_entry\": \"forte.data.ontology.top.MultiPackLink\",\n \"description\": \"A `Link` type entry which represent a relation between two event mentions across the packs.\",\n \"attributes\": [\n {\n \"name\": \"rel_type\",\n \"type\": \"str\",\n \"description\": \"The type of the relation.\"\n }\n ],\n \"parent_type\": \"ft.onto.base_ontology.EventMention\",\n \"child_type\": \"ft.onto.base_ontology.EventMention\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.ConstituentNode\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `ConstituentNode` to represent constituents in constituency parsing. This can also sentiment values annotated on the nodes.\",\n \"attributes\": [\n {\n \"name\": \"label\",\n \"type\": \"str\"\n },\n {\n \"name\": \"sentiment\",\n \"type\": \"Dict\",\n \"key_type\": \"str\",\n \"value_type\": \"float\"\n },\n {\n \"name\": \"is_root\",\n \"type\": \"bool\"\n },\n {\n \"name\": \"is_leaf\",\n \"type\": \"bool\"\n },\n {\n \"name\": \"parent_node\",\n \"type\": \"ft.onto.base_ontology.ConstituentNode\"\n },\n {\n \"name\": \"children_nodes\",\n \"type\": \"List\",\n \"item_type\": \"ft.onto.base_ontology.ConstituentNode\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Title\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `Title`, normally used to represent a title.\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Body\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `Body`, normally used to represent a document body.\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.MCOption\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\"\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.MCQuestion\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"attributes\": [\n {\n \"name\": \"options\",\n \"type\": \"List\",\n \"item_type\": \"ft.onto.base_ontology.MCOption\"\n },\n {\n \"name\": \"answers\",\n \"type\": \"List\",\n \"item_type\": \"int\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.MRCQuestion\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"An `Annotation` type which represents an MRC question.\",\n \"attributes\": [\n {\n \"name\": \"qid\",\n \"type\": \"int\"\n },\n {\n \"name\": \"answers\",\n \"type\": \"List\",\n \"item_type\": \"ft.onto.base_ontology.Phrase\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.Recording\",\n \"parent_entry\": \"forte.data.ontology.top.AudioAnnotation\",\n \"description\": \"A span based annotation `Recording`, normally used to represent a recording.\",\n \"attributes\": [\n {\n \"name\": \"recording_class\",\n \"type\": \"List\",\n \"item_type\": \"str\",\n \"description\": \"A list of class names that the recording belongs to.\"\n }\n ]\n },\n {\n \"entry_name\": \"ft.onto.base_ontology.AudioUtterance\",\n \"parent_entry\": \"forte.data.ontology.top.AudioAnnotation\",\n \"description\": \"A span based annotation `AudioUtterance`, normally used to represent an utterance in dialogue.\",\n \"attributes\": [\n {\n \"name\": \"speaker\",\n \"type\": \"str\"\n }\n ]\n },\n {\n \"entry_name\": \"ftx.medical.clinical_ontology.NegationContext\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"A span based annotation `NegationContext`, used to represent the negation context of a named entity.\",\n \"attributes\": [\n {\n \"name\": \"polarity\",\n \"type\": \"bool\"\n }\n ]\n },\n {\n \"entry_name\": \"ftx.medical.clinical_ontology.MedicalEntityMention\",\n \"parent_entry\": \"ft.onto.base_ontology.EntityMention\",\n \"description\": \"A span based annotation class MedicalEntityMention, used to represent an Entity Mention in medical domain\",\n \"attributes\": [\n {\n \"name\": \"umls_link\",\n \"type\": \"str\"\n },\n {\n \"name\": \"umls_entities\",\n \"type\": \"List\",\n \"item_type\": \"ftx.medical.clinical_ontology.UMLSConceptLink\"\n }\n ]\n },\n {\n \"entry_name\": \"ftx.medical.clinical_ontology.MedicalArticle\",\n \"parent_entry\": \"forte.data.ontology.top.Annotation\",\n \"description\": \"An annotation based representation for the whole medical text chunk/document\",\n \"attributes\": [\n {\n \"name\": \"icd_version\",\n \"type\": \"int\",\n \"description\": \"The version of ICD-Coding being used.\"\n },\n {\n \"name\": \"icd_code\",\n \"type\": \"str\",\n \"description\": \"The ICD code assigned to current medical article.\"\n }\n ]\n }\n ]\n}\n", "config": "{\"legendConfigs\":{\"ft.onto.base_ontology.Token\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"pos\":false,\"ud_xpos\":false,\"lemma\":false,\"chunk\":false,\"ner\":false,\"sense\":false}},\"ft.onto.base_ontology.Subword\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{}},\"ft.onto.base_ontology.Classification\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{}},\"ft.onto.base_ontology.Document\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{}},\"ft.onto.base_ontology.Sentence\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"speaker\":false}},\"ft.onto.base_ontology.Phrase\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"phrase_type\":false}},\"ft.onto.base_ontology.UtteranceContext\":{\"is_selected\":false,\"is_shown\":false},\"ft.onto.base_ontology.Utterance\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"speaker\":false}},\"ft.onto.base_ontology.PredicateArgument\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"ner_type\":false,\"predicate_lemma\":false}},\"ft.onto.base_ontology.EntityMention\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"ner_type\":false}},\"ft.onto.base_ontology.EventMention\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"event_type\":false}},\"ft.onto.base_ontology.PredicateMention\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"predicate_lemma\":false,\"framenet_id\":false}},\"ft.onto.base_ontology.PredicateLink\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"arg_type\":false}},\"ft.onto.base_ontology.Dependency\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"dep_label\":false,\"rel_type\":false}},\"ft.onto.base_ontology.EnhancedDependency\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"dep_label\":false}},\"ft.onto.base_ontology.RelationLink\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"rel_type\":false}},\"ft.onto.base_ontology.CrossDocEntityRelation\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"rel_type\":false}},\"ft.onto.base_ontology.CoreferenceGroup\":{\"is_selected\":false,\"is_shown\":false},\"ft.onto.base_ontology.EventRelation\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"rel_type\":false}},\"ft.onto.base_ontology.CrossDocEventRelation\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"rel_type\":false}},\"ft.onto.base_ontology.ConstituentNode\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"label\":false}},\"ft.onto.base_ontology.Title\":{\"is_selected\":false,\"is_shown\":false},\"ft.onto.base_ontology.Body\":{\"is_selected\":false,\"is_shown\":false},\"ft.onto.base_ontology.MCOption\":{\"is_selected\":false,\"is_shown\":false},\"ft.onto.base_ontology.MCQuestion\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{}},\"ft.onto.base_ontology.MRCQuestion\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{}},\"ft.onto.base_ontology.Recording\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{}},\"ft.onto.base_ontology.AudioUtterance\":{\"is_selected\":false,\"is_shown\":false,\"attributes\":{\"speaker\":false}},\"ftx.medical.clinical_ontology.NegationContext\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{}},\"ftx.medical.clinical_ontology.MedicalEntityMention\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"umls_link\":false}},\"ftx.medical.clinical_ontology.MedicalArticle\":{\"is_selected\":false,\"is_shown\":true,\"attributes\":{\"icd_code\":false}}},\"scopeConfigs\":{\"ft.onto.base_ontology.Token\":false,\"ft.onto.base_ontology.Subword\":false,\"ft.onto.base_ontology.Document\":false,\"ft.onto.base_ontology.Sentence\":false,\"ft.onto.base_ontology.Phrase\":false,\"ft.onto.base_ontology.UtteranceContext\":false,\"ft.onto.base_ontology.Utterance\":false,\"ft.onto.base_ontology.PredicateArgument\":false,\"ft.onto.base_ontology.EntityMention\":false,\"ft.onto.base_ontology.EventMention\":false,\"ft.onto.base_ontology.PredicateMention\":false,\"ft.onto.base_ontology.ConstituentNode\":false,\"ft.onto.base_ontology.Title\":false,\"ft.onto.base_ontology.Body\":false,\"ft.onto.base_ontology.MCOption\":false,\"ft.onto.base_ontology.MCQuestion\":false,\"ft.onto.base_ontology.MRCQuestion\":false,\"ftx.medical.clinical_ontology.NegationContext\":false,\"ftx.medical.clinical_ontology.MedicalEntityMention\":false,\"ftx.medical.clinical_ontology.MedicalArticle\":false},\"layoutConfigs\":{\"center-middle\":\"default-nlp\",\"left\":\"default-meta\",\"right\":\"default-attribute\",\"center-bottom\":\"disable\"},\"remoteConfigs\":{\"pipelineUrl\":\"\",\"doValidation\":false,\"expectedName\":\"\",\"inputFormat\":\"string\",\"expectedRecords\":{}}}"} 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Similarly, these other JSON files are also not valid JSON.
| ```bash | ||
| pip install forte.elastic | ||
| pip install forte.spacy | ||
| pip install forte.nltk |
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The instruction should include stave installation, which is simply pip install stave
| @@ -30,32 +39,43 @@ You also need to set up elastic searcher by following guide below to run the pip | |||
| https://www.elastic.co/guide/en/elasticsearch/reference/current/starting-elasticsearch.html | |||
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Elasticsearch is actually quite easy to set up, probably just download, unzip and install. It would be helpful if we can show some simple setup steps here (and of course we can leave more reading to the elastic search site).
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| def main( | ||
| input_path: str, output_path: str, max_packs: int = -1, run_ner_pipeline=0 | ||
| ): |
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If I ran this I will have ModuleNotFoundError: No module named 'ftx.medical, instructions to add the ontology?
| "drop_record": True, | ||
| "zip_pack": True, | ||
| }, | ||
| if run_ner_pipeline == 1: |
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Why are we placing two scripts into this one main function? One is this NER pipeline, and the other is the search pipeline. Just make them two scripts so that we don't have to worry about to use this run_ner_pipeline parameter
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| def update_stave_db( | ||
| default_project_json, chat_project_json, chat_doc_json, config | ||
| ): |
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Can we explain what the function is doing? And what are the parameters?
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@hunterhector I am assuming we are planning to abandon this PR, now that we have a PR in ForteHealth to add this example there? Or do we want to push it here too? |
If everything is moved there we should remove one of them (probably this one). Otherwise, we will have to maintain multiple versions |
We will then have to remove the whole example here then? Because it won't work the old way now that Stave uses RemoteProcessors. As in, removing the clinical_processing_pipeline folder itself from forte/examples; or we will have to strip some functionalities and just keep a non stave interaction example, but that again would be an effective copy of our MIMIC3 example in ForteHealth? https://github.com/asyml/ForteHealth/blob/master/examples/mimic_iii/medical_pipeline.py |
I think we can just remove the whole thing since we have a complete example in the other repo |
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close since most of the code is moved out and this pr is inactive |
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This PR fixes #745.
Description of changes
We provide a remote service pipeline that handles interaction between the chatbot and the elastic search indexer, to get the results visualized through stave on the UI.
We also create 2 stave projects in the script, one for annotation viewing and the other to act as the search engine/chat bot.