diff options
Diffstat (limited to 'gn3/llms')
| -rw-r--r-- | gn3/llms/__init__.py | 0 | ||||
| -rw-r--r-- | gn3/llms/client.py | 207 | ||||
| -rw-r--r-- | gn3/llms/doc_ids.json | 1409 | ||||
| -rw-r--r-- | gn3/llms/errors.py | 57 | ||||
| -rw-r--r-- | gn3/llms/gn_bib.json | 5287 | ||||
| -rw-r--r-- | gn3/llms/process.py | 111 | ||||
| -rw-r--r-- | gn3/llms/response.py | 75 | ||||
| -rw-r--r-- | gn3/llms/sugar_doc_ids.json | 7796 |
8 files changed, 14942 insertions, 0 deletions
diff --git a/gn3/llms/__init__.py b/gn3/llms/__init__.py new file mode 100644 index 0000000..e69de29 --- /dev/null +++ b/gn3/llms/__init__.py diff --git a/gn3/llms/client.py b/gn3/llms/client.py new file mode 100644 index 0000000..41aa6b4 --- /dev/null +++ b/gn3/llms/client.py @@ -0,0 +1,207 @@ +# pylint: skip-file +import json +import string +import os +import datetime +import time +import requests +from requests import Session +from urllib.parse import urljoin +from requests.packages.urllib3.util.retry import Retry +from requests import HTTPError +from requests import Session +from requests.adapters import HTTPAdapter +from gn3.settings import FAHAMU_AUTH_TOKEN + +basedir = os.path.join(os.path.dirname(__file__)) + + +class TimeoutHTTPAdapter(HTTPAdapter): + def __init__(self, timeout, *args, **kwargs): + """TimeoutHTTPAdapter constructor. + Args: + timeout (int): How many seconds to wait for the server to send data before + giving up. + """ + self.timeout = timeout + super().__init__(*args, **kwargs) + + def send(self, request, **kwargs): + """Override :obj:`HTTPAdapter` send method to add a default timeout.""" + timeout = kwargs.get("timeout") + if timeout is None: + kwargs["timeout"] = self.timeout + + return super().send(request, **kwargs) + + +class GeneNetworkQAClient(Session): + """GeneNetworkQA Client + + This class provides a client object interface to the GeneNetworkQA API. + It extends the `requests.Session` class and includes authorization, base URL, + request timeouts, and request retries. + + Args: + account (str): Base address subdomain. + api_key (str): API key. + version (str, optional): API version, defaults to "v3". + timeout (int, optional): Timeout value, defaults to 5. + total_retries (int, optional): Total retries value, defaults to 5. + backoff_factor (int, optional): Retry backoff factor value, defaults to 30. + + Usage: + from genenetworkqa import GeneNetworkQAClient + gnqa = GeneNetworkQAClient(account="account-name", api_key="XXXXXXXXXXXXXXXXXXX...") + """ + + BASE_URL = 'https://genenetwork.fahamuai.com/api/tasks' + + def __init__(self, account, api_key, version="v3", timeout=5, total_retries=5, backoff_factor=30): + super().__init__() + self.headers.update({"Authorization": "Bearer " + FAHAMU_AUTH_TOKEN}) + self.answer_url = f"{self.BASE_URL}/answers" + self.feedback_url = f"{self.BASE_URL}/feedback" + + adapter = TimeoutHTTPAdapter( + timeout=timeout, + max_retries=Retry( + total=total_retries, + status_forcelist=[429, 500, 502, 503, 504], + backoff_factor=backoff_factor, + ), + ) + + self.mount("https://", adapter) + self.mount("http://", adapter) + + + + @staticmethod + def format_bibliography_info(bib_info): + + if isinstance(bib_info, str): + # Remove '.txt' + bib_info = bib_info.removesuffix('.txt') + elif isinstance(bib_info, dict): + # Format string bibliography information + bib_info = "{0}. ".format(bib_info.get('author', ''), + bib_info.get('title', ''), + bib_info.get('year', ''), + bib_info.get('doi', '')) + return bib_info + + @staticmethod + def ask_the_documents(extend_url, my_auth): + try: + response = requests.post( + base_url + extend_url, data={}, headers=my_auth) + response.raise_for_status() + except requests.exceptions.RequestException as e: + # Handle the exception appropriately, e.g., log the error + raise RuntimeError(f"Error making the request: {e}") + + if response.status_code != 200: + return negative_status_msg(response), 0 + + task_id = get_task_id_from_result(response) + response = get_answer_using_task_id(task_id, my_auth) + + if response.status_code != 200: + + return negative_status_msg(response), 0 + + return response, 1 + + @staticmethod + def negative_status_msg(response): + return f"Problems\n\tStatus code => {response.status_code}\n\tReason => {response.reason}" + + def ask(self, exUrl, *args, **kwargs): + askUrl = self.BASE_URL + exUrl + res = self.custom_request('POST', askUrl, *args, **kwargs) + if (res.status_code != 200): + return self.negativeStatusMsg(res), 0 + task_id = self.getTaskIDFromResult(res) + return res, task_id + + def get_answer(self, taskid, *args, **kwargs): + query = self.answer_url + self.extendTaskID(taskid) + res = self.custom_request('GET', query, *args, **kwargs) + if (res.status_code != 200): + return self.negativeStatusMsg(res), 0 + return res, 1 + + def custom_request(self, method, url, *args, **kwargs): + max_retries = 3 + retry_delay = 10 + + response = super().request(method, url, *args, **kwargs) + + for i in range(max_retries): + try: + + response.raise_for_status() + except requests.exceptions.RequestException as exc: + code = exc.response.status_code + if code == 422: + raise UnprocessableEntity(exc.request, exc.response) + # from exc + elif i == max_retries - 1: + raise exc + if response.ok: + # Give time to get all the data + time.sleep(retry_delay*3) + return response + else: + time.sleep(retry_delay) + return response + + @staticmethod + def get_task_id_from_result(response): + task_id = json.loads(response.text) + result = f"?task_id={task_id.get('task_id', '')}" + return result + + @staticmethod + def get_answer_using_task_id(extend_url, my_auth): + try: + response = requests.get( + answer_url + extend_url, data={}, headers=my_auth) + response.raise_for_status() + return response + except requests.exceptions.RequestException as error: + # Handle the exception appropriately, e.g., log the error + raise error + + @staticmethod + def filter_response_text(val): + """ + Filters out non-printable characters from the input string and parses it as JSON. + + Args: + val (str): Input string to be filtered and parsed. + + Returns: + dict: Parsed JSON object. + # remove this + """ + return json.loads(''.join([str(char) for char in val if char in string.printable])) + + def getTaskIDFromResult(self, res): + return json.loads(res.text) + + def extendTaskID(self, task_id): + return '?task_id=' + str(task_id['task_id']) + + def get_gnqa(self, query): + res, task_id = api_client.ask('?ask=' + query) + res, success = api_client.get_answer(task_id) + + if success == 1: + resp_text = filter_response_text(res.text) + answer = resp_text.get('data', {}).get('answer', '') + context = resp_text.get('data', {}).get('context', '') + return answer, context + else: + return res, "Unfortunately, I have nothing." diff --git a/gn3/llms/doc_ids.json b/gn3/llms/doc_ids.json new file mode 100644 index 0000000..c742962 --- /dev/null +++ b/gn3/llms/doc_ids.json @@ -0,0 +1,1409 @@ +{ + "713ad3a2-efa9-44af-8639-f4e67efc7001": "2001 Nadkarni BayesCausal Approach.txt", + "87e43e53-85e4-4ad6-8e5f-c6b5e3b99202": "2022 -Tabbaa- Mouse pop genetics.pdf", + "152b2818-67d3-4041-a347-d1b355ca4ce8": "2003 -WebQTL rapid exploratory analysis of gene_expression and genetic networks for brain and_behavior.txt", + "9c8e07d4-2d6f-4e0b-8cf1-6920047554fa": "2022 -Yu- Sex Diff Key Genes Mouse.pdf", + "26abfbd2-7c02-4696-b208-039f8ec5a287": "2003 - 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Genetic Analysis of the Hypothalamic CorticotropinReleasing Factor System.txt", + "4e2485fb-8490-4422-a794-592b28a956b9": "2005 - Nonparametric imputation of missing values for estimating equation based inference.txt", + "644157d6-d149-4994-87fb-3c45e6fd5e0a": "2005 - Sp1 and NFkB pathways are regulated in brain inresponse to acute and chronic ethanol.txt", + "60e08224-f0e8-409c-b00a-b9e7358d3548": "2005 - Cerebellar Gene Expression Profiling and eQTL Analysis in Inbred Mouse Strains Selected for Ethanol Sensitivity.txt", + "a7aa1a3e-4681-4596-b9d0-384dbb260857": "2005 - Metastasis Predictive Signature Profiles Pre-exist in Normal Tissues.txt", + "62a4ee72-b305-4027-be68-1c156fb7adbe": "2005 - Genetic tests of biologic systems in affective disorders.txt", + "7ab1ee39-84b7-4def-91d6-5d79c4d46598": "2005 - Inbred mouse strains C57BL6J and DBA2J vary in sensitivity to a subset of bitter stimuli.txt", + "16f93624-6e07-44bb-ae0c-1404994f31ae": "2005 - Sensitivity to the locomotor-stimulant effects of ethanol and allopregnanolone a quantitative trait locus study of common genetic influence.txt", + "54881d38-e18b-41a8-90d5-b1f990859811": "2005 - 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The Syntaxin Binding Protein 1 Gene (Stxbp1) Is a Candidate for an Ethanol Preference Drinking Locus on Mouse Chromosome 2.txt", + "3490ee08-29dd-4c88-8e58-fd47fb8f0413": "2005 -Chesler- WebQTL pain related phenotypes.txt", + "17690cd7-3e21-47df-b697-06726b3f0b69": "2005 -Knott- Regression based QTL mapping.txt", + "83a4ab87-f4a5-40b9-9297-5a3596e3636f": "2005 -Ljungberg- Numerical algos for Multi QTL.txt", + "969427e9-5901-402d-9d30-216c3c2f528c": "2005 -Bystrykh- Uncovering_regulatory_pathways_that_affe.txt", + "0022bfa1-c2e9-41e9-a96a-0e89688bcbe0": "2005 -Hu- QTL PigQTLDB.txt", + "4439ac39-e421-482f-9aa9-9ad11fa641c1": "2005 -Integrated gene expression profiling and linkage analysis in the rat.txt", + "682c5755-d492-46f6-80e7-fc3055450028": "2005 -Boughter- Inbred mouse strains better stimuli.txt", + "d1f04d58-2589-4183-aee4-569820dae052": "2005 - quantitative-trait-analysis-in-the-investigation-of-function-and.txt", + "447fc5a6-3f29-475e-9e88-a422f0fe03d3": "2005 -Lovinger- Lab models of alcoholism.txt", + "fdd4c745-dacc-4cef-b7b9-05b774ba930d": "2005 -Searls- DataIntegration.txt", + "12a26064-293b-41ff-93c3-763dc2a160df": "2005 -Tao- Spinal density-93.txt", + "945d04d0-6650-470f-a2ef-f88142749087": "2007 - 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Identification of a QTL in Mus musculus for Alcohol Preference, Withdrawal, and Ap3m2 Expression Using Integrative Functional Genomics and Precision Genetics.txt", + "80a77e9d-0d80-4548-9253-c14b8bb5cff7": "2014 - Pharmacological Inhibition of Poly(ADP-Ribose) Polymerases Improves Fitness and Mitochondrial Function in Skeletal Muscle.txt", + "d3dae048-6a34-4ab5-9c47-4f11da232b97": "2008 - Studies on Syntaxin 12 and Alcohol Preference Involving C57BL6J and DBA2J Strains of Mice.txt", + "0140d814-c394-4293-89bf-81f94fd22012": "2006 - Characterization of genetic differences within the centrally projecting Edinger–Westphal nucleus of C57BL6J and DBA2J mice by expression profiling_William J Giardino, Dawn M Cote, Ju Li, Andrey.txt", + "32338b01-15af-4ec9-9bc4-e9c58b53068e": "2015 - Genetic properties of the MAGIC maize population a new platform for high definition QTL mapping in Zea mays.txt", + "a68c1746-5f14-4226-af75-10c0988b2d38": "2005 - Quantitative Trait Locus (QTL) mapping of mechanical sensitivity and peripheral nerve injury-induced neuropathic mechanical allodynia in Recombinant Inbred (RI) mice using www.webqtl.org.txt", + "5964906e-b016-4a60-b043-db826b438048": "2008 - Variation in mouse basolateral amygdala volume is associated with differences in stress reactivity and fear learning.txt", + "12780adb-bba7-43fe-9e36-2dc6b13afa93": "2016 - Influenza H3N2 infection of the collaborative cross founder strains reveals highly divergent host responses and identifies a unique phenotype in CASTEiJ mice.txt", + "3517925b-cdcd-477c-9632-09dadec2dffd": "2016 - Decreased expression levels of Ifi genes is associated to the increased resistance to spontaneous arthritis disease in mice deficiency of IL-1RA.txt", + "e70edf15-a163-4db3-9346-6d3b69cdc6d3": "2012 - Hepatocellular carcinoma as extracolonic manifestation of Lynch syndrome indicates SEC63 as potential target gene in hepatocarcinogenesis.txt", + "a6c28701-9fcd-4e0a-9d1d-26c63b28a6e7": "2012 - Genetic Control of a Central Pattern Generator Rhythmic Oromotor Movement in Mice Is Controlled by a Major Locus near Atp1a2.txt", + "7a81de58-67b5-4185-bc89-bcf50a7032d4": "2017 - Sex difference in the expression and gene network of epidermal growth factor receptor in pituitary gland in mice.txt", + "7ca1b7d0-cbae-4c68-b8e8-610435d84f9f": "2013 - Congenic Mice Provide Evidence for a Genetic Locus That Modulates Spontaneous Arthritis Caused by Deficiency of IL-1RA.txt", + "d2749f7d-2943-4c3e-ae5a-ac3999aad956": "2005 - Regression-based quantitative trait loci mapping robust, efficient and effective.txt", + "e2799196-122f-4b4f-a2a6-68adf24a236f": "2008 - Using hippocampal microRNA expression differences between mouse inbred strains to characterise miRNA function.txt", + "adf2ef89-dd1c-4b90-8eea-9d14a3952f6a": "2013 - Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli_Irit Gat-Viks, Nicolas Chevrier, [...], and Aviv.txt", + "448232de-41b9-4c26-82fc-d3e2126ad1dd": "2011 - THREE APPROACHES TO INVESTIGATING AN EPIGENETIC BASIS TO NICOTINE CONSUMPTION IN ADOLESCENT MICE AGOUTI VIABLE YELLOW PROGRAMMING, METHYL DONOR SUPPLEMENTATION, AND MATERNAL CARE.txt", + "a67372ac-02b7-41c4-bb55-5152444c5479": "2006 - Gene expression profiling in the striatum of inbred mouse strains with distinct opioid-related phenotypes.txt", + "91f1c2e6-da3e-4709-ab7f-117297f1aea8": "2012 - Using Genome-Wide Expression Profiling to Define Gene Networks Relevant to the Study of Complex Traits From RNA Integrity to Network Topology.txt", + "dee4f645-0cce-42f8-8cb5-66efb1378d82": "2004 - P2P-R expression is genetically coregulated with components of the translation machinery and with PUM2, a translational repressor that associates with the P2P-R mRNA.txt", + "6d78d290-1edb-40aa-9bf9-a77998e47671": "2012 - Methods for scoring the collective effect of SNPs Minor alleles of common SNPs quantitatively affect traits diseases and are under both positive and negative selection.txt", + "e34e7f49-66e0-4c99-8f7d-efe109589bf3": "53b7b8006154d7cb2f4be3d20696a79d.pdf", + "d74b9d37-258f-440c-afdd-cb3ed7c14f34": "glm.pdf" +}
\ No newline at end of file diff --git a/gn3/llms/errors.py b/gn3/llms/errors.py new file mode 100644 index 0000000..006e034 --- /dev/null +++ b/gn3/llms/errors.py @@ -0,0 +1,57 @@ + +# pylint: skip-file +import json + +from requests import HTTPError + +class UnprocessableEntity(HTTPError): + """An HTTP 422 Unprocessable Entity error occurred. + + https://help.helpjuice.com/en_US/api-v3/api-v3#errors + + The request could not be processed, usually due to a missing or invalid parameter. + + The response will also include an error object with an explanation of fields that + are missing or invalid. Here is an example: + + .. code-block:: + + HTTP/1.1 422 Unprocessable Entity + + + { + "errors": [ + { + "email": "is not valid." + } + ] + } + """ + + def __init__(self, request, response): + """UnprocessableEntity constructor. + + Parses out error information from the error object and passes on to the + :obj:`HTTPError` constructor. + + Args: + exc (:obj:`HTTPError`): Original exception. + """ + rq_json = next(iter(json.loads(request.body.decode()).values())) + errors = response.json() + + for field, error in errors.items(): + rq_field = rq_json.get(field, None) + if not rq_field: + continue + + if isinstance(error, list): + error = error.insert(0, rq_field) + elif isinstance(error, str): + error = f"{rq_field} {error}" + + msg = json.dumps(errors) + super(HTTPError, self).__init__(msg, request=request, response=response) + + +
\ No newline at end of file diff --git a/gn3/llms/gn_bib.json b/gn3/llms/gn_bib.json new file mode 100644 index 0000000..8758fa1 --- /dev/null +++ b/gn3/llms/gn_bib.json @@ -0,0 +1,5287 @@ +{ + "parker_systems2017": + { + "filename": "2017-Parker-Systems Genetic Analysis in GeneNetwork.org.pdf", + "TITLE": "Systems genetic analysis in GeneNetwork.org", + "volume": 79, + "issn": "2691-1299", + "url": "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpns.23", + "doi": "10.1002/cpns.23", + "language": "en", + "number": 1, + "urldate": "2023-02-01", + "journal": "Current Protocols in Neuroscience", + "AUTHOR": "Parker, Clarissa C. and Dickson, Price E.and Philip, Vivek M. and Thomas, Mary and Chesler, Elissa J.", + "month": "Apr", + "year": 2017, + "pages": "8-39" + }, + "andreux_systems2012": + { + "filename": "2012-Andreux-BXDMurineReferencePanel.pdf", + "TITLE": "Systems Genetics of Metabolism: The Use of the BXD Murine Reference Panel for Multiscalar Integration of Traits", + "volume": 150, + "issn": "1097-4172", + "url": "https://www.cell.com/fulltext/S0092-8674(12)01007-0", + "doi": "doi.org/10.1016/j.cell.2012.08.012", + "language": "en", + "number": 6, + "urldate": "2023-01-23", + "journal": "Cell", + "AUTHOR": "Andreux, Penelope A. and Williams, Evan G. and Koutnikova, Hana and Houtkooper, Riekelt H. and Champy, Marie-France and Henry, Hugues and Schoonjans, Kristina and Williams, Robert W. and Auwerx, Johan", + "month": "Sep", + "year": 2012, + "pages": "1287--1299," + }, + "druka_towards2008": + { + "filename": "2008-Druka-IntegrationofPhenotypicGeneNetwork.pdf", + "TITLE": "Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork", + "volume": 9, + "issn": "1471-2156", + "url": "https://bmcgenomdata.biomedcentral.com/articles/10.1186/1471-2156-9-73", + "doi": "10.1186/1471-2156-9-73", + "language": "en", + "number": 1, + "urldate": "2023-01-18", + "journal": "BMC Genetics", + 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protein tau gene.pdf", + "TITLE": "Expression QTL and regulatory network analysis of microtubule-associated protein tau gene", + "volume": 15, + "issn": "1353-8020", + "url": "https://www.sciencedirect.com/science/article/abs/pii/S1353802009000248", + "doi": "10.1016/j.parkreldis.2008.10.010", + "language": "en", + "number": 7, + "urldate": "2023-07-27", + "journal": "Parkinsonism and Related Disorders", + "AUTHOR": "Shen, Qin and Wang, Xusheng and Chen, Ying and Xu, Lingli and Wang, Xiaodong and Lu, Lu", + "month": "Aug", + "year": 2009, + "pages": "525--531" + }, + "wang_joint2016": + { + "filename": "2016-Wang-Phenome-wide association to test gene.pdf", + "TITLE": "Joint mouse-human phenome-wide association to test gene function and disease risk", + "volume": 7, + "issn": "2041-1723", + "url": "https://www.nature.com/articles/ncomms10464", + "doi": "10.1038/ncomms10464", + "language": "en", + "number": 1, + "urldate": "2023-01-27", + "journal": "Nature Communications", + "AUTHOR": 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"https://www.cambridge.org/core/journals/development-and-psychopathology/article/abs/agerelated-changes-of-gene-expression-in-the-neocortex-preliminary-data-on-rnaseq-of-the-transcriptome-in-three-functionally-distinct-cortical-areas/07FD49218DF8284CF43799367858326B", + "doi": "10.1017/S0954579412000818", + "language": "en", + "number": 4, + "urldate": "2023-01-24", + "journal": "Development and psychopathology", + "AUTHOR": "Naumova, Oksana Yu and Palejev, Dean and Vlasova, Natalia V and Lee, Maria and Rychkov, Sergei Yu and Babich, Olga N and Vaccarino, Flora M and Grigorenko, Elena L", + "year": 2012, + "month": "Nov", + "pages": "1427--1442" + }, + "munguba_effects2013": + { + "filename": "2013-Munguba-Effects of Glaucoma on Chrna6 Expression in the Retina.pdf", + "TITLE": "Effects of glaucoma on Chrna6 expression in the retina", + "volume": 38, + "issn": "0271-3683, 1460-2202", + "url": "https://www.tandfonline.com/doi/full/10.3109/02713683.2012.724512", + "doi": "10.3109/02713683.2012.724512", + "language": "en", + "number": 1, + "urldate": "2023-02-06", + "journal": "Current eye research", + "AUTHOR": "Munguba, Gustavo C and Geisert, Eldon E and Williams, Robert W and Tapia, Mary L and Lam, Daisy K and Bhattacharya, Sanjoy K and Lee, Richard K", + "year": 2013, + "month": "Feb", + "pages": "150--157" + }, + "marenco_nif2010": + { + "filename": "2010-Marenco-The NIF DISCO Framework Facilitating Automated Integration of Neuroscience Content on the Web.pdf", + "TITLE": "The NIF DISCO framework: facilitating automated integration of neuroscience content on the web", + "volume": 8, + "issn": "1539-2791, 1559-0089", + "url": "https://link.springer.com/article/10.1007/s12021-010-9068-8", + "doi": "10.1007/s12021-010-9068-8", + "language": "en", + "urldate": "2023-01-22", + "journal": "Neuroinformatics", + "AUTHOR": "Marenco, Luis and Wang, Rixin and Shepherd, Gordon M and Miller, Perry L", + "year": 2010, + "month": "Jun", + "pages": "101--112" + }, + "crabbe_human2010": + { + "filename": "2010-Crabbe-Human and laboratory rodent low response to alcohol Is better consilience possible.pdf", + "TITLE": "Human and laboratory rodent low response to alcohol: is better consilience possible?", + "volume": 15, + "issn": "1355-6215, 1369-1600", + "url": "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1369-1600.2009.00191.x", + "doi": "10.1111/j.1369-1600.2009.00191.x", + "language": "en", + "number": 2, + "urldate": "2023-02-06", + "journal": "Addiction biology", + "AUTHOR": "Crabbe, John C and Bell, Richard L and Ehlers, Cindy L", + "year": 2010, + "month": "Apr", + "pages": "125--144" + }, + "loos_impact2016": + { + "filename": "2016-Loos-Impact of genetic variation on synaptic protein levels in genetically diverse mice.pdf", + "TITLE": "Impact of genetic variation on synaptic protein levels in genetically diverse mice", + "volume": 16, + "issn": "1615-9853, 1615-9861", + "url": "https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201500154", + "doi": "10.1002/pmic.201500154", + "language": "en", + "number": 7, + "urldate": "2023-02-06", + "journal": "Proteomics", + "AUTHOR": "Loos, Maarten and Li, Ka Wan and van der Schors, Roel and Gouwenberg, Yvonne and van der Loo, Rolinka and Williams, Robert W and Smit, August B and Spijker, Sabine", + "year": 2016, + "month": "Apr", + "pages": "1123--1130" + }, + "shpyleva_cerebellar2014": + { + "filename": "2014-Shpyleva-Cerebellar oxidative DNA damage and altered DNA methylation in the BTBR T+ tfJ mouse model of autism and similarities with human post mortem cerebellum.pdf", + "TITLE": "Cerebellar oxidative DNA damage and altered DNA methylation in the BTBR T+ tf/J mouse model of autism and similarities with human post mortem cerebellum", + "volume": 9, + "issn": "1615-9853, 1615-9861", + "url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0113712", + "doi": "10.1371/journal.pone.0113712", + "language": "en", + "number": 11, + "urldate": "2023-02-06", + "journal": "Plos one", + "AUTHOR": "Shpyleva, Svitlana and Ivanovsky, Samuil and de Conti, Aline and Melnyk, Stepan and Tryndyak, Volodymyr and Beland, Frederick A and James, S Jill and Pogribny, Igor P", + "year": 2014, + "month": 11, + "pages": "e113712" + }, + "thomas_quantitative2020": + { + "filename": "2020-Thomas-Quantitative trait locus mapping identifies Col4a6 as a novel regulator of striatal dopamine level and axonal branching in mice.pdf", + "TITLE": "Quantitative trait locus mapping identifies Col4a6 as a novel regulator of striatal dopamine level and axonal branching in mice", + "issn": "2692-8205", + "url": "https://www.biorxiv.org/content/10.1101/2020.06.28.176206v1.abstract", + "doi": "10.1101/2020.06.28.176206 ", + "language": "en", + "urldate": "2023-02-06", + "journal": "bioRvix", + "AUTHOR": "Thomas, M{\\'e}lanie H and Gui, Yujuan and Garcia, Pierre and Karout, Mona and Jaeger, Christian and Hodak, Zdenka and Michelucci, Alessandro and Kollmus, Heike and Centeno, Arthur and Schughart, Klaus", + "year": 2020, + "month": "Jun", + "pages": "2020-06" + }, + "hoffman_using2011": + { + "filename": "2011-Hoffman-Using the PhenoGen Website for “In Silico” Analysis of Morphine-Induced Analgesia Identifying Candidate Genes.pdf", + "TITLE": "Using the Phenogen website for ‘in silico’analysis of morphine-induced analgesia: Identifying candidate genes", + "volume": 16, + "issn": "1355-6215, 1369-1600", + "url": "https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1369-1600.2010.00254.x", + "doi": "10.1111/j.1369-1600.2010.00254.x", + "language": "en", + "number": 3, + "urldate": "2023-02-06", + "journal": "Addiction biology", + "AUTHOR": "Hoffman, Paula L and Bennett, Beth and Saba, Laura M and Bhave, Sanjiv V and Carosone-Link, Phyllis J and Hornbaker, Cheryl K and Kechris, Katerina J and Williams, Robert W and Tabakoff, Boris", + "year": 2011, + "month": "Jul", + "pages": "393--404" + }, + "ashbrook_born2018": + { + "filename": "2018-Ashbrook-Born to Cry A Genetic Dissection of Infant Vocalization.pdf", + "TITLE": "Born to cry: A genetic dissection of infant vocalization", + "volume": 12, + "issn": "16625153", + "url": "https://www.frontiersin.org/articles/10.3389/fnbeh.2018.00250/full", + "doi": "10.3389/fnbeh.2018.00250", + "language": "en", + "urldate": "2023-02-01", + "journal": "Frontiers in Behavioral Neuroscience", + "AUTHOR": "Ashbrook, David George and Roy, Snigdha and Clifford, Brittany G and Riede, Tobias and Scattoni, Maria Luisa and Heck, Detlef H and Lu, Lu and Williams, Robert W", + "year": 2018, + "month": "Oct", + "pages": "250" + }, + "bernstein_differential2015": + { + "filename": "2015 - Differential regional and cellular distribution of TFF3 peptide in the human brain.pdf", + "TITLE": "Differential regional and cellular distribution of TFF3 peptide in the human brain", + "volume": 47, + "issn": "09394451, 14382199", + "url": "https://link.springer.com/article/10.1007/s00726-015-1938-9", + "doi": "10.1007/s00726-015-1938-9", + "language": "en", + "urldate": "2023-01-18", + "journal": "Amino Acids", + "AUTHOR": "Bernstein, Hans-Gert and Dobrowolny, Henrik and Tr{\"u}bner, Kurt and Steiner, Johann and Bogerts, Bernhard and Hoffmann, Werner", + "year": 2015, + "month": "May", + "pages": "1053--1063" + }, + "roy2019evaluation": + { + "filename":"2019-Roy-Evaluation of Sirtuin-3 probe quality and co-expressed genes", + "TITLE":"Evaluation of Sirtuin-3 probe quality and co-expressed genes using literature cohesion", + "AUTHOR":"Roy, Sujoy and Zaman, Kazi I and Williams, Robert W and Homayouni, Ramin", + "JOURNAL": "BMC bioinformatics", + "URL": "https://link.springer.com/article/10.1186/s12859-019-2621-z", + "DOI": "10.1186/s12859-019-2621-z", + "ISSN": "1471-2105", + "URLDATE": "2023-08-04", + "VOLUME": "20", + "PAGES": "31--43", + "YEAR": 2019, + "MONTH": 3, + "PUBLISHER": "Springer" + } +} diff --git a/gn3/llms/process.py b/gn3/llms/process.py new file mode 100644 index 0000000..4220d7a --- /dev/null +++ b/gn3/llms/process.py @@ -0,0 +1,111 @@ + +# pylint: skip-file + +import requests +import sys +import time +import string +import json +import os +from gn3.llms.client import GeneNetworkQAClient +from gn3.llms.response import DocIDs + + +baseUrl = 'https://genenetwork.fahamuai.com/api/tasks' +answerUrl = baseUrl + '/answers' +basedir = os.path.abspath(os.path.dirname(__file__)) +apiClient = GeneNetworkQAClient(requests.Session(), api_key='') + + + + + + + + + +def formatBibliographyInfo(bibInfo): + if isinstance(bibInfo, str): + # remove '.txt' + bibInfo = bibInfo.removesuffix('.txt') + elif isinstance(bibInfo, dict): + # format string bibliography information + bibInfo = "{0}. ".format(bibInfo['author'], bibInfo['title'], bibInfo['year'], bibInfo['doi']) + return bibInfo + + +def askTheDocuments( extendUrl, my_auth ): + try: + res = requests.post(baseUrl+extendUrl, + data={}, + headers=my_auth) + res.raise_for_status() + except: + raise # what + if (res.status_code != 200): + return negativeStatusMsg(res), 0 + task_id = getTaskIDFromResult(res) + res = getAnswerUsingTaskID(task_id, my_auth) + if (res.status_code != 200): + return negativeStatusMsg(res), 0 + return res, 1 + +def getAnswerUsingTaskID( extendUrl, my_auth ): + try: + res = requests.get(answerUrl+extendUrl, data={}, headers=my_auth) + res.raise_for_status() + except: + raise + return res + +def openAPIConfig(): + f = open(os.path.join(basedir, "api.config.json") , "rb" ) + result = json.load(f) + f.close() + return result + + +def getTaskIDFromResult(res): + task_id = json.loads(res.text) + result = '?task_id=' + str(task_id['task_id']) + return result + +def negativeStatusMsg(res): + return 'Problems\n\tStatus code => {0}\n\tReason=> {res.reason}'.format(res.status_code, res.reason) + +def filterResponseText(val): + return json.loads(''.join([str(char) for char in val if char in string.printable])) + +def getGNQA(query): + res, task_id = apiClient.ask('?ask=' + query) + res, success = apiClient.get_answer(task_id) + + if ( success == 1 ): + respText = filterResponseText(res.text) + if respText.get("data") is None: + return "Unfortunately I have nothing on the query",[] + answer = respText['data']['answer'] + context = respText['data']['context'] + references = parse_context(context) + return answer,references + else: + return res, "Unfortunately I have nothing." + + + +def parse_context(context): + """parse content map id to reference""" + result = [] + for doc_ids,summary in context.items(): + comboTxt = "" + for entry in summary: + comboTxt += '\t' + entry['text'] + + docInfo = DocIDs().getInfo(doc_ids) + if doc_ids !=docInfo: + bibInfo = formatBibliographyInfo(docInfo) + + else: + bibInfo = doc_ids + result.append({"doc_id":doc_ids,"bibInfo":bibInfo,"comboTxt":comboTxt}) + return result
\ No newline at end of file diff --git a/gn3/llms/response.py b/gn3/llms/response.py new file mode 100644 index 0000000..9172860 --- /dev/null +++ b/gn3/llms/response.py @@ -0,0 +1,75 @@ + +# pylint: skip-file +import string +import json +import os + + +basedir = os.path.abspath(os.path.dirname(__file__)) + + +class DocIDs(): + def __init__(self): + # open doc ids for GN refs + self.doc_ids = self.loadFile("doc_ids.json") + # open doc ids for Diabetes references + self.sugar_doc_ids = self.loadFile("sugar_doc_ids.json") + # format is not what I prefer, it needs to be rebuilt + self.formatDocIDs(self.sugar_doc_ids) + + def loadFile(self, file_name): + file_path = os.path.join(basedir, file_name) + if os.path.isfile(file_path): + f = open(file_path, "rb") + result = json.load(f) + f.close() + return result + else: + raise Exception("\n{0} -- File does not exist\n".format(file_path)) + + def formatDocIDs(self, values): + for _key, _val in values.items(): + if isinstance(_val, list): + for theObject in _val: + docName = self.formatDocumentName(theObject['filename']) + docID = theObject['id'] + self.doc_ids.update({docID: docName}) + + def formatDocumentName(self, val): + result = val.removesuffix('.pdf') + result = result.removesuffix('.txt') + result = result.replace('_', ' ') + return result + + + def getInfo(self, doc_id): + if doc_id in self.doc_ids.keys(): + return self.doc_ids[doc_id] + else: + return doc_id + +class RespContext(): + def __init__(self, context): + self.cntxt = context + self.theObj = {} + + def parseIntoObject(self, info): + # check for obj, arr, or val + for key, val in info.items(): + if isinstance(val, list): + self.parseIntoObject(val) + elif isinstance(val, str) or isinstance(val, int): + self.theObj[key] = val + self.theObj[key] = self.val + + +def createAccordionFromJson(theContext): + result = '' + # loop thru json array + ndx = 0 + for docID, summaryLst in theContext.items(): + # item is a key with a list + comboTxt = '' + for entry in summaryLst: + comboTxt += '\t' + entry['text'] + return result
\ No newline at end of file diff --git a/gn3/llms/sugar_doc_ids.json b/gn3/llms/sugar_doc_ids.json new file mode 100644 index 0000000..686867b --- /dev/null +++ b/gn3/llms/sugar_doc_ids.json @@ -0,0 +1,7796 @@ +{ + "data": [ + { + "filename": "2019 - Machine-learning to stratify diabetic patients using novel cardiac biomarkers and integrative genomics.pdf", + "id": "5d9d5e09-f80b-496a-b6b2-dfc7d7cf7f2b" + }, + { + "filename": "2015 - The 6 year incidence of diabetes-associated autoantibodies in genetically at-risk children the TEDDY study.pdf", + "id": "733e85a8-8ba1-4aae-8ce0-8597faaeefc7" + }, + { + "filename": "2003 - A functional polymorphism in the promoterenhancer region of the FOXP3Scurfin gene associated with type 1 diabetes.pdf", + "id": "7d331e2e-0bed-4d06-880f-f882c6d07214" + }, + { + "filename": "2018 - Genome-wide association studies of albuminuria towards genetic stratification in diabetes.pdf", + "id": "2ad3a7ba-8f21-4a1d-a92d-a3b3c9aa02e0" + }, + { + "filename": "2020 - Fine-tuning of Genome-Wide Polygenic Risk Scores and Prediction of Gestational Diabetes in South Asian Women.pdf", + "id": "a644f3d8-5b62-4416-b787-66c0de198beb" + }, + { + "filename": "2001 Nadkarni BayesCausal Approach.txt", + "id": "713ad3a2-efa9-44af-8639-f4e67efc7001" + }, + { + "filename": "2021 - Genomic Medicine in Diabetes Improving the Diagnostic Rate of Monogenic Diabetes.pdf", + "id": "7f5fa726-75d1-47c9-a6d7-dae36b0cb211" + }, + { + "filename": "2022 -Tabbaa- Mouse pop genetics.pdf", + "id": "87e43e53-85e4-4ad6-8e5f-c6b5e3b99202" + }, + { + "filename": "2019 - A genome wide association study implicates that the TTC39C gene is associated with diabetic maculopathy with decreased visual acuity.pdf", + "id": "8b086e53-79f4-498a-91e0-48f6217388d7" + }, + { + "filename": "2013 - Mutations in the genes encoding the transcription factors Hepatocyte Nuclear Factor 1.pdf", + "id": "09218e05-177e-438a-9526-a7572ecfbf6a" + }, + { + "filename": "2003 -WebQTL rapid exploratory analysis 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