From b0778fb1cb1f622bfc4cf4813d871ca497c14c7d Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Wed, 17 Mar 2021 15:35:17 +0100 Subject: [PATCH 01/26] Add datadiscovery fields --- .../documents/datadiscovery_germplasm.json | 29 ++++++- .../documents/datadiscovery_study.json | 75 ++++++++++++++++++- 2 files changed, 102 insertions(+), 2 deletions(-) diff --git a/config/transform-elasticsearch/documents/datadiscovery_germplasm.json b/config/transform-elasticsearch/documents/datadiscovery_germplasm.json index 3d9dc74..59a38a0 100644 --- a/config/transform-elasticsearch/documents/datadiscovery_germplasm.json +++ b/config/transform-elasticsearch/documents/datadiscovery_germplasm.json @@ -4,8 +4,12 @@ "document-transform": { "@type": [ "Germplasm" ], + "entryType": [ "Germplasm" ], "@id": "{.germplasmPUI}", + "identifier": "{.germplasmPUI}", + "name": "{.germplasmName}", + "accessionHolder": "{.holdingInstitute.instituteName}", "schema:includedInDataCatalog": "{.source}", "schema:identifier": "{.germplasmDbId}", "schema:name": { @@ -16,6 +20,7 @@ ] }, "schema:url": "{.documentationURL}", + "url": "{.documentationURL}", "schema:description": { "{join}": [ "\"", @@ -30,6 +35,28 @@ " {.comment}" ] }, + "description": { + "{join}": [ + "\"", + { "{or}": ["{.germplasmName}", "{.defaultDisplayName}"] }, + "\" is a", + " {.genus + .species + .subtaxa}", + " ({.commonCropName})", + " accession", + " (number: \"{.accessionNumber}\")", + " managed by {.holdingInstitute.instituteName}", + ".", + " {.comment}" + ] + }, + + "species": { + "{or}": [ + "{.genusSpecies}", + "{.genus}", + "{.species}" + ] + }, "germplasm": { "cropName": { @@ -67,4 +94,4 @@ } } } -} +} \ No newline at end of file diff --git a/config/transform-elasticsearch/documents/datadiscovery_study.json b/config/transform-elasticsearch/documents/datadiscovery_study.json index 97080a9..a101379 100644 --- a/config/transform-elasticsearch/documents/datadiscovery_study.json +++ b/config/transform-elasticsearch/documents/datadiscovery_study.json @@ -41,14 +41,57 @@ } ] }, + "entryType": { + "{list}": [ + { + "{or}": [ + { + "{replace}":{ + "possible_terms": [ + "Genotyping", "Genotyping Study", + "allele size", "genotype" + ] + }, + "{with}": { + "replaced_by": "Genotyping Study" + } + }, + { + "{replace}":{ + "possible_terms": [ + "Phenotypes", "Phenotyping", "Field Experiement", + "Greenhouse (29\u00baC/20\u00baC)", "Green house", + "Growth chamber", "Phenotyping Study", "Provenance trial", + "Half sibling progeny trial", "Clonal trial", "Progeny trial", + "Other", "Provenance and half sibling progeny trial", + "Species comparison", "Seed orchard", "Demonstration test", + "Full sibling progeny trial", "Juveniles comparison", + "Clonal archiva, clone bank", "Conservation plot", + "Biomasse test - sylvabiom", "Response study", "raw" + ] + }, + "{with}": { + "replaced_by": "Phenotyping Study" + } + }, + "Study" + ] + } + ] + }, "@id": "{.studyPUI}", + "identifier": "{.studyPUI}", "schema:includedInDataCatalog": "{.source}", "schema:identifier": "{.studyDbId}", "schema:name": { "{or}": ["{.studyName}", "{.name}"] }, + "name": { + "{or}": ["{.studyName}", "{.name}"] + }, "schema:url": "{.documentationURL}", + "url": "{.documentationURL}", "schema:description": { "{join}": [ "\"", @@ -71,6 +114,36 @@ " {.studyDescription}" ] }, + "description": { + "{join}": [ + "\"", + { "{or}": ["{.studyName}", "{.name}"] }, + "\" is a ", + { "{or}": ["{.studyTypeName}", "{.studyType}", "study"] }, + { "{or}": [" conducted from {.startDate} to {.endDate}", " running since {.startDate}"] }, + { "{or}": [ + { "{join}": [ + " (seasons: ", {"{join}": ["{.seasons.season}", "{.seasons.year}"], "{separator}": ", "}, ")"], + "{accept_none}": false }, + { "{join}": [" (seasons: ", {"{join}": "{.seasons}", "{separator}": ", "}, ")"], "{accept_none}": false } + ]}, + { "{or}": [ + " in {.locationURI => .locationName} ({.locationURI => .countryName})", + " in {.locationURI => .countryName}" + ]}, + ". this study is part of the {.programName} program", + ".", + " {.studyDescription}" + ] + }, + + "species": { + "{or}": [ + "{.germplasmURIs => .genus + .species + .subtaxa}", + "{.germplasmURIs => .genus + .species}", + "{.germplasmURIs => .genus}" + ] + }, "germplasm": { "cropName": { @@ -109,4 +182,4 @@ } } } -} +} \ No newline at end of file From 0721f8ae135e306cee39bce787260a3a975de364 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Thu, 8 Apr 2021 11:46:40 +0200 Subject: [PATCH 02/26] fix: Correcting DataDiscovery template - GNP-6003 --- .../documents/datadiscovery_germplasm.json | 17 +- .../documents/datadiscovery_study.json | 243 +++++++++--------- 2 files changed, 136 insertions(+), 124 deletions(-) diff --git a/config/transform-elasticsearch/documents/datadiscovery_germplasm.json b/config/transform-elasticsearch/documents/datadiscovery_germplasm.json index 59a38a0..a3121be 100644 --- a/config/transform-elasticsearch/documents/datadiscovery_germplasm.json +++ b/config/transform-elasticsearch/documents/datadiscovery_germplasm.json @@ -4,12 +4,11 @@ "document-transform": { "@type": [ "Germplasm" ], - "entryType": [ "Germplasm" ], + "entryType": "Germplasm", "@id": "{.germplasmPUI}", "identifier": "{.germplasmPUI}", "name": "{.germplasmName}", - "accessionHolder": "{.holdingInstitute.instituteName}", "schema:includedInDataCatalog": "{.source}", "schema:identifier": "{.germplasmDbId}", "schema:name": { @@ -37,13 +36,12 @@ }, "description": { "{join}": [ - "\"", { "{or}": ["{.germplasmName}", "{.defaultDisplayName}"] }, - "\" is a", + " is a", " {.genus + .species + .subtaxa}", " ({.commonCropName})", " accession", - " (number: \"{.accessionNumber}\")", + " (number: {.accessionNumber})", " managed by {.holdingInstitute.instituteName}", ".", " {.comment}" @@ -92,6 +90,13 @@ "{.studyURIs => .observationVariableDbIds}" ] } + }, + "node": "{.source}", + "databaseName": { + "{join}": [ + "brapi@", + "{.source}" + ] } } -} \ No newline at end of file +} diff --git a/config/transform-elasticsearch/documents/datadiscovery_study.json b/config/transform-elasticsearch/documents/datadiscovery_study.json index a101379..2107076 100644 --- a/config/transform-elasticsearch/documents/datadiscovery_study.json +++ b/config/transform-elasticsearch/documents/datadiscovery_study.json @@ -1,142 +1,139 @@ { "document-type": "datadiscovery", "source-entity": "study", - "document-transform": { - "@type": { - "{list}": [ - { - "{or}": [ - { - "{replace}":{ - "possible_terms": [ - "Genotyping", "Genotyping Study", - "allele size", "genotype" - ] - }, - "{with}": { - "replaced_by": "Genotyping Study" - } - }, - { - "{replace}":{ - "possible_terms": [ - "Phenotypes", "Phenotyping", "Field Experiement", - "Greenhouse (29\u00baC/20\u00baC)", "Green house", - "Growth chamber", "Phenotyping Study", "Provenance trial", - "Half sibling progeny trial", "Clonal trial", "Progeny trial", - "Other", "Provenance and half sibling progeny trial", - "Species comparison", "Seed orchard", "Demonstration test", - "Full sibling progeny trial", "Juveniles comparison", - "Clonal archiva, clone bank", "Conservation plot", - "Biomasse test - sylvabiom", "Response study", "raw" - ] - }, - "{with}": { - "replaced_by": "Phenotyping Study" - } - }, - "Study" - ] - } - ] - }, "entryType": { - "{list}": [ + "{or}": [ { - "{or}": [ - { - "{replace}":{ - "possible_terms": [ - "Genotyping", "Genotyping Study", - "allele size", "genotype" - ] - }, - "{with}": { - "replaced_by": "Genotyping Study" - } - }, - { - "{replace}":{ - "possible_terms": [ - "Phenotypes", "Phenotyping", "Field Experiement", - "Greenhouse (29\u00baC/20\u00baC)", "Green house", - "Growth chamber", "Phenotyping Study", "Provenance trial", - "Half sibling progeny trial", "Clonal trial", "Progeny trial", - "Other", "Provenance and half sibling progeny trial", - "Species comparison", "Seed orchard", "Demonstration test", - "Full sibling progeny trial", "Juveniles comparison", - "Clonal archiva, clone bank", "Conservation plot", - "Biomasse test - sylvabiom", "Response study", "raw" - ] - }, - "{with}": { - "replaced_by": "Phenotyping Study" - } - }, - "Study" - ] - } + "{replace}": { + "possible_terms": [ + "Genotyping", + "Genotyping Study", + "allele size", + "genotype" + ] + }, + "{with}": { + "replaced_by": "Genotyping Study" + } + }, + { + "{replace}": { + "possible_terms": [ + "", + null, + "Phenotypes", + "Phenotyping", + "Field Experiement", + "Greenhouse (29\u00baC/20\u00baC)", + "Green house", + "Growth chamber", + "Phenotyping Study", + "Provenance trial", + "Half sibling progeny trial", + "Clonal trial", + "Progeny trial", + "Other", + "Provenance and half sibling progeny trial", + "Species comparison", + "Seed orchard", + "Demonstration test", + "Full sibling progeny trial", + "Juveniles comparison", + "Clonal archiva, clone bank", + "Conservation plot", + "Biomasse test - sylvabiom", + "Response study", + "raw" + ] + }, + "{with}": { + "replaced_by": "Phenotyping Study" + } + }, + "Study" ] }, "@id": "{.studyPUI}", "identifier": "{.studyPUI}", - "schema:includedInDataCatalog": "{.source}", "schema:identifier": "{.studyDbId}", "schema:name": { - "{or}": ["{.studyName}", "{.name}"] + "{or}": [ + "{.studyName}", + "{.name}" + ] }, "name": { - "{or}": ["{.studyName}", "{.name}"] + "{or}": [ + "{.studyName}", + "{.name}" + ] }, "schema:url": "{.documentationURL}", "url": "{.documentationURL}", - "schema:description": { - "{join}": [ - "\"", - { "{or}": ["{.studyName}", "{.name}"] }, - "\" is a ", - { "{or}": ["{.studyTypeName}", "{.studyType}", "study"] }, - { "{or}": [" conducted from {.startDate} to {.endDate}", " running since {.startDate}"] }, - { "{or}": [ - { "{join}": [ - " (seasons: ", {"{join}": ["{.seasons.season}", "{.seasons.year}"], "{separator}": ", "}, ")"], - "{accept_none}": false }, - { "{join}": [" (seasons: ", {"{join}": "{.seasons}", "{separator}": ", "}, ")"], "{accept_none}": false } - ]}, - { "{or}": [ - " in {.locationURI => .locationName} ({.locationURI => .countryName})", - " in {.locationURI => .countryName}" - ]}, - ". this study is part of the {.programName} program", - ".", - " {.studyDescription}" - ] - }, "description": { "{join}": [ - "\"", - { "{or}": ["{.studyName}", "{.name}"] }, - "\" is a ", - { "{or}": ["{.studyTypeName}", "{.studyType}", "study"] }, - { "{or}": [" conducted from {.startDate} to {.endDate}", " running since {.startDate}"] }, - { "{or}": [ - { "{join}": [ - " (seasons: ", {"{join}": ["{.seasons.season}", "{.seasons.year}"], "{separator}": ", "}, ")"], - "{accept_none}": false }, - { "{join}": [" (seasons: ", {"{join}": "{.seasons}", "{separator}": ", "}, ")"], "{accept_none}": false } - ]}, - { "{or}": [ - " in {.locationURI => .locationName} ({.locationURI => .countryName})", - " in {.locationURI => .countryName}" - ]}, + { + "{or}": [ + "{.studyName}", + "{.name}" + ] + }, + " is a ", + { + "{or}": [ + "{.studyTypeName}", + "{.studyType}", + "study" + ] + }, + { + "{or}": [ + " conducted from {.startDate} to {.endDate}", + " running since {.startDate}" + ] + }, + { + "{or}": [ + { + "{join}": [ + " (seasons: ", + { + "{join}": [ + "{.seasons.season}", + "{.seasons.year}" + ], + "{separator}": ", " + }, + ")" + ], + "{accept_none}": false + }, + { + "{join}": [ + " (seasons: ", + { + "{join}": "{.seasons}", + "{separator}": ", " + }, + ")" + ], + "{accept_none}": false + } + ] + }, + { + "{or}": [ + " in {.locationURI => .locationName} ({.locationURI => .countryName})", + " in {.locationURI => .countryName}" + ] + }, ". this study is part of the {.programName} program", ".", " {.studyDescription}" ] }, - "species": { "{or}": [ "{.germplasmURIs => .genus + .species + .subtaxa}", @@ -144,7 +141,6 @@ "{.germplasmURIs => .genus}" ] }, - "germplasm": { "cropName": { "{list}": [ @@ -154,7 +150,12 @@ "{.germplasmURIs => .genus + .species}", "{.germplasmURIs => .genus + .species + .subtaxa}", "{.germplasmURIs => .taxonSynonyms}" - ], "{transform}": ["capitalize", "flatten", "distinct"] + ], + "{transform}": [ + "capitalize", + "flatten", + "distinct" + ] }, "germplasmList": { "{flatten_distinct}": [ @@ -173,13 +174,19 @@ ] } }, - "trait": { "observationVariableIds": { "{flatten_distinct}": [ "{.observationVariableDbIds}" ] } + }, + "node": "{.source}", + "databaseName": { + "{join}": [ + "brapi@", + "{.source}" + ] } } -} \ No newline at end of file +} From 08ea07cc41a73796e2cc21017e8e86b38c3350e4 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Mon, 12 Apr 2021 14:28:57 +0200 Subject: [PATCH 03/26] feat: Replace bulk files by json files --- etl/transform/elasticsearch.py | 57 ++++++++++++++++------------------ 1 file changed, 26 insertions(+), 31 deletions(-) diff --git a/etl/transform/elasticsearch.py b/etl/transform/elasticsearch.py index e36ca62..4f79e2e 100755 --- a/etl/transform/elasticsearch.py +++ b/etl/transform/elasticsearch.py @@ -132,43 +132,41 @@ def validate_documents(document_tuples, validation_schemas, logger): logger.debug(f"Validated {document_count} documents.") -def generate_bulk_headers(document_tuples): +def dump_in_json_files(source_dir, logger, documents_tuples): """ - Consumes an iterable of document type and document tuples and produces an iterable of tuples - (of bulk index header and document) + Consumes an iterable of document tuples """ - for document_type, document in document_tuples: - document_id = document['@id'] - bulk_header = {'index': {'_type': document_type, '_id': document_id}} - yield bulk_header, document - - -def dump_in_bulk_files(source_bulk_dir, logger, documents_tuples): - """ - Consumes an iterable of header and document tuples and dump into the JSONSplitStore - """ - logger.debug("Saving documents to bulk files...") + logger.debug("Saving documents to json files...") - json_stores = dict() + json_list = list() document_count = 0 for document_header, document in documents_tuples: - document_type = document_header['index']['_type'] - if document_type not in json_stores: - json_stores[document_type] = JSONSplitStore(source_bulk_dir, document_type) - - json_store = json_stores[document_type] + json_list.append(document) document_count += 1 if is_checkpoint(document_count): logger.debug(f"checkpoint: {document_count} documents saved") - # Dump batch of headers and documents in bulk file - json_store.dump(document_header, document) + save_json(document_count, source_dir, json_list) + + logger.debug(f"Total of {document_count} documents saved in json files.") + - # Close all json stores - for json_store in json_stores.values(): - json_store.close() - logger.debug(f"Total of {document_count} documents saved in bulk files.") +def save_json(document_count, source_dir, json_list): + file_number = 1 + saved_documents = 0 + if document_count <= 1000: + with open(source_dir +'.json', 'w') as f: + json.dump(json_list, f, ensure_ascii=False) + f.close() + + else: + while saved_documents < document_count: + with open(source_dir + '-' + str(file_number) + '.json', 'w') as f: + json.dump(json_list[saved_documents:file_number*10000], f, ensure_ascii=False) + f.close() + file_number += 1 + saved_documents += 10000 def get_document_configs_by_entity(document_configs): @@ -273,11 +271,8 @@ def transform_source(source, transform_config, source_json_dir, source_bulk_dir, # Validate the document schemas validated_documents = validate_documents(documents, validation_schemas, logger) - # Generate Elasticsearch bulk headers before each documents - documents_with_headers = generate_bulk_headers(validated_documents) - - # Write the documents in bulk files - dump_in_bulk_files(source_bulk_dir, logger, documents_with_headers) + # Write the documents in jsonfiles + dump_in_json_files(source_bulk_dir, logger, validated_documents) # shutil.rmtree(tmp_index_dir, ignore_errors=True) logger.info(f"SUCCEEDED Transforming BrAPI {source_name}.") From ccf18f5dbd8a91a522b1a1e00672fc41e113d48b Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Tue, 4 May 2021 14:28:49 +0200 Subject: [PATCH 04/26] Initial test creation --- tests/transform/integration/__init__.py | 0 .../fixtures/brapi_pheno_source/contact.json | 7 + .../brapi_pheno_source/germplasm.json | 665 ++++++++++++++++++ .../fixtures/brapi_pheno_source/location.json | 3 + .../observationVariable.json | 32 + .../fixtures/brapi_pheno_source/study.json | 27 + .../fixtures/brapi_pheno_source/trial.json | 4 + .../fixtures/test_es_integration.py | 12 + 8 files changed, 750 insertions(+) create mode 100644 tests/transform/integration/__init__.py create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/contact.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/location.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/observationVariable.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/study.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/trial.json create mode 100644 tests/transform/integration/fixtures/test_es_integration.py diff --git a/tests/transform/integration/__init__.py b/tests/transform/integration/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/contact.json b/tests/transform/integration/fixtures/brapi_pheno_source/contact.json new file mode 100644 index 0000000..3ab614f --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/contact.json @@ -0,0 +1,7 @@ +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Participating Investigator", "orcid": "0000-0001-6104-8479", "name": "Giorgio Pea", "contactDbId": "4010106321", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0002-1544-0979", "name": "Aye L. Hlaing", "contactDbId": "1213155226", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0003-3547-0195", "name": "Htay H. Aung", "contactDbId": "58550283", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Corresponding author", "email": "marioenrico.pe@santannapisa.it", "orcid": "0000-0001-6197-2282", "name": "Mario Enrico P\u00e8", "contactDbId": "3191909450", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "VIB - Center for Plant Systems Biology", "type": "Author", "email": "joke.baute@vib.be", "orcid": "0000-0003-0507-6904", "name": "Joke Baute", "contactDbId": "2601524745", "trialDbIds": ["4", "1", "3"], "source": "VIB"} +{"institutionName": "VIB - Center for Plant Systems Biology", "type": "Collecting data", "email": "joblo@psb.vib-ugent.be", "orcid": "0000-0003-0047-4380", "name": "Jolien De Block", "contactDbId": "3728271192", "trialDbIds": ["4", "1", "3"], "source": "VIB"} +{"institutionName": "VIB - Center for Plant Systems Biology", "type": "Corresponding author", "email": "dirk.inze@ugent.vib.be", "orcid": "0000-0002-3217-8407", "name": "Dirk Inz\u00e9", "contactDbId": "2564201848", "trialDbIds": ["4", "1", "3"], "source": "VIB"} diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json b/tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json new file mode 100644 index 0000000..6c7dfda --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json @@ -0,0 +1,665 @@ +{"countryOfOriginCode": "BE", "instituteCode": "VIB", "accessionNumber": "208", "defaultDisplayName": "A632 RIL 8-way ", "germplasmDbId": "Zea_VIB_A632RIL8way___208", "germplasmName": "A632 RIL 8-way ", "commonCropName": "Maize", "instituteName": "VIB", "species": "mays", "genus": "Zea", "source": "VIB", "studyDbIds": ["VIB_study___51"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1300", "defaultDisplayName": "ami-13-1", "germplasmDbId": "Arabidopsis_VIB_ami131___1300", "germplasmName": "ami-13-1", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1301", "defaultDisplayName": "ami-4-6", "germplasmDbId": "Arabidopsis_VIB_ami46___1301", "germplasmName": "ami-4-6", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1302", "defaultDisplayName": "ami-Col", "germplasmDbId": "Arabidopsis_VIB_amiCol___1302", "germplasmName": "ami-Col", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} +{"countryOfOriginCode": "BE", 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"RIL_2-way_growth_chamber", "trialDescription": "Assessed Variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complemented with measurements capturing growth dynamics, and cellular measurements.", "startDate": "2011-09-21", "trialDbId": "1", "source": "VIB", "studyDbIds": ["VIB_study___30", "VIB_study___31", "VIB_study___32", "VIB_study___33", "VIB_study___34", "VIB_study___27", "VIB_study___36", "VIB_study___28", "VIB_study___29", "VIB_study___39", "VIB_study___37", "VIB_study___35", "VIB_study___38"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} +{"publications": [{"publicationReference": "https://www.plantphysiol.org/cgi/doi/10.1104/pp.15.01883", "publicationPUI": "10.1104/pp.15.01883"}], "trialName": "RIL_8-way_growth_chamber", "trialDescription": "Indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations.", "startDate": "2012-06-16", "trialDbId": "3", "source": "VIB", "studyDbIds": ["VIB_study___48", "VIB_study___46", "VIB_study___47", "VIB_study___49", "VIB_study___44", "VIB_study___51", "VIB_study___45", "VIB_study___41", "VIB_study___50", "VIB_study___42", "VIB_study___40", "VIB_study___43"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} diff --git a/tests/transform/integration/fixtures/test_es_integration.py b/tests/transform/integration/fixtures/test_es_integration.py new file mode 100644 index 0000000..0f14c0e --- /dev/null +++ b/tests/transform/integration/fixtures/test_es_integration.py @@ -0,0 +1,12 @@ +import unittest + + +class MyTestCase(unittest.TestCase): + + + def test_something(self): + self.assertEqual(True, False) + + +#if __name__ == '__main__': +# unittest.main() From adc2de6c790e57dc378daddcbce5a503e59a2afa Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Tue, 4 May 2021 17:16:28 +0200 Subject: [PATCH 05/26] test_fixture WIP --- .../VIB_datadiscovery_expected.json | 1 + .../brapi_pheno_source/VIB_expected.json | 1 + .../VIB_germplasm_expected.json | 1343 ++++++++++++ .../VIB_location_expected.json | 1343 ++++++++++++ .../VIB_observation_variable_expected.json | 1807 +++++++++++++++++ .../VIB_study_expected.json | 1371 +++++++++++++ .../VIB_trial_expected.json | 1343 ++++++++++++ .../brapi_pheno_source/germplasm.json | 665 ------ .../{ => json/VIB}/contact.json | 6 +- .../json/VIB/germplasm.json | 4 + .../brapi_pheno_source/json/VIB/location.json | 2 + .../json/VIB/observationVariable.json | 14 + .../brapi_pheno_source/json/VIB/study.json | 3 + .../brapi_pheno_source/json/VIB/trial.json | 2 + .../fixtures/brapi_pheno_source/location.json | 3 - .../observationVariable.json | 32 - .../fixtures/brapi_pheno_source/study.json | 27 - .../fixtures/brapi_pheno_source/trial.json | 4 - .../fixtures/test_es_integration.py | 12 - .../integration/test_es_integration.py | 19 + 20 files changed, 7256 insertions(+), 746 deletions(-) create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_germplasm_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_observation_variable_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_trial_expected.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json rename tests/transform/integration/fixtures/brapi_pheno_source/{ => json/VIB}/contact.json (89%) create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/germplasm.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/location.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/observationVariable.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/study.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/trial.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/location.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/observationVariable.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/study.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/trial.json delete mode 100644 tests/transform/integration/fixtures/test_es_integration.py create mode 100644 tests/transform/integration/test_es_integration.py diff --git 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"Columbia/", "instituteCode": "VIB", "accessionNumber": "1311", "defaultDisplayName": "Zm-3-1", "germplasmDbId": "Arabidopsis_VIB_Zm31___1311", "germplasmName": "Zm-3-1", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/contact.json b/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/contact.json similarity index 89% rename from tests/transform/integration/fixtures/brapi_pheno_source/contact.json rename to tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/contact.json index 3ab614f..118db6b 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/contact.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/contact.json @@ -2,6 +2,6 @@ {"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0002-1544-0979", "name": "Aye L. 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a/tests/transform/integration/fixtures/brapi_pheno_source/trial.json b/tests/transform/integration/fixtures/brapi_pheno_source/trial.json deleted file mode 100644 index 5bacfc8..0000000 --- a/tests/transform/integration/fixtures/brapi_pheno_source/trial.json +++ /dev/null @@ -1,4 +0,0 @@ -{"publications": [{"publicationReference": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0716-z", "publicationPUI": "10.1186/s13059-015-0716-z"}], "trialName": "RIL_8-way_Field_trial", "endDate": "2012-08-01", "trialDescription": "1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines.", "startDate": "2012-05-01", "trialDbId": "2", "source": "VIB", "studyDbIds": ["VIB_study___55"], "contactDbIds": ["3191909450", "1213155226", "58550283", "4010106321"]} -{"publications": [{"publicationReference": "https://academic.oup.com/pcp/article/58/5/962/3069849", "publicationPUI": "10.1093/pcp/pcx035"}], "trialName": "D4_wiwam2", "endDate": 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"VIB_study___39", "VIB_study___37", "VIB_study___35", "VIB_study___38"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} -{"publications": [{"publicationReference": "https://www.plantphysiol.org/cgi/doi/10.1104/pp.15.01883", "publicationPUI": "10.1104/pp.15.01883"}], "trialName": "RIL_8-way_growth_chamber", "trialDescription": "Indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations.", "startDate": "2012-06-16", "trialDbId": "3", "source": "VIB", "studyDbIds": ["VIB_study___48", "VIB_study___46", "VIB_study___47", "VIB_study___49", "VIB_study___44", "VIB_study___51", "VIB_study___45", "VIB_study___41", "VIB_study___50", "VIB_study___42", "VIB_study___40", "VIB_study___43"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} diff --git a/tests/transform/integration/fixtures/test_es_integration.py b/tests/transform/integration/fixtures/test_es_integration.py deleted file mode 100644 index 0f14c0e..0000000 --- a/tests/transform/integration/fixtures/test_es_integration.py +++ /dev/null @@ -1,12 +0,0 @@ -import unittest - - -class MyTestCase(unittest.TestCase): - - - def test_something(self): - self.assertEqual(True, False) - - -#if __name__ == '__main__': -# unittest.main() diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py new file mode 100644 index 0000000..83d437a --- /dev/null +++ b/tests/transform/integration/test_es_integration.py @@ -0,0 +1,19 @@ +import unittest +import subprocess +import os + +class MyTestCase(unittest.TestCase): + + + def setUp(self): + current_path = os.path.dirname(__file__) + root_dir = os.path.normpath(os.path.join(current_path, "../../../")) + result = subprocess.run([root_dir + "/main.py", "trans", "es", root_dir + "/tests/transform/integration/fixtures/VIB.json", "--data-dir", root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + + #("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") + + def test_toto(self): + self.assertEqual(1,1) + +#if __name__ == '__main__': +# unittest.main() From b17fefe15231d040deef35ebdee54e708172dbf1 Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Tue, 4 May 2021 17:38:47 +0200 Subject: [PATCH 06/26] Add fixture files --- .../VIB_datadiscovery_expected.json | 503 ++++++- .../VIB_germplasm_expected.json | 1231 ----------------- 2 files changed, 502 insertions(+), 1232 deletions(-) diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json index b0994bf..7765a08 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json @@ -1 +1,502 @@ -[{"ontology_name": "NA", "observationVariableDbId": "188", 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Consumes an iterable of document tuples + Consumes an iterable of document tuples and clean email """ logger.debug("Saving documents to json files...") json_list = list() document_count = 0 for document_header, document in documents_tuples: + if "contact" in document: + old_mail = document["contact"]["email"] + safe_mail = old_mail.replace('@', '_') + document["contact"]["email"] = safe_mail json_list.append(document) document_count += 1 @@ -272,7 +276,7 @@ def transform_source(source, transform_config, source_json_dir, source_bulk_dir, validated_documents = validate_documents(documents, validation_schemas, logger) # Write the documents in jsonfiles - dump_in_json_files(source_bulk_dir, logger, validated_documents) + dump_clean_in_json_files(source_bulk_dir, logger, validated_documents) # shutil.rmtree(tmp_index_dir, ignore_errors=True) logger.info(f"SUCCEEDED Transforming BrAPI {source_name}.") diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json index fa1f634..0e4c968 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json @@ -46,1298 +46,5 @@ "urn:VIB/study/VIB_study___46" ], "locationName": "growth chamber" - 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"schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "3728271192", - "schema:name": null, - "trialURIs": [ - "urn:VIB/trial/3" - ] - }, - { - "institutionName": "VIB - Center for Plant Systems Biology", - "type": "Corresponding author", - "email": "dirk.inze@ugent.vib.be", - "orcid": "0000-0002-3217-8407", - "name": "Dirk Inzé", - "contactDbId": "dXJuOlZJQi9jb250YWN0LzI1NjQyMDE4NDg=", - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "source": "VIB", - "contactURI": "urn:VIB/contact/2564201848", - "@type": "contact", - "@id": "urn:VIB/contact/2564201848", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "2564201848", - "schema:name": null, - "trialURIs": [ - "urn:VIB/trial/3" - ] } ] \ No newline at end of file From e2ce4773f5e5d102da5252f341a634183862f66f Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Tue, 4 May 2021 17:44:08 +0200 Subject: [PATCH 08/26] test source --- tests/transform/integration/fixtures/VIB.json | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 tests/transform/integration/fixtures/VIB.json diff --git a/tests/transform/integration/fixtures/VIB.json b/tests/transform/integration/fixtures/VIB.json new file mode 100644 index 0000000..2da1ad6 --- /dev/null +++ b/tests/transform/integration/fixtures/VIB.json @@ -0,0 +1,11 @@ +{ + "@context": { + "schema": "http://schema.org/", + "brapi": "https://brapi.org/rdf/" + }, + "@type": "schema:DataCatalog", + "@id": "http://pippa.psb.ugent.be", + "schema:identifier": "VIB", + "schema:name": "VIB PIPPA", + "brapi:endpointUrl": "https://pippa.psb.ugent.be/BrAPIPPA/brapi/v1/" +} From ed495d9c780145a320d58b03e470972273ee59e5 Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Wed, 5 May 2021 09:42:42 +0200 Subject: [PATCH 09/26] Tests WIP --- .../integration/test_es_integration.py | 62 ++++++++++++++++++- 1 file changed, 59 insertions(+), 3 deletions(-) diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index 83d437a..9acf664 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -1,19 +1,75 @@ import unittest import subprocess import os +import json + +from etl.transform.uri import read_json_lines + + + class MyTestCase(unittest.TestCase): + _are_file_generated = False def setUp(self): - current_path = os.path.dirname(__file__) - root_dir = os.path.normpath(os.path.join(current_path, "../../../")) - result = subprocess.run([root_dir + "/main.py", "trans", "es", root_dir + "/tests/transform/integration/fixtures/VIB.json", "--data-dir", root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + self._current_path = os.path.dirname(__file__) + self._root_dir = os.path.normpath(os.path.join(self._current_path, "../../../")) + if not self._are_file_generated: + result = subprocess.run([self._root_dir + "/main.py", "trans", + "es", + self._root_dir + "/tests/transform/integration/fixtures/VIB.json", + "--data-dir", + self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + self._are_file_generated = True + + self._actual_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/json-bulk/" + self._expected_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/" + + + #("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") + def test_files_should_be_generated(self): + self.assertIsNotNone(self._actual_data_dir) + self.assertTrue(os.path.exists(self._actual_data_dir)) + self.assertTrue(os.path.exists(self._actual_data_dir+"VIB.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-germplasm.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-study.json")) + + def test_all_germplasms_generated(self): + self.assertTrue(True) + #all_germplasms = json_load(self._actual_data_dir+"VIB.json")) + #all_germplams 4 germplasm, contient un id attendu + + def test_json_files_equals(self): + # https://www.geeksforgeeks.org/how-to-compare-json-objects-regardless-of-order-in-python/ + # https://pypi.org/project/deepdiff/ + with open(self._actual_data_dir+"VIB.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(self.sorting_dict(actual_vib), self.sorting_dict(expected_vib)) + + def test_toto(self): self.assertEqual(1,1) + + + def sorting_dict(self, item): + + if isinstance(item, dict): + return sorted((key, self.sorting_dict(values)) for key, values in item.items()) + if isinstance(item, list): + return sorted(self.sorting_dict(x) for x in item) + else: + return item + + + #if __name__ == '__main__': # unittest.main() From 3146d662bce03bf8956dfda1cf734923cf9daa60 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Fri, 7 May 2021 17:51:42 +0200 Subject: [PATCH 10/26] fix: Save documents by type --- etl/transform/elasticsearch.py | 39 +++++++++++++++++++--------------- 1 file changed, 22 insertions(+), 17 deletions(-) diff --git a/etl/transform/elasticsearch.py b/etl/transform/elasticsearch.py index 4f79e2e..f047152 100755 --- a/etl/transform/elasticsearch.py +++ b/etl/transform/elasticsearch.py @@ -138,35 +138,40 @@ def dump_in_json_files(source_dir, logger, documents_tuples): """ logger.debug("Saving documents to json files...") - json_list = list() + json_dict = dict() document_count = 0 for document_header, document in documents_tuples: - json_list.append(document) + + if document_header not in json_dict: + json_dict[document_header] = [] + + json_dict[document_header].append(document) document_count += 1 if is_checkpoint(document_count): logger.debug(f"checkpoint: {document_count} documents saved") - save_json(document_count, source_dir, json_list) + save_json(source_dir, json_dict) logger.debug(f"Total of {document_count} documents saved in json files.") -def save_json(document_count, source_dir, json_list): - file_number = 1 - saved_documents = 0 - if document_count <= 1000: - with open(source_dir +'.json', 'w') as f: - json.dump(json_list, f, ensure_ascii=False) - f.close() - - else: - while saved_documents < document_count: - with open(source_dir + '-' + str(file_number) + '.json', 'w') as f: - json.dump(json_list[saved_documents:file_number*10000], f, ensure_ascii=False) +def save_json(source_dir, json_dict): + for type, document in json_dict.items(): + if len(document) < 10000: + with open(source_dir + "/" + type +'.json', 'w') as f: + json.dump(document, f, ensure_ascii=False) f.close() - file_number += 1 - saved_documents += 10000 + + else: + file_number = 1 + saved_documents = 0 + while saved_documents < len(document): + with open(source_dir + "/" + type + '-' + str(file_number) + '.json', 'w') as f: + json.dump(document[saved_documents:file_number*10000], f, ensure_ascii=False) + f.close() + file_number += 1 + saved_documents += 10000 def get_document_configs_by_entity(document_configs): From 4890164de2d1ff0a39f1fc062fc2e08cf46161e0 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Mon, 10 May 2021 16:22:38 +0200 Subject: [PATCH 11/26] feat: Add germplasm test --- .../integration/test_es_integration.py | 42 +++++++------------ 1 file changed, 16 insertions(+), 26 deletions(-) diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index 9acf664..a12de9c 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -2,16 +2,14 @@ import subprocess import os import json - +from deepdiff import DeepDiff from etl.transform.uri import read_json_lines - - class MyTestCase(unittest.TestCase): _are_file_generated = False - + def setUp(self): self._current_path = os.path.dirname(__file__) self._root_dir = os.path.normpath(os.path.join(self._current_path, "../../../")) @@ -27,32 +25,33 @@ def setUp(self): self._expected_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/" - - - #("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") - def test_files_should_be_generated(self): self.assertIsNotNone(self._actual_data_dir) self.assertTrue(os.path.exists(self._actual_data_dir)) self.assertTrue(os.path.exists(self._actual_data_dir+"VIB.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-germplasm.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-study.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/germplasm.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/study.json")) + def test_all_germplasms_generated(self): self.assertTrue(True) - #all_germplasms = json_load(self._actual_data_dir+"VIB.json")) - #all_germplams 4 germplasm, contient un id attendu + with open(self._actual_data_dir+"/VIB/germplasm.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_germplasm_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + def test_json_files_equals(self): - # https://www.geeksforgeeks.org/how-to-compare-json-objects-regardless-of-order-in-python/ - # https://pypi.org/project/deepdiff/ with open(self._actual_data_dir+"VIB.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_expected.json") as expected_vib_f: expected_vib = json.load(expected_vib_f) - self.assertEqual(self.sorting_dict(actual_vib), self.sorting_dict(expected_vib)) + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) def test_toto(self): @@ -60,16 +59,7 @@ def test_toto(self): - def sorting_dict(self, item): - - if isinstance(item, dict): - return sorted((key, self.sorting_dict(values)) for key, values in item.items()) - if isinstance(item, list): - return sorted(self.sorting_dict(x) for x in item) - else: - return item - - - #if __name__ == '__main__': # unittest.main() + +#("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") From a0ccc369ee6887fcfa6e6eb77decb6d5c80db9f2 Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Tue, 4 May 2021 14:28:49 +0200 Subject: [PATCH 12/26] Initial test creation --- tests/transform/integration/__init__.py | 0 .../fixtures/brapi_pheno_source/contact.json | 7 + .../brapi_pheno_source/germplasm.json | 665 ++++++++++++++++++ .../fixtures/brapi_pheno_source/location.json | 3 + .../observationVariable.json | 32 + .../fixtures/brapi_pheno_source/study.json | 27 + .../fixtures/brapi_pheno_source/trial.json | 4 + .../fixtures/test_es_integration.py | 12 + 8 files changed, 750 insertions(+) create mode 100644 tests/transform/integration/__init__.py create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/contact.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/location.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/observationVariable.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/study.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/trial.json create mode 100644 tests/transform/integration/fixtures/test_es_integration.py diff --git a/tests/transform/integration/__init__.py b/tests/transform/integration/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/contact.json b/tests/transform/integration/fixtures/brapi_pheno_source/contact.json new file mode 100644 index 0000000..3ab614f --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/contact.json @@ -0,0 +1,7 @@ +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Participating Investigator", "orcid": "0000-0001-6104-8479", "name": "Giorgio Pea", "contactDbId": "4010106321", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0002-1544-0979", "name": "Aye L. Hlaing", "contactDbId": "1213155226", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0003-3547-0195", "name": "Htay H. Aung", "contactDbId": "58550283", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Corresponding author", "email": "marioenrico.pe@santannapisa.it", "orcid": "0000-0001-6197-2282", "name": "Mario Enrico P\u00e8", "contactDbId": "3191909450", "trialDbIds": ["2"], "source": "VIB"} +{"institutionName": "VIB - Center for Plant Systems Biology", "type": "Author", "email": "joke.baute@vib.be", "orcid": "0000-0003-0507-6904", "name": "Joke Baute", "contactDbId": "2601524745", "trialDbIds": ["4", "1", "3"], "source": "VIB"} +{"institutionName": "VIB - Center for Plant Systems Biology", "type": "Collecting data", "email": "joblo@psb.vib-ugent.be", "orcid": "0000-0003-0047-4380", "name": "Jolien De Block", "contactDbId": "3728271192", "trialDbIds": ["4", "1", "3"], "source": "VIB"} +{"institutionName": "VIB - Center for Plant Systems Biology", "type": "Corresponding author", "email": "dirk.inze@ugent.vib.be", "orcid": "0000-0002-3217-8407", "name": "Dirk Inz\u00e9", "contactDbId": "2564201848", "trialDbIds": ["4", "1", "3"], "source": "VIB"} diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json b/tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json new file mode 100644 index 0000000..6c7dfda --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json @@ -0,0 +1,665 @@ +{"countryOfOriginCode": "BE", "instituteCode": "VIB", "accessionNumber": "208", "defaultDisplayName": "A632 RIL 8-way ", "germplasmDbId": "Zea_VIB_A632RIL8way___208", "germplasmName": "A632 RIL 8-way ", "commonCropName": "Maize", "instituteName": "VIB", "species": "mays", "genus": "Zea", "source": "VIB", "studyDbIds": ["VIB_study___51"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1300", "defaultDisplayName": "ami-13-1", "germplasmDbId": "Arabidopsis_VIB_ami131___1300", "germplasmName": "ami-13-1", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1301", "defaultDisplayName": "ami-4-6", "germplasmDbId": "Arabidopsis_VIB_ami46___1301", "germplasmName": "ami-4-6", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1302", "defaultDisplayName": "ami-Col", "germplasmDbId": "Arabidopsis_VIB_amiCol___1302", "germplasmName": "ami-Col", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} +{"countryOfOriginCode": "BE", "instituteCode": "VIB", "accessionNumber": "202", "defaultDisplayName": "B104 RIL 8-way ", "germplasmDbId": "Zea_VIB_B104RIL8way___202", "germplasmName": "B104 RIL 8-way ", "commonCropName": "Maize", "instituteName": "VIB", "species": "mays", "genus": "Zea", "source": "VIB", "studyDbIds": ["VIB_study___51"]} +{"countryOfOriginCode": "BE", "instituteCode": "VIB", "accessionNumber": "9", "defaultDisplayName": "B73 RIL 2-way ", "germplasmDbId": "Zea_VIB_B73RIL2way___9", "germplasmName": "B73 RIL 2-way ", "commonCropName": "Maize", "instituteName": "VIB", "species": "mays", "genus": "Zea", "source": "VIB", "studyDbIds": ["VIB_study___30", "VIB_study___31", "VIB_study___32", "VIB_study___33", "VIB_study___34", "VIB_study___27", "VIB_study___36", "VIB_study___28", "VIB_study___29", "VIB_study___39", "VIB_study___37", "VIB_study___35", "VIB_study___38"]} +{"countryOfOriginCode": "BE", "instituteCode": "VIB", "accessionNumber": "109", "defaultDisplayName": "B73 RIL 8-way ", "germplasmDbId": "Zea_VIB_B73RIL8way___109", "germplasmName": "B73 RIL 8-way ", "commonCropName": "Maize", "instituteName": "VIB", "species": "mays", "genus": "Zea", "source": "VIB", "studyDbIds": ["VIB_study___48", "VIB_study___46", "VIB_study___47", "VIB_study___49", "VIB_study___44", "VIB_study___51", "VIB_study___45", "VIB_study___41", "VIB_study___50", "VIB_study___42", "VIB_study___40", "VIB_study___43"]} +{"countryOfOriginCode": "BE", "instituteCode": "VIB", "accessionNumber": "205", "defaultDisplayName": "CML91 RIL 8-way ", "germplasmDbId": "Zea_VIB_CML91RIL8way___205", "germplasmName": "CML91 RIL 8-way ", "commonCropName": "Maize", "instituteName": "VIB", "species": "mays", "genus": "Zea", "source": "VIB", "studyDbIds": ["VIB_study___51"]} +{"countryOfOriginCode": "BE", "pedigree": "Columbia/", "instituteCode": "VIB", "accessionNumber": "1303", "defaultDisplayName": "delta Col", "germplasmDbId": "Arabidopsis_VIB_deltaCol___1303", "germplasmName": "delta Col", "commonCropName": "Arabidopsis", 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"Arabidopsis_VIB_amiCol___1302", "Arabidopsis_VIB_delta69___1305", "Arabidopsis_VIB_OECol___1308", "Arabidopsis_VIB_Zm31___1311", "Arabidopsis_VIB_OE71___1307", "Arabidopsis_VIB_deltaCol___1303", "Arabidopsis_VIB_ami46___1301", "Arabidopsis_VIB_OE21___1306", "Arabidopsis_VIB_Zm111___1310", "Arabidopsis_VIB_ZmCol___1309"], "observationVariableDbIds": ["15", "18", "16", "44", "20", "46", "45", "40", "13", "21", "27", "8", "14", "42", "25", "26", "24", "43"], "locationDbIds": ["6"], "trialDbIds": ["4"]} diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/trial.json b/tests/transform/integration/fixtures/brapi_pheno_source/trial.json new file mode 100644 index 0000000..5bacfc8 --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/trial.json @@ -0,0 +1,4 @@ +{"publications": [{"publicationReference": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0716-z", "publicationPUI": "10.1186/s13059-015-0716-z"}], "trialName": 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"RIL_2-way_growth_chamber", "trialDescription": "Assessed Variation in 103 lines of the Zea mays B73xH99 RIL population for a set of final leaf size and whole shoot traits at the seedling stage, complemented with measurements capturing growth dynamics, and cellular measurements.", "startDate": "2011-09-21", "trialDbId": "1", "source": "VIB", "studyDbIds": ["VIB_study___30", "VIB_study___31", "VIB_study___32", "VIB_study___33", "VIB_study___34", "VIB_study___27", "VIB_study___36", "VIB_study___28", "VIB_study___29", "VIB_study___39", "VIB_study___37", "VIB_study___35", "VIB_study___38"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} +{"publications": [{"publicationReference": "https://www.plantphysiol.org/cgi/doi/10.1104/pp.15.01883", "publicationPUI": "10.1104/pp.15.01883"}], "trialName": "RIL_8-way_growth_chamber", "trialDescription": "Indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations.", "startDate": "2012-06-16", "trialDbId": "3", "source": "VIB", "studyDbIds": ["VIB_study___48", "VIB_study___46", "VIB_study___47", "VIB_study___49", "VIB_study___44", "VIB_study___51", "VIB_study___45", "VIB_study___41", "VIB_study___50", "VIB_study___42", "VIB_study___40", "VIB_study___43"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} diff --git a/tests/transform/integration/fixtures/test_es_integration.py b/tests/transform/integration/fixtures/test_es_integration.py new file mode 100644 index 0000000..0f14c0e --- /dev/null +++ b/tests/transform/integration/fixtures/test_es_integration.py @@ -0,0 +1,12 @@ +import unittest + + +class MyTestCase(unittest.TestCase): + + + def test_something(self): + self.assertEqual(True, False) + + +#if __name__ == '__main__': +# unittest.main() From 6c02c1ae332ef6e6e54ffadedb9fe3941d075ca3 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Tue, 4 May 2021 17:16:28 +0200 Subject: [PATCH 13/26] test_fixture WIP --- .../VIB_datadiscovery_expected.json | 1 + .../brapi_pheno_source/VIB_expected.json | 1 + .../VIB_germplasm_expected.json | 1343 ++++++++++++ .../VIB_location_expected.json | 1343 ++++++++++++ .../VIB_observation_variable_expected.json | 1807 +++++++++++++++++ .../VIB_study_expected.json | 1371 +++++++++++++ .../VIB_trial_expected.json | 1343 ++++++++++++ .../brapi_pheno_source/germplasm.json | 665 ------ .../{ => json/VIB}/contact.json | 6 +- .../json/VIB/germplasm.json | 4 + .../brapi_pheno_source/json/VIB/location.json | 2 + .../json/VIB/observationVariable.json | 14 + .../brapi_pheno_source/json/VIB/study.json | 3 + .../brapi_pheno_source/json/VIB/trial.json | 2 + .../fixtures/brapi_pheno_source/location.json | 3 - .../observationVariable.json | 32 - .../fixtures/brapi_pheno_source/study.json | 27 - .../fixtures/brapi_pheno_source/trial.json | 4 - .../fixtures/test_es_integration.py | 12 - .../integration/test_es_integration.py | 19 + 20 files changed, 7256 insertions(+), 746 deletions(-) create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_germplasm_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_observation_variable_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_trial_expected.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/germplasm.json rename tests/transform/integration/fixtures/brapi_pheno_source/{ => json/VIB}/contact.json (89%) create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/germplasm.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/location.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/observationVariable.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/study.json create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/trial.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/location.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/observationVariable.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/study.json delete mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/trial.json delete mode 100644 tests/transform/integration/fixtures/test_es_integration.py create mode 100644 tests/transform/integration/test_es_integration.py diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json new file mode 100644 index 0000000..b0994bf --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json @@ -0,0 +1 @@ +[{"ontology_name": "NA", "observationVariableDbId": "188", "institution": "VIB", "scale": {"decimalPlaces": 2, "dataType": "numeric", "validValues": {"max": 1000}, "name": "mm"}, "observationVariableName": "CDZSL_188", "name": "cellDivisionZoneLengthLeaf", "trait": {"name": "cellDivisionZoneLengthLeaf", "description": "size of the cell division zone at the basis of a leaf"}, "source": "VIB", "studyDbIds": ["dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX180Ng==", "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX180OA=="], "observationVariableURI": "urn:VIB/observationVariable/188", "@type": "observationVariable", "@id": "urn:VIB/observationVariable/188", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "188", "schema:name": "CDZSL_188", "studyURIs": ["urn:VIB/study/VIB_study___46", "urn:VIB/study/VIB_study___48"]}, {"ontology_name": "NA", "observationVariableDbId": "217", "institution": "VIB", "scale": {"decimalPlaces": 2, "dataType": "numeric", "name": "mm"}, "observationVariableName": "EH_217", "name": "earHeight", "trait": {"name": "earHeight"}, "source": "VIB", "studyDbIds": ["dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX181NQ=="], "observationVariableURI": "urn:VIB/observationVariable/217", "@type": "observationVariable", "@id": "urn:VIB/observationVariable/217", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "217", "schema:name": "EH_217", "studyURIs": ["urn:VIB/study/VIB_study___55"]}, {"ontology_name": "NA", "observationVariableDbId": "195", "institution": "VIB", "scale": {"decimalPlaces": 2, "dataType": "numeric", "validValues": {"max": 100000}, "name": "mm"}, 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"Columbia/", "instituteCode": "VIB", "accessionNumber": "1311", "defaultDisplayName": "Zm-3-1", "germplasmDbId": "Arabidopsis_VIB_Zm31___1311", "germplasmName": "Zm-3-1", "commonCropName": "Arabidopsis", "instituteName": "VIB", "species": "thaliana", "genus": "Arabidopsis", "source": "VIB", "studyDbIds": ["VIB_study___56"]} diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/contact.json b/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/contact.json similarity index 89% rename from tests/transform/integration/fixtures/brapi_pheno_source/contact.json rename to tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/contact.json index 3ab614f..118db6b 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/contact.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/contact.json @@ -2,6 +2,6 @@ {"institutionName": "Institute of Life Sciences, Scuola Superiore Sant\u2019Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0002-1544-0979", "name": "Aye L. 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a/tests/transform/integration/fixtures/brapi_pheno_source/trial.json b/tests/transform/integration/fixtures/brapi_pheno_source/trial.json deleted file mode 100644 index 5bacfc8..0000000 --- a/tests/transform/integration/fixtures/brapi_pheno_source/trial.json +++ /dev/null @@ -1,4 +0,0 @@ -{"publications": [{"publicationReference": "https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0716-z", "publicationPUI": "10.1186/s13059-015-0716-z"}], "trialName": "RIL_8-way_Field_trial", "endDate": "2012-08-01", "trialDescription": "1,636 MAGIC maize recombinant inbred lines derived from eight genetically diverse founder lines.", "startDate": "2012-05-01", "trialDbId": "2", "source": "VIB", "studyDbIds": ["VIB_study___55"], "contactDbIds": ["3191909450", "1213155226", "58550283", "4010106321"]} -{"publications": [{"publicationReference": "https://academic.oup.com/pcp/article/58/5/962/3069849", "publicationPUI": "10.1093/pcp/pcx035"}], "trialName": "D4_wiwam2", "endDate": 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"VIB_study___39", "VIB_study___37", "VIB_study___35", "VIB_study___38"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} -{"publications": [{"publicationReference": "https://www.plantphysiol.org/cgi/doi/10.1104/pp.15.01883", "publicationPUI": "10.1104/pp.15.01883"}], "trialName": "RIL_8-way_growth_chamber", "trialDescription": "Indepth phenotyping of the fourth leaf at later stages of development in 197 recombinant inbred lines of two different maize (Zea mays) populations.", "startDate": "2012-06-16", "trialDbId": "3", "source": "VIB", "studyDbIds": ["VIB_study___48", "VIB_study___46", "VIB_study___47", "VIB_study___49", "VIB_study___44", "VIB_study___51", "VIB_study___45", "VIB_study___41", "VIB_study___50", "VIB_study___42", "VIB_study___40", "VIB_study___43"], "contactDbIds": ["2601524745", "2564201848", "3728271192"]} diff --git a/tests/transform/integration/fixtures/test_es_integration.py b/tests/transform/integration/fixtures/test_es_integration.py deleted file mode 100644 index 0f14c0e..0000000 --- a/tests/transform/integration/fixtures/test_es_integration.py +++ /dev/null @@ -1,12 +0,0 @@ -import unittest - - -class MyTestCase(unittest.TestCase): - - - def test_something(self): - self.assertEqual(True, False) - - -#if __name__ == '__main__': -# unittest.main() diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py new file mode 100644 index 0000000..83d437a --- /dev/null +++ b/tests/transform/integration/test_es_integration.py @@ -0,0 +1,19 @@ +import unittest +import subprocess +import os + +class MyTestCase(unittest.TestCase): + + + def setUp(self): + current_path = os.path.dirname(__file__) + root_dir = os.path.normpath(os.path.join(current_path, "../../../")) + result = subprocess.run([root_dir + "/main.py", "trans", "es", root_dir + "/tests/transform/integration/fixtures/VIB.json", "--data-dir", root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + + #("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") + + def test_toto(self): + self.assertEqual(1,1) + +#if __name__ == '__main__': +# unittest.main() From 996146f632ea7e417da4d41076b09478553f3948 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Tue, 4 May 2021 17:40:50 +0200 Subject: [PATCH 14/26] clean expected files --- .../VIB_location_expected.json | 1293 ---------------- .../VIB_observation_variable_expected.json | 1341 ----------------- .../VIB_study_expected.json | 720 --------- .../VIB_trial_expected.json | 965 +----------- 4 files changed, 1 insertion(+), 4318 deletions(-) diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json index fa1f634..0e4c968 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_location_expected.json @@ -46,1298 +46,5 @@ "urn:VIB/study/VIB_study___46" ], "locationName": "growth chamber" - }, - { - "trialDbId": "dXJuOlZJQi90cmlhbC8y", - "startDate": "2012-05-01", - "studyType": "Phenotyping Study", - "studyDbId": "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX181NQ==", - "trialName": "RIL_8-way_Field_trial", - "name": "Enrico Pe field trial", - "endDate": "2012-08-01", - "locationDbId": "dXJuOlZJQi9sb2NhdGlvbi81", - "locationName": "Field trial", - "active": false, - "source": "VIB", - "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/55", - "studyName": "Enrico Pe field trial", - "studyDescription": "Short description of the experimental design, possibly including statistical design.", - "germplasmDbIds": [ - "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfRVAzM18yMF9fXzExODQ=" - ], - "observationVariableDbIds": [ - "216", - "215", - "217", - "218" - ], - 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--- tests/transform/integration/fixtures/VIB.json | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 tests/transform/integration/fixtures/VIB.json diff --git a/tests/transform/integration/fixtures/VIB.json b/tests/transform/integration/fixtures/VIB.json new file mode 100644 index 0000000..2da1ad6 --- /dev/null +++ b/tests/transform/integration/fixtures/VIB.json @@ -0,0 +1,11 @@ +{ + "@context": { + "schema": "http://schema.org/", + "brapi": "https://brapi.org/rdf/" + }, + "@type": "schema:DataCatalog", + "@id": "http://pippa.psb.ugent.be", + "schema:identifier": "VIB", + "schema:name": "VIB PIPPA", + "brapi:endpointUrl": "https://pippa.psb.ugent.be/BrAPIPPA/brapi/v1/" +} From eee5f2ed70d66a46d6be5a4f1313b4ff34d6da88 Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Tue, 4 May 2021 17:38:47 +0200 Subject: [PATCH 16/26] Add fixture files --- .../VIB_datadiscovery_expected.json | 503 ++++++- .../VIB_germplasm_expected.json | 1231 ----------------- 2 files changed, 502 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"schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "3728271192", - "schema:name": null, - "trialURIs": [ - "urn:VIB/trial/3" - ] - }, - { - "institutionName": "VIB - Center for Plant Systems Biology", - "type": "Corresponding author", - "email": "dirk.inze@ugent.vib.be", - "orcid": "0000-0002-3217-8407", - "name": "Dirk Inzé", - "contactDbId": "dXJuOlZJQi9jb250YWN0LzI1NjQyMDE4NDg=", - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "source": "VIB", - "contactURI": "urn:VIB/contact/2564201848", - "@type": "contact", - "@id": "urn:VIB/contact/2564201848", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "2564201848", - "schema:name": null, - "trialURIs": [ - "urn:VIB/trial/3" - ] } ] \ No newline at end of file From ef231b7f8477a5ad2652ed4e1f39b6946c3c8ed8 Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Wed, 5 May 2021 09:42:42 +0200 Subject: [PATCH 17/26] Tests WIP --- .../integration/test_es_integration.py | 62 ++++++++++++++++++- 1 file changed, 59 insertions(+), 3 deletions(-) diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index 83d437a..9acf664 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -1,19 +1,75 @@ import unittest import subprocess import os +import json + +from etl.transform.uri import read_json_lines + + + class MyTestCase(unittest.TestCase): + _are_file_generated = False def setUp(self): - current_path = os.path.dirname(__file__) - root_dir = os.path.normpath(os.path.join(current_path, "../../../")) - result = subprocess.run([root_dir + "/main.py", "trans", "es", root_dir + "/tests/transform/integration/fixtures/VIB.json", "--data-dir", root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + self._current_path = os.path.dirname(__file__) + self._root_dir = os.path.normpath(os.path.join(self._current_path, "../../../")) + if not self._are_file_generated: + result = subprocess.run([self._root_dir + "/main.py", "trans", + "es", + self._root_dir + "/tests/transform/integration/fixtures/VIB.json", + "--data-dir", + self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + self._are_file_generated = True + + self._actual_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/json-bulk/" + self._expected_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/" + + + #("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") + def test_files_should_be_generated(self): + self.assertIsNotNone(self._actual_data_dir) + self.assertTrue(os.path.exists(self._actual_data_dir)) + self.assertTrue(os.path.exists(self._actual_data_dir+"VIB.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-germplasm.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-study.json")) + + def test_all_germplasms_generated(self): + self.assertTrue(True) + #all_germplasms = json_load(self._actual_data_dir+"VIB.json")) + #all_germplams 4 germplasm, contient un id attendu + + def test_json_files_equals(self): + # https://www.geeksforgeeks.org/how-to-compare-json-objects-regardless-of-order-in-python/ + # https://pypi.org/project/deepdiff/ + with open(self._actual_data_dir+"VIB.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(self.sorting_dict(actual_vib), self.sorting_dict(expected_vib)) + + def test_toto(self): self.assertEqual(1,1) + + + def sorting_dict(self, item): + + if isinstance(item, dict): + return sorted((key, self.sorting_dict(values)) for key, values in item.items()) + if isinstance(item, list): + return sorted(self.sorting_dict(x) for x in item) + else: + return item + + + #if __name__ == '__main__': # unittest.main() From 6fc7acbee4659d869c86b10a2277a1d6f12bff17 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Mon, 10 May 2021 16:22:38 +0200 Subject: [PATCH 18/26] feat: Add germplasm test --- .../integration/test_es_integration.py | 42 +++++++------------ 1 file changed, 16 insertions(+), 26 deletions(-) diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index 9acf664..a12de9c 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -2,16 +2,14 @@ import subprocess import os import json - +from deepdiff import DeepDiff from etl.transform.uri import read_json_lines - - class MyTestCase(unittest.TestCase): _are_file_generated = False - + def setUp(self): self._current_path = os.path.dirname(__file__) self._root_dir = os.path.normpath(os.path.join(self._current_path, "../../../")) @@ -27,32 +25,33 @@ def setUp(self): self._expected_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/" - - - #("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") - def test_files_should_be_generated(self): self.assertIsNotNone(self._actual_data_dir) self.assertTrue(os.path.exists(self._actual_data_dir)) self.assertTrue(os.path.exists(self._actual_data_dir+"VIB.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-germplasm.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"VIB-study.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/germplasm.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/study.json")) + def test_all_germplasms_generated(self): self.assertTrue(True) - #all_germplasms = json_load(self._actual_data_dir+"VIB.json")) - #all_germplams 4 germplasm, contient un id attendu + with open(self._actual_data_dir+"/VIB/germplasm.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_germplasm_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + def test_json_files_equals(self): - # https://www.geeksforgeeks.org/how-to-compare-json-objects-regardless-of-order-in-python/ - # https://pypi.org/project/deepdiff/ with open(self._actual_data_dir+"VIB.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_expected.json") as expected_vib_f: expected_vib = json.load(expected_vib_f) - self.assertEqual(self.sorting_dict(actual_vib), self.sorting_dict(expected_vib)) + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) def test_toto(self): @@ -60,16 +59,7 @@ def test_toto(self): - def sorting_dict(self, item): - - if isinstance(item, dict): - return sorted((key, self.sorting_dict(values)) for key, values in item.items()) - if isinstance(item, list): - return sorted(self.sorting_dict(x) for x in item) - else: - return item - - - #if __name__ == '__main__': # unittest.main() + +#("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") From 1d7521f01990d389050cc5f27af17305c7e51c55 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Wed, 12 May 2021 17:02:39 +0200 Subject: [PATCH 19/26] fix: remove extra line --- etl/transform/elasticsearch.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/etl/transform/elasticsearch.py b/etl/transform/elasticsearch.py index 57735fa..d3e398b 100755 --- a/etl/transform/elasticsearch.py +++ b/etl/transform/elasticsearch.py @@ -147,12 +147,12 @@ def dump_clean_in_json_files(source_dir, logger, documents_tuples): json_dict[document_header].append(document) + # Hide email if "contact" in document: old_mail = document["contact"]["email"] if old_mail is not None: safe_mail = old_mail.replace('@', '_') document["contact"]["email"] = safe_mail - json_list.append(document) document_count += 1 if is_checkpoint(document_count): From 9e922bd426c1985aca407f3d3dd198135a1c6d2e Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Wed, 12 May 2021 17:06:36 +0200 Subject: [PATCH 20/26] fix: replace the email masking --- etl/transform/elasticsearch.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/etl/transform/elasticsearch.py b/etl/transform/elasticsearch.py index d3e398b..8c683ba 100755 --- a/etl/transform/elasticsearch.py +++ b/etl/transform/elasticsearch.py @@ -142,11 +142,6 @@ def dump_clean_in_json_files(source_dir, logger, documents_tuples): document_count = 0 for document_header, document in documents_tuples: - if document_header not in json_dict: - json_dict[document_header] = [] - - json_dict[document_header].append(document) - # Hide email if "contact" in document: old_mail = document["contact"]["email"] @@ -154,6 +149,11 @@ def dump_clean_in_json_files(source_dir, logger, documents_tuples): safe_mail = old_mail.replace('@', '_') document["contact"]["email"] = safe_mail + if document_header not in json_dict: + json_dict[document_header] = [] + + json_dict[document_header].append(document) + document_count += 1 if is_checkpoint(document_count): logger.debug(f"checkpoint: {document_count} documents saved") From 74dd3429afec29cf024e2b1568e747e955422968 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Wed, 12 May 2021 18:01:57 +0200 Subject: [PATCH 21/26] feat: add document types tests --- .../VIB_study_expected.json | 488 ------------------ .../integration/test_es_integration.py | 62 ++- 2 files changed, 60 insertions(+), 490 deletions(-) diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json index a16976c..b4daf60 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json @@ -159,493 +159,5 @@ "urn:VIB/trial/3" ], "schema:url": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/48" - }, - { - "countryOfOriginCode": "BE", - "instituteCode": "VIB", - "accessionNumber": "1184", - "defaultDisplayName": "RIL_8W_EP33_20", - "germplasmDbId": "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfRVAzM18yMF9fXzExODQ=", - "germplasmName": "RIL_8W_EP33_20", - "commonCropName": "Maize", - "instituteName": "VIB", - "species": "mays", - "genus": "Zea", - "source": "VIB", - "studyDbIds": [ - "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX181NQ==" - ], - "germplasmURI": "urn:VIB/germplasm/Zea_VIB_RIL_8W_EP33_20___1184", - "@type": "germplasm", - "@id": "urn:VIB/germplasm/Zea_VIB_RIL_8W_EP33_20___1184", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "Zea_VIB_RIL_8W_EP33_20___1184", - "schema:name": "RIL_8W_EP33_20", - "studyURIs": [ - "urn:VIB/study/VIB_study___55" - ], - "genusSpecies": "Zea mays" - }, - { - "countryOfOriginCode": "BE", - "instituteCode": "VIB", - "accessionNumber": "160", - "defaultDisplayName": "RIL_8W_59 RIL 8-way ", - "germplasmDbId": "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfNTlSSUw4d2F5X19fMTYw", - "germplasmName": "RIL_8W_59 RIL 8-way ", - "commonCropName": "Maize", - "instituteName": "VIB", - "species": "mays", - "genus": "Zea", - "source": "VIB", - "studyDbIds": [ - "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX181NQ==", - "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX180Ng==" - ], - "germplasmURI": "urn:VIB/germplasm/Zea_VIB_RIL_8W_59RIL8way___160", - "@type": "germplasm", - "@id": "urn:VIB/germplasm/Zea_VIB_RIL_8W_59RIL8way___160", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "Zea_VIB_RIL_8W_59RIL8way___160", - "schema:name": "RIL_8W_59 RIL 8-way ", - "studyURIs": [ - "urn:VIB/study/VIB_study___55", - "urn:VIB/study/VIB_study___46" - ], - "genusSpecies": "Zea mays" - }, - { - "countryOfOriginCode": "BE", - "instituteCode": "VIB", - "accessionNumber": "183", - "defaultDisplayName": "RIL_8W_75 RIL 8-way ", - "germplasmDbId": "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfNzVSSUw4d2F5X19fMTgz", - "germplasmName": "RIL_8W_75 RIL 8-way ", - "commonCropName": "Maize", - "instituteName": "VIB", - "species": "mays", - "genus": "Zea", - "source": "VIB", - "studyDbIds": [ - "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX180OA==", - "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX181NQ==" - ], - "germplasmURI": "urn:VIB/germplasm/Zea_VIB_RIL_8W_75RIL8way___183", - "@type": "germplasm", - "@id": "urn:VIB/germplasm/Zea_VIB_RIL_8W_75RIL8way___183", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "Zea_VIB_RIL_8W_75RIL8way___183", - "schema:name": "RIL_8W_75 RIL 8-way ", - "studyURIs": [ - "urn:VIB/study/VIB_study___48", - "urn:VIB/study/VIB_study___55" - ], - "genusSpecies": "Zea mays" - }, - { - "countryOfOriginCode": "BE", - "instituteCode": "VIB", - "accessionNumber": "177", - "defaultDisplayName": "RIL_8W_81 RIL 8-way ", - "germplasmDbId": "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfODFSSUw4d2F5X19fMTc3", - "germplasmName": "RIL_8W_81 RIL 8-way ", - "commonCropName": "Maize", - "instituteName": "VIB", - "species": "mays", - "genus": "Zea", - "source": "VIB", - 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"urn:VIB/location/5" - ], - "trialURIs": [ - "urn:VIB/trial/2" - ] - } - ], - "contacts": [ - { - "institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", - "type": "Corresponding author", - "email": "marioenrico.pe@santannapisa.it", - "orcid": "0000-0001-6197-2282", - "name": "Mario Enrico Pè", - "contactDbId": "dXJuOlZJQi9jb250YWN0LzMxOTE5MDk0NTA=", - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8y" - ], - "source": "VIB", - "contactURI": "urn:VIB/contact/3191909450", - "@type": "contact", - "@id": "urn:VIB/contact/3191909450", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "3191909450", - "trialURIs": [ - "urn:VIB/trial/2" - ] - }, - { - "institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", - "type": "Collecting data", - "orcid": "0000-0002-1544-0979", - "name": "Aye L. 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"urn:VIB/contact/3728271192" - ], - "studies": [ - { - "trialDbId": "dXJuOlZJQi90cmlhbC8z", - "startDate": "2013-08-20", - "studyType": "Phenotyping Study", - "studyDbId": "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX180OA==", - "trialName": "RIL_8-way_growth_chamber", - "name": "RIL 8-way batch 9", - "endDate": "2013-09-16", - "locationDbId": "dXJuOlZJQi9sb2NhdGlvbi8x", - "locationName": "growth chamber", - "active": false, - "source": "VIB", - "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/48", - "studyName": "RIL 8-way batch 9", - "studyDescription": "Short description of the experimental design, possibly including statistical design.", - "germplasmDbIds": [ - "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfNzVSSUw4d2F5X19fMTgz", - "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfODFSSUw4d2F5X19fMTc3" - ], - "observationVariableDbIds": [ - "65", - "66", - "50", - "54", - "52", - "186", - "188", - "60", - "71", - "195" - ], - "locationDbIds": [ - "dXJuOlZJQi9sb2NhdGlvbi8x" - ], - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "studyURI": "urn:VIB/study/VIB_study___48", - "@type": "study", - "@id": "urn:VIB/study/VIB_study___48", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "VIB_study___48", - "schema:name": "RIL 8-way batch 9", - "trialURI": "urn:VIB/trial/3", - "locationURI": "urn:VIB/location/1", - "germplasmURIs": [ - "urn:VIB/germplasm/Zea_VIB_RIL_8W_75RIL8way___183", - "urn:VIB/germplasm/Zea_VIB_RIL_8W_81RIL8way___177" - ], - "locationURIs": [ - "urn:VIB/location/1" - ], - "trialURIs": [ - "urn:VIB/trial/3" - ] - }, - { - "trialDbId": "dXJuOlZJQi90cmlhbC8z", - "startDate": "2013-06-25", - "studyType": "Phenotyping Study", - "studyDbId": "dXJuOlZJQi9zdHVkeS9WSUJfc3R1ZHlfX180Ng==", - "trialName": "RIL_8-way_growth_chamber", - "name": "RIL 8-way batch 7", - "endDate": "2013-07-22", - "locationDbId": "dXJuOlZJQi9sb2NhdGlvbi8x", - "locationName": "growth chamber", - "active": false, - "source": "VIB", - "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/46", - "studyName": "RIL 8-way batch 7", - "studyDescription": "Short description of the experimental design, possibly including statistical design.", - "germplasmDbIds": [ - "dXJuOlZJQi9nZXJtcGxhc20vWmVhX1ZJQl9SSUxfOFdfNTlSSUw4d2F5X19fMTYw" - ], - "observationVariableDbIds": [ - "65", - "66", - "50", - "54", - "52", - "186", - "188", - "60", - "71", - "195" - ], - "locationDbIds": [ - "dXJuOlZJQi9sb2NhdGlvbi8x" - ], - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "studyURI": "urn:VIB/study/VIB_study___46", - "@type": "study", - "@id": "urn:VIB/study/VIB_study___46", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "VIB_study___46", - "schema:name": "RIL 8-way batch 7", - "trialURI": "urn:VIB/trial/3", - "locationURI": "urn:VIB/location/1", - "germplasmURIs": [ - "urn:VIB/germplasm/Zea_VIB_RIL_8W_59RIL8way___160" - ], - "locationURIs": [ - "urn:VIB/location/1" - ], - "trialURIs": [ - "urn:VIB/trial/3" - ] - } - ], - "contacts": [ - { - "institutionName": "VIB - Center for Plant Systems Biology", - "type": "Author", - "email": "joke.baute@vib.be", - "orcid": "0000-0003-0507-6904", - "name": "Joke Baute", - "contactDbId": "dXJuOlZJQi9jb250YWN0LzI2MDE1MjQ3NDU=", - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "source": "VIB", - "contactURI": "urn:VIB/contact/2601524745", - "@type": "contact", - "@id": "urn:VIB/contact/2601524745", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "2601524745", - "trialURIs": [ - "urn:VIB/trial/3" - ] - }, - { - "institutionName": "VIB - Center for Plant Systems Biology", - "type": "Corresponding author", - "email": "dirk.inze@ugent.vib.be", - "orcid": "0000-0002-3217-8407", - "name": "Dirk Inzé", - "contactDbId": "dXJuOlZJQi9jb250YWN0LzI1NjQyMDE4NDg=", - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "source": "VIB", - "contactURI": "urn:VIB/contact/2564201848", - "@type": "contact", - "@id": "urn:VIB/contact/2564201848", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "2564201848", - "trialURIs": [ - "urn:VIB/trial/3" - ] - }, - { - "institutionName": "VIB - Center for Plant Systems Biology", - "type": "Collecting data", - "email": "joblo@psb.vib-ugent.be", - "orcid": "0000-0003-0047-4380", - "name": "Jolien De Block", - "contactDbId": "dXJuOlZJQi9jb250YWN0LzM3MjgyNzExOTI=", - "trialDbIds": [ - "dXJuOlZJQi90cmlhbC8z" - ], - "source": "VIB", - "contactURI": "urn:VIB/contact/3728271192", - "@type": "contact", - "@id": "urn:VIB/contact/3728271192", - "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", - "schema:identifier": "3728271192", - "trialURIs": [ - "urn:VIB/trial/3" - ] - } - ] } ] \ No newline at end of file diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index a12de9c..6bc71cc 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -31,6 +31,11 @@ def test_files_should_be_generated(self): self.assertTrue(os.path.exists(self._actual_data_dir+"VIB.json")) self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/germplasm.json")) self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/study.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/contact.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/datadiscovery.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/location.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/observationVariable.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/trial.json")) def test_all_germplasms_generated(self): @@ -44,6 +49,61 @@ def test_all_germplasms_generated(self): self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + def test_all_datadiscovery_generated(self): + self.assertTrue(True) + with open(self._actual_data_dir+"/VIB/datadiscovery.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_datadiscovery_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + + + def test_all_locations_generated(self): + self.assertTrue(True) + with open(self._actual_data_dir+"/VIB/location.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_location_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + + + def test_all_observationVariables_generated(self): + self.assertTrue(True) + with open(self._actual_data_dir+"/VIB/observationVariable.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_observation_variable_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + + + def test_all_studys_generated(self): + self.assertTrue(True) + with open(self._actual_data_dir+"/VIB/study.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_study_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + + + def test_all_trials_generated(self): + self.assertTrue(True) + with open(self._actual_data_dir+"/VIB/trial.json") as actual_vib_f: + actual_vib = json.load(actual_vib_f) + + with open(self._expected_data_dir+"VIB_trial_expected.json") as expected_vib_f: + expected_vib = json.load(expected_vib_f) + + self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + + def test_json_files_equals(self): with open(self._actual_data_dir+"VIB.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -54,8 +114,6 @@ def test_json_files_equals(self): self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) - def test_toto(self): - self.assertEqual(1,1) From dc605c5c4223426b3a7fda86008dbc01154d8752 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Wed, 19 May 2021 11:25:05 +0200 Subject: [PATCH 22/26] Remove unnecessary lines --- tests/transform/integration/test_es_integration.py | 9 --------- 1 file changed, 9 deletions(-) diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index 6bc71cc..67ca5a0 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -3,7 +3,6 @@ import os import json from deepdiff import DeepDiff -from etl.transform.uri import read_json_lines class MyTestCase(unittest.TestCase): @@ -113,11 +112,3 @@ def test_json_files_equals(self): self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) - - - - -#if __name__ == '__main__': -# unittest.main() - -#("pipenv run ./main.py trans es --data-dir sandbox/ sources/VIB.json sources/NIB.json") From 6f2e594e20ebc0e1d807b97584d569181a916e16 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Tue, 1 Jun 2021 15:17:29 +0200 Subject: [PATCH 23/26] Simplify for Faidare indexing --- etl/transform/elasticsearch.py | 20 +++++++------------- 1 file changed, 7 insertions(+), 13 deletions(-) diff --git a/etl/transform/elasticsearch.py b/etl/transform/elasticsearch.py index 8c683ba..e1d9b73 100755 --- a/etl/transform/elasticsearch.py +++ b/etl/transform/elasticsearch.py @@ -165,20 +165,14 @@ def dump_clean_in_json_files(source_dir, logger, documents_tuples): def save_json(source_dir, json_dict): for type, document in json_dict.items(): - if len(document) < 10000: - with open(source_dir + "/" + type +'.json', 'w') as f: - json.dump(document, f, ensure_ascii=False) + file_number = 1 + saved_documents = 0 + while saved_documents < len(document): + with open(source_dir + "/" + type + '-' + str(file_number) + '.json', 'w') as f: + json.dump(document[saved_documents:file_number*10000], f, ensure_ascii=False) f.close() - - else: - file_number = 1 - saved_documents = 0 - while saved_documents < len(document): - with open(source_dir + "/" + type + '-' + str(file_number) + '.json', 'w') as f: - json.dump(document[saved_documents:file_number*10000], f, ensure_ascii=False) - f.close() - file_number += 1 - saved_documents += 10000 + file_number += 1 + saved_documents += 10000 def get_document_configs_by_entity(document_configs): From d3693e4ad6dfd8e319ca526afe81acdcbdc540c6 Mon Sep 17 00:00:00 2001 From: Maud Marty Date: Tue, 22 Jun 2021 11:49:59 +0200 Subject: [PATCH 24/26] fix: file name correction --- .../integration/test_es_integration.py | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index 67ca5a0..b8a638a 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -28,18 +28,18 @@ def test_files_should_be_generated(self): self.assertIsNotNone(self._actual_data_dir) self.assertTrue(os.path.exists(self._actual_data_dir)) self.assertTrue(os.path.exists(self._actual_data_dir+"VIB.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/germplasm.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/study.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/contact.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/datadiscovery.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/location.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/observationVariable.json")) - self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/trial.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/germplasm-1.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/study-1.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/contact-1.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/datadiscovery-1.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/location-1.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/observationVariable-1.json")) + self.assertTrue(os.path.exists(self._actual_data_dir+"/VIB/trial-1.json")) def test_all_germplasms_generated(self): self.assertTrue(True) - with open(self._actual_data_dir+"/VIB/germplasm.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/germplasm-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_germplasm_expected.json") as expected_vib_f: @@ -50,7 +50,7 @@ def test_all_germplasms_generated(self): def test_all_datadiscovery_generated(self): self.assertTrue(True) - with open(self._actual_data_dir+"/VIB/datadiscovery.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/datadiscovery-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_datadiscovery_expected.json") as expected_vib_f: @@ -61,7 +61,7 @@ def test_all_datadiscovery_generated(self): def test_all_locations_generated(self): self.assertTrue(True) - with open(self._actual_data_dir+"/VIB/location.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/location-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_location_expected.json") as expected_vib_f: @@ -72,7 +72,7 @@ def test_all_locations_generated(self): def test_all_observationVariables_generated(self): self.assertTrue(True) - with open(self._actual_data_dir+"/VIB/observationVariable.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/observationVariable-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_observation_variable_expected.json") as expected_vib_f: @@ -83,7 +83,7 @@ def test_all_observationVariables_generated(self): def test_all_studys_generated(self): self.assertTrue(True) - with open(self._actual_data_dir+"/VIB/study.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/study-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_study_expected.json") as expected_vib_f: @@ -94,7 +94,7 @@ def test_all_studys_generated(self): def test_all_trials_generated(self): self.assertTrue(True) - with open(self._actual_data_dir+"/VIB/trial.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/trial-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) with open(self._expected_data_dir+"VIB_trial_expected.json") as expected_vib_f: From a693528216f588a70fc93f6dd36cd5aa79f278ee Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Mon, 16 Aug 2021 16:52:00 +0200 Subject: [PATCH 25/26] Add explicit error message --- etl/transform/uri.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/etl/transform/uri.py b/etl/transform/uri.py index 6355f98..38e52c9 100644 --- a/etl/transform/uri.py +++ b/etl/transform/uri.py @@ -292,6 +292,10 @@ def get_in_index(link_id): # upper() to solve case sensitive issues (eg. "ea00371") in WUR data return uri_index[link_id.upper()].decode() except KeyError as e: + print( + f"Could not find '{alias or linked_entity}' with id '{link_id}' " + f"found in '{link_path}' of object:\n{data}" + ) raise MissingDataLink( f"Could not find '{alias or linked_entity}' with id '{link_id}' " f"found in '{link_path}' of object:\n{data}" From ea737b8267fad9ad29502264c45dedea9e5d1ef1 Mon Sep 17 00:00:00 2001 From: Cyril Pommier Date: Tue, 17 Aug 2021 18:05:02 +0200 Subject: [PATCH 26/26] Improve performances for test execution. Improve test coverage by checking email transformation. --- etl/transform/elasticsearch.py | 12 +- .../VIB_contact_expected.json | 1 + .../VIB_datadiscovery_expected.json | 13 +- .../VIB_study_expected.json | 335 +++++++++--------- .../VIB_trial_expected.json | 23 +- .../brapi_pheno_source/json/VIB/study.json | 2 +- .../integration/test_es_integration.py | 38 +- 7 files changed, 230 insertions(+), 194 deletions(-) create mode 100644 tests/transform/integration/fixtures/brapi_pheno_source/VIB_contact_expected.json diff --git a/etl/transform/elasticsearch.py b/etl/transform/elasticsearch.py index e1d9b73..b718079 100755 --- a/etl/transform/elasticsearch.py +++ b/etl/transform/elasticsearch.py @@ -143,11 +143,13 @@ def dump_clean_in_json_files(source_dir, logger, documents_tuples): for document_header, document in documents_tuples: # Hide email - if "contact" in document: - old_mail = document["contact"]["email"] - if old_mail is not None: - safe_mail = old_mail.replace('@', '_') - document["contact"]["email"] = safe_mail + if ("email" in document): + document["email"]= document["email"].replace('@', '_') + + if ("contacts" in document): + for contact in document["contacts"]: + if "email" in contact : + contact["email"]= contact["email"].replace('@', '_') if document_header not in json_dict: json_dict[document_header] = [] diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_contact_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_contact_expected.json new file mode 100644 index 0000000..6d797cb --- /dev/null +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_contact_expected.json @@ -0,0 +1 @@ +[{"institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", "type": "Participating Investigator", "orcid": "0000-0001-6104-8479", "name": "Giorgio Pea", "contactDbId": "dXJuOlZJQi9jb250YWN0LzQwMTAxMDYzMjE=", "trialDbIds": ["dXJuOlZJQi90cmlhbC8y"], "source": "VIB", "contactURI": "urn:VIB/contact/4010106321", "@type": "contact", "@id": "urn:VIB/contact/4010106321", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "4010106321", "schema:name": null, "trialURIs": ["urn:VIB/trial/2"]}, {"institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0002-1544-0979", "name": "Aye L. Hlaing", "contactDbId": "dXJuOlZJQi9jb250YWN0LzEyMTMxNTUyMjY=", "trialDbIds": ["dXJuOlZJQi90cmlhbC8y"], "source": "VIB", "contactURI": "urn:VIB/contact/1213155226", "@type": "contact", "@id": "urn:VIB/contact/1213155226", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "1213155226", "schema:name": null, "trialURIs": ["urn:VIB/trial/2"]}, {"institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", "type": "Collecting data", "orcid": "0000-0003-3547-0195", "name": "Htay H. Aung", "contactDbId": "dXJuOlZJQi9jb250YWN0LzU4NTUwMjgz", "trialDbIds": ["dXJuOlZJQi90cmlhbC8y"], "source": "VIB", "contactURI": "urn:VIB/contact/58550283", "@type": "contact", "@id": "urn:VIB/contact/58550283", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "58550283", "schema:name": null, "trialURIs": ["urn:VIB/trial/2"]}, {"institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", "type": "Corresponding author", "email": "marioenrico.pe_santannapisa.it", "orcid": "0000-0001-6197-2282", "name": "Mario Enrico Pè", "contactDbId": "dXJuOlZJQi9jb250YWN0LzMxOTE5MDk0NTA=", "trialDbIds": ["dXJuOlZJQi90cmlhbC8y"], "source": "VIB", "contactURI": "urn:VIB/contact/3191909450", "@type": "contact", "@id": "urn:VIB/contact/3191909450", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "3191909450", "schema:name": null, "trialURIs": ["urn:VIB/trial/2"]}, {"institutionName": "VIB - Center for Plant Systems Biology", "type": "Author", "email": "joke.baute_vib.be", "orcid": "0000-0003-0507-6904", "name": "Joke Baute", "contactDbId": "dXJuOlZJQi9jb250YWN0LzI2MDE1MjQ3NDU=", "trialDbIds": ["dXJuOlZJQi90cmlhbC8z"], "source": "VIB", "contactURI": "urn:VIB/contact/2601524745", "@type": "contact", "@id": "urn:VIB/contact/2601524745", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "2601524745", "schema:name": null, "trialURIs": ["urn:VIB/trial/3"]}, {"institutionName": "VIB - Center for Plant Systems Biology", "type": "Collecting data", "email": "joblo_psb.vib-ugent.be", "orcid": "0000-0003-0047-4380", "name": "Jolien De Block", "contactDbId": "dXJuOlZJQi9jb250YWN0LzM3MjgyNzExOTI=", "trialDbIds": ["dXJuOlZJQi90cmlhbC8z"], "source": "VIB", "contactURI": "urn:VIB/contact/3728271192", "@type": "contact", "@id": "urn:VIB/contact/3728271192", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "3728271192", "schema:name": null, "trialURIs": ["urn:VIB/trial/3"]}, {"institutionName": "VIB - Center for Plant Systems Biology", "type": "Corresponding author", "email": "dirk.inze_ugent.vib.be", "orcid": "0000-0002-3217-8407", "name": "Dirk Inzé", "contactDbId": "dXJuOlZJQi9jb250YWN0LzI1NjQyMDE4NDg=", "trialDbIds": ["dXJuOlZJQi90cmlhbC8z"], "source": "VIB", "contactURI": "urn:VIB/contact/2564201848", "@type": "contact", "@id": "urn:VIB/contact/2564201848", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", "schema:identifier": "2564201848", "schema:name": null, "trialURIs": ["urn:VIB/trial/3"]}] diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json index 7765a08..b563628 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_datadiscovery_expected.json @@ -201,6 +201,17 @@ "dXJuOlZJQi90cmlhbC8z" ], "studyURI": "urn:VIB/study/VIB_study___48", + "contacts": [ + { + "contactDbId": "dXJuOlZJQi9jb250YWN0LzVmNGU1NTA5", + "email": "bob_bob.com", + "instituteName": "The BrAPI Institute", + "name": "Bob Robertson", + "orcid": "http://orcid.org/0000-0001-8640-1750", + "type": "PI", + "contactURI": "urn:VIB/contact/5f4e5509" + } + ], "@type": "study", "@id": "urn:VIB/study/VIB_study___48", "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", @@ -499,4 +510,4 @@ "node": "VIB", "databaseName": "brapi@VIB" } -] \ No newline at end of file +] diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json index b4daf60..10f12fa 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_study_expected.json @@ -1,163 +1,174 @@ [ - { - 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"contactDbId": "dXJuOlZJQi9jb250YWN0LzVmNGU1NTA5", + "email": "bob_bob.com", + "instituteName": "The BrAPI Institute", + "name": "Bob Robertson", + "orcid": "http://orcid.org/0000-0001-8640-1750", + "type": "PI", + "contactURI": "urn:VIB/contact/5f4e5509" + } + ], + "studyURI": "urn:VIB/study/VIB_study___48", + "@type": "study", + "@id": "urn:VIB/study/VIB_study___48", + "schema:includedInDataCatalog": "http://pippa.psb.ugent.be", + "schema:identifier": "VIB_study___48", + "schema:name": "RIL 8-way batch 9", + "trialURI": "urn:VIB/trial/3", + "locationURI": "urn:VIB/location/1", + "germplasmURIs": [ + "urn:VIB/germplasm/Zea_VIB_RIL_8W_75RIL8way___183", + "urn:VIB/germplasm/Zea_VIB_RIL_8W_81RIL8way___177" + ], + "locationURIs": [ + "urn:VIB/location/1" + ], + "trialURIs": [ + "urn:VIB/trial/3" + ], + "schema:url": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/48" + } +] diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_trial_expected.json b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_trial_expected.json index 6a4ed67..cd61fe3 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/VIB_trial_expected.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/VIB_trial_expected.json @@ -1,4 +1,4 @@ -[ +[ { "publications": [ { @@ -90,7 +90,7 @@ { "institutionName": "Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy", "type": "Corresponding author", - "email": "marioenrico.pe@santannapisa.it", + "email": "marioenrico.pe_santannapisa.it", "orcid": "0000-0001-6197-2282", "name": "Mario Enrico Pè", "contactDbId": "dXJuOlZJQi9jb250YWN0LzMxOTE5MDk0NTA=", @@ -240,6 +240,17 @@ "trialDbIds": [ "dXJuOlZJQi90cmlhbC8z" ], + "contacts": [ + { + "contactDbId": "dXJuOlZJQi9jb250YWN0LzVmNGU1NTA5", + "email": "bob@bob.com", + "instituteName": "The BrAPI Institute", + "name": "Bob Robertson", + "orcid": "http://orcid.org/0000-0001-8640-1750", + "type": "PI", + "contactURI": "urn:VIB/contact/5f4e5509" + } + ], "studyURI": "urn:VIB/study/VIB_study___48", "@type": "study", "@id": "urn:VIB/study/VIB_study___48", @@ -318,7 +329,7 @@ { "institutionName": "VIB - Center for Plant Systems Biology", "type": "Author", - "email": "joke.baute@vib.be", + "email": "joke.baute_vib.be", "orcid": "0000-0003-0507-6904", "name": "Joke Baute", "contactDbId": "dXJuOlZJQi9jb250YWN0LzI2MDE1MjQ3NDU=", @@ -338,7 +349,7 @@ { "institutionName": "VIB - Center for Plant Systems Biology", "type": "Corresponding author", - "email": "dirk.inze@ugent.vib.be", + "email": "dirk.inze_ugent.vib.be", "orcid": "0000-0002-3217-8407", "name": "Dirk Inzé", "contactDbId": "dXJuOlZJQi9jb250YWN0LzI1NjQyMDE4NDg=", @@ -358,7 +369,7 @@ { "institutionName": "VIB - Center for Plant Systems Biology", "type": "Collecting data", - "email": "joblo@psb.vib-ugent.be", + "email": "joblo_psb.vib-ugent.be", "orcid": "0000-0003-0047-4380", "name": "Jolien De Block", "contactDbId": "dXJuOlZJQi9jb250YWN0LzM3MjgyNzExOTI=", @@ -377,4 +388,4 @@ } ] } -] \ No newline at end of file +] diff --git a/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/study.json b/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/study.json index 46f574b..31793ac 100644 --- a/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/study.json +++ b/tests/transform/integration/fixtures/brapi_pheno_source/json/VIB/study.json @@ -1,3 +1,3 @@ {"trialDbId": "2", "startDate": "2012-05-01", "studyType": "Phenotyping Study", "studyDbId": "VIB_study___55", "trialName": "RIL_8-way_Field_trial", "name": "Enrico Pe field trial", "endDate": "2012-08-01", "locationDbId": "5", "locationName": "Field trial", "active": false, "source": "VIB", "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/55", "studyName": "Enrico Pe field trial", "studyDescription": "Short description of the experimental design, possibly including statistical design.", "germplasmDbIds": ["Zea_VIB_RIL_8W_EP33_20___1184"], "observationVariableDbIds": ["216", "215", "217", "218"], "locationDbIds": ["5"], "trialDbIds": ["2"]} {"trialDbId": "3", "startDate": "2013-06-25", "studyType": "Phenotyping Study", "studyDbId": "VIB_study___46", "trialName": "RIL_8-way_growth_chamber", "name": "RIL 8-way batch 7", "endDate": "2013-07-22", "locationDbId": "1", "locationName": "growth chamber", "active": false, "source": "VIB", "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/46", "studyName": "RIL 8-way batch 7", "studyDescription": "Short description of the experimental design, possibly including statistical design.", "germplasmDbIds": ["Zea_VIB_RIL_8W_59RIL8way___160"], "observationVariableDbIds": ["65", "66", "50", "54", "52", "186", "188", "60", "71", "195"], "locationDbIds": ["1"], "trialDbIds": ["3"]} -{"trialDbId": "3", "startDate": "2013-08-20", "studyType": "Phenotyping Study", "studyDbId": "VIB_study___48", "trialName": "RIL_8-way_growth_chamber", "name": "RIL 8-way batch 9", "endDate": "2013-09-16", "locationDbId": "1", "locationName": "growth chamber", "active": false, "source": "VIB", "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/48", "studyName": "RIL 8-way batch 9", "studyDescription": "Short description of the experimental design, possibly including statistical design.", "germplasmDbIds": ["Zea_VIB_RIL_8W_75RIL8way___183", "Zea_VIB_RIL_8W_81RIL8way___177"], "observationVariableDbIds": ["65", "66", "50", "54", "52", "186", "188", "60", "71", "195"], "locationDbIds": ["1"], "trialDbIds": ["3"]} +{"trialDbId": "3", "startDate": "2013-08-20", "studyType": "Phenotyping Study", "studyDbId": "VIB_study___48", "trialName": "RIL_8-way_growth_chamber", "name": "RIL 8-way batch 9", "endDate": "2013-09-16", "locationDbId": "1", "locationName": "growth chamber", "active": false, "source": "VIB", "documentationURL": "https://pippa.psb.ugent.be/pippa_experiments/consult_experiment_basic_info/48", "studyName": "RIL 8-way batch 9", "studyDescription": "Short description of the experimental design, possibly including statistical design.", "germplasmDbIds": ["Zea_VIB_RIL_8W_75RIL8way___183", "Zea_VIB_RIL_8W_81RIL8way___177"], "observationVariableDbIds": ["65", "66", "50", "54", "52", "186", "188", "60", "71", "195"], "locationDbIds": ["1"], "trialDbIds": ["3"], "contacts": [{ "contactDbId": "5f4e5509", "email": "bob@bob.com", "instituteName": "The BrAPI Institute", "name": "Bob Robertson", "orcid": "http://orcid.org/0000-0001-8640-1750", "type": "PI"}]} diff --git a/tests/transform/integration/test_es_integration.py b/tests/transform/integration/test_es_integration.py index b8a638a..5a9d786 100644 --- a/tests/transform/integration/test_es_integration.py +++ b/tests/transform/integration/test_es_integration.py @@ -7,18 +7,19 @@ class MyTestCase(unittest.TestCase): - _are_file_generated = False + #_are_file_generated = False - def setUp(self): + @classmethod + def setUpClass(self): self._current_path = os.path.dirname(__file__) self._root_dir = os.path.normpath(os.path.join(self._current_path, "../../../")) - if not self._are_file_generated: - result = subprocess.run([self._root_dir + "/main.py", "trans", - "es", - self._root_dir + "/tests/transform/integration/fixtures/VIB.json", - "--data-dir", - self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) - self._are_file_generated = True + #if not self._are_file_generated: + result = subprocess.run([self._root_dir + "/main.py", "trans", + "es", + self._root_dir + "/tests/transform/integration/fixtures/VIB.json", + "--data-dir", + self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source"]) + #self._are_file_generated = True self._actual_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/json-bulk/" self._expected_data_dir = self._root_dir + "/tests/transform/integration/fixtures/brapi_pheno_source/" @@ -38,7 +39,7 @@ def test_files_should_be_generated(self): def test_all_germplasms_generated(self): - self.assertTrue(True) + with open(self._actual_data_dir+"VIB/germplasm-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -49,7 +50,7 @@ def test_all_germplasms_generated(self): def test_all_datadiscovery_generated(self): - self.assertTrue(True) + with open(self._actual_data_dir+"VIB/datadiscovery-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -60,7 +61,7 @@ def test_all_datadiscovery_generated(self): def test_all_locations_generated(self): - self.assertTrue(True) + with open(self._actual_data_dir+"VIB/location-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -71,7 +72,7 @@ def test_all_locations_generated(self): def test_all_observationVariables_generated(self): - self.assertTrue(True) + with open(self._actual_data_dir+"VIB/observationVariable-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -82,7 +83,7 @@ def test_all_observationVariables_generated(self): def test_all_studys_generated(self): - self.assertTrue(True) + with open(self._actual_data_dir+"VIB/study-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -93,7 +94,7 @@ def test_all_studys_generated(self): def test_all_trials_generated(self): - self.assertTrue(True) + with open(self._actual_data_dir+"VIB/trial-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) @@ -102,13 +103,12 @@ def test_all_trials_generated(self): self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) + def test_all_contacts_generated(self): - def test_json_files_equals(self): - with open(self._actual_data_dir+"VIB.json") as actual_vib_f: + with open(self._actual_data_dir+"VIB/contact-1.json") as actual_vib_f: actual_vib = json.load(actual_vib_f) - with open(self._expected_data_dir+"VIB_expected.json") as expected_vib_f: + with open(self._expected_data_dir+"VIB_contact_expected.json") as expected_vib_f: expected_vib = json.load(expected_vib_f) self.assertEqual(DeepDiff(actual_vib, expected_vib), {}) -