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Merge pull request #48 from cancervariants/eb-working
Elastic Beanstalk Deployment
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| container_commands: | ||
| 00_export_eb_env_var: | ||
| command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)" | ||
| 01_install_awscli: | ||
| command: "yum install -y awscli" | ||
| 02_install_unzip: | ||
| command: "yum install -y unzip" | ||
| 03_s3_download: | ||
| command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} ./variant/data/seqrepo.zip --region us-east-2" | ||
| 04_unzip_seqrepo: | ||
| command: "unzip ./variant/data/seqrepo.zip -d ./variant/data" | ||
| 05_seqrepo_permission: | ||
| command: "chmod -R 777 ./variant/data/seqrepo" | ||
| 06_macosx_permission: | ||
| command: "chmod -R +wr ./variant/data/__MACOSX" | ||
| 07_seqrepo_zip_permission: | ||
| command: "chmod +wr ./variant/data/seqrepo.zip" | ||
| 08_remove_macosx: | ||
| command: "rm -R ./variant/data/__MACOSX" | ||
| 09_remove_seqrepo_zip: | ||
| command: "rm ./variant/data/seqrepo.zip" | ||
| 10_data_permission: | ||
| command: "chmod -R +wrx ./variant/data" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1 @@ | ||
| web: gunicorn -w 4 -k uvicorn.workers.UvicornWorker main:app | ||
| web: gunicorn -k uvicorn.workers.UvicornWorker main:app |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,34 @@ | ||
| """Module for testing Protein Substitution Translator.""" | ||
| """Module for testing amino acid Substitution Translator.""" | ||
| import unittest | ||
| from variant.classifiers import AminoAcidSubstitutionClassifier | ||
| from variant.translators import AminoAcidSubstitution | ||
| from variant.validators import AminoAcidSubstitution as AASUB_V | ||
| from .translator_base import TranslatorBase | ||
| from variant.tokenizers import GeneSymbol | ||
| from variant.tokenizers.caches import GeneSymbolCache, AminoAcidCache | ||
| from variant.data_sources import SeqRepoAccess, TranscriptMappings | ||
| from variant import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH | ||
|
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||
|
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| class TestAminoAcidSubstitutionTranslator(TranslatorBase, unittest.TestCase): | ||
| """A class to test the Protein Substitution Translator.""" | ||
| """A class to test the amino acid Substitution Translator.""" | ||
|
|
||
| def classifier_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return amino acid substitution instance.""" | ||
| return AminoAcidSubstitutionClassifier() | ||
|
|
||
| def validator_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return amino acid substitution instance.""" | ||
| return AASUB_V(SeqRepoAccess(SEQREPO_DATA_PATH), | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH)) | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH), | ||
| GeneSymbol(GeneSymbolCache()), | ||
| AminoAcidCache() | ||
| ) | ||
|
|
||
| def translator_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return amino acid substitution instance.""" | ||
| return AminoAcidSubstitution() | ||
|
|
||
| def fixture_name(self): | ||
| """Return the fixture name for protein substitution.""" | ||
| """Return the fixture name for amino acid substitution.""" | ||
| return 'amino_acid_substitution' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,34 @@ | ||
| """Module for testing Protein Substitution Translator.""" | ||
| """Module for testing polypeptide truncation Translator.""" | ||
| import unittest | ||
| from variant.classifiers import PolypeptideTruncationClassifier | ||
| from variant.translators import PolypeptideTruncation | ||
| from variant.validators import PolypeptideTruncation as PT_V | ||
| from .translator_base import TranslatorBase | ||
| from variant.tokenizers import GeneSymbol | ||
| from variant.tokenizers.caches import GeneSymbolCache, AminoAcidCache | ||
| from variant.data_sources import SeqRepoAccess, TranscriptMappings | ||
| from variant import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH | ||
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||
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| class TestPolypeptideTruncationTranslator(TranslatorBase, unittest.TestCase): | ||
| """A class to test the Protein Substitution Translator.""" | ||
| """A class to test the polypeptide truncation Translator.""" | ||
|
|
||
| def classifier_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return polypeptide truncation instance.""" | ||
| return PolypeptideTruncationClassifier() | ||
|
|
||
| def validator_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return polypeptide truncation instance.""" | ||
| return PT_V(SeqRepoAccess(SEQREPO_DATA_PATH), | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH)) | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH), | ||
| GeneSymbol(GeneSymbolCache()), | ||
| AminoAcidCache() | ||
| ) | ||
|
|
||
| def translator_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return polypeptide truncation instance.""" | ||
| return PolypeptideTruncation() | ||
|
|
||
| def fixture_name(self): | ||
| """Return the fixture name for protein substitution.""" | ||
| return 'amino_acid_substitution' | ||
| """Return the fixture name for polypeptide truncation.""" | ||
| return 'polypeptide_truncation' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,29 +1,34 @@ | ||
| """Module for testing Protein Substitution Translator.""" | ||
| """Module for testing Silent Mutation Translator.""" | ||
| import unittest | ||
| from variant.classifiers import SilentMutationClassifier | ||
| from variant.translators import SilentMutation | ||
| from variant.validators import SilentMutation as SM_V | ||
| from .translator_base import TranslatorBase | ||
| from variant.tokenizers import GeneSymbol | ||
| from variant.tokenizers.caches import GeneSymbolCache, AminoAcidCache | ||
| from variant.data_sources import SeqRepoAccess, TranscriptMappings | ||
| from variant import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH | ||
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| class TestAminoAcidSubstitutionTranslator(TranslatorBase, unittest.TestCase): | ||
| """A class to test the Protein Substitution Translator.""" | ||
| class TestSilentMutationTranslator(TranslatorBase, unittest.TestCase): | ||
| """A class to test the silent mutation Translator.""" | ||
|
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||
| def classifier_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return silent mutation instance.""" | ||
| return SilentMutationClassifier() | ||
|
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| def validator_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return silent mutation instance.""" | ||
| return SM_V(SeqRepoAccess(SEQREPO_DATA_PATH), | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH)) | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH), | ||
| GeneSymbol(GeneSymbolCache()), | ||
| AminoAcidCache() | ||
| ) | ||
|
|
||
| def translator_instance(self): | ||
| """Return protein substitution instance.""" | ||
| """Return silent mutation instance.""" | ||
| return SilentMutation() | ||
|
|
||
| def fixture_name(self): | ||
| """Return the fixture name for protein substitution.""" | ||
| return 'amino_acid_substitution' | ||
| """Return the fixture name for silent mutation.""" | ||
| return 'silent_mutation' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,24 +1,28 @@ | ||
| """Module for testing Amino Acid Substitution Validator.""" | ||
| """Module for testing Polypeptide Truncation Validator.""" | ||
| import unittest | ||
| from variant.validators import PolypeptideTruncation | ||
| from variant.classifiers import PolypeptideTruncationClassifier | ||
| from .validator_base import ValidatorBase | ||
| from variant.tokenizers import GeneSymbol | ||
| from variant.tokenizers.caches import GeneSymbolCache, AminoAcidCache | ||
| from variant.data_sources import TranscriptMappings, SeqRepoAccess | ||
| from variant import SEQREPO_DATA_PATH, TRANSCRIPT_MAPPINGS_PATH | ||
|
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||
|
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| class TestPolypeptideTruncationValidator(ValidatorBase, unittest.TestCase): | ||
| """A class to test the Protein Substitution Validator.""" | ||
| """A class to test the Polypeptide Truncation Validator.""" | ||
|
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||
| def validator_instance(self): | ||
| """Return amino acid substitution instance.""" | ||
| """Return Polypeptide Truncation instance.""" | ||
| return PolypeptideTruncation(SeqRepoAccess(SEQREPO_DATA_PATH), | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH)) # noqa: E501 | ||
| TranscriptMappings(TRANSCRIPT_MAPPINGS_PATH), # noqa: E501 | ||
| GeneSymbol(GeneSymbolCache()), | ||
| AminoAcidCache()) | ||
|
|
||
| def classifier_instance(self): | ||
| """Return the protein substitution classifier instance.""" | ||
| """Return the Polypeptide Truncation classifier instance.""" | ||
| return PolypeptideTruncationClassifier() | ||
|
|
||
| def fixture_name(self): | ||
| """Return the fixture name for protein substitution.""" | ||
| """Return the fixture name for Polypeptide Truncation.""" | ||
| return 'polypeptide_truncation' |
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