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Merge pull request #23 from bento-platform/releases/v3.5
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v3.5.0 rc-1
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@brouillette
brouillette authored Apr 26, 2022
2 parents 630d3fb + 9a16c59 commit 2bbee4f
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5 changes: 4 additions & 1 deletion .gitignore
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Expand Up @@ -7,7 +7,7 @@

# Volume directories
data/
data-*/
data-x/

# vcfs
*/vcfs/*.txt
Expand Down Expand Up @@ -54,3 +54,6 @@ bin/*
# ignore .gtf files
*/*.gtf*
*/*/*.gtf*

# ignore vendor
vendor/
18 changes: 15 additions & 3 deletions Makefile
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Expand Up @@ -22,41 +22,53 @@ export HOST_USER_GID=$(shell id -g)

# initialize services
init:
# Gateway:
@# Gateway:
@# - DRS Authentication
@htpasswd -cb gateway/drs.htpasswd ${GOHAN_DRS_BASIC_AUTH_USERNAME} ${GOHAN_DRS_BASIC_AUTH_PASSWORD}

@echo

# Authorization:
@# Authorization:
@# - API OPA policies
@echo Configuring authorzation policies
@envsubst < ./etc/api.policy.rego.tpl > ./authorization/api.policy.rego

@$(MAKE) init-data-dirs
@$(MAKE) init-vendor

init-vendor:
@echo "Initializing Go Module Vendor"
@cd src/api && go mod vendor && \
cd ../tests && go mod vendor

init-data-dirs:
@echo "Initializing data directories.." && \
# api-drs bridge: \
mkdir -p ${GOHAN_API_DRS_BRIDGE_HOST_DIR} && \
chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_API_DRS_BRIDGE_HOST_DIR} && \
chmod -R 770 ${GOHAN_API_DRS_BRIDGE_HOST_DIR} && \
\
# drs: \
mkdir -p ${GOHAN_DRS_DATA_DIR} && \
chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_DRS_DATA_DIR} && \
chmod -R 770 ${GOHAN_DRS_DATA_DIR} && \
\
# elasticsearch: \
mkdir -p ${GOHAN_ES_DATA_DIR} && \
chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_ES_DATA_DIR} && \
chmod -R 770 ${GOHAN_ES_DATA_DIR} && \
chmod -R 770 ./data && \
chmod -R 770 ${GOHAN_ES_DATA_DIR} && \
\
# tmp: \
# (setup for when gohan needs to preprocess vcf's at ingestion time): \
mkdir -p ${GOHAN_API_VCF_PATH}/tmp && \
chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_API_VCF_PATH}/tmp && \
chmod -R 770 ${GOHAN_API_VCF_PATH}/tmp && \
chmod -R 770 ${GOHAN_API_VCF_PATH}/tmp && \
mkdir -p ${GOHAN_API_GTF_PATH} && \
chown -R ${HOST_USER_UID}:${HOST_USER_GID} ${GOHAN_API_GTF_PATH} && \
chmod -R 770 ${GOHAN_API_GTF_PATH}/ && \
chmod -R 770 ${GOHAN_API_GTF_PATH}/tmp && \
echo ".. done!"


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120 changes: 119 additions & 1 deletion README.md
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Expand Up @@ -207,7 +207,7 @@ Requests
> - chromosome : **string** `( 1-23, X, Y, MT )`
> - lowerBound : **number**
> - upperBound : **number**
> - reference : **string** `an allele ( "A" | "C" | "G" | "T" or some combination thereof )`
> - reference : **string** `an allele ( "A" | "C" | "G" | "T" | "N" or some combination thereof )`
> - alternative : **string** `an allele`
> - ids : **string** `(a comma-deliminated list of variant ID alphanumeric codes)`
> - size : **number** `(maximum number of results per id)`
Expand Down Expand Up @@ -369,6 +369,124 @@ Response
<br />
**`/tables`**
<br />
Request
> &nbsp;&nbsp;**GET** `/tables`<br/>
<br/>
Response
>```json
> [
> {
> "id": `string`,
> "name": `string`,
> "data_type": `string`,
> "dataset": `string`,
> "assembly_ids": `[]string`,
> "metadata": {...},
> "schema": {...},
> },
> ...
> ]
> ```
<br />
<br />
Request
> &nbsp;&nbsp;**POST** `/tables`<br/>
>```json
> {
> "name": `string`,
> "data_type": `string`,
> "dataset": `string`,
> "metadata": {...},
> }
> ```
<br/>
Response
>```json
> {
> "id": `string`,
> "name": `string`,
> "data_type": `string`,
> "dataset": `string`,
> "assembly_ids": `[]string`,
> "metadata": {...},
> "schema": {...},
> }
> ```
<br />
<br />
Request
> &nbsp;&nbsp;**GET** `/tables/:id`<br/>
> &nbsp;&nbsp;&nbsp;path params:
> - id : **string (UUID)** `(required)`
<br/>
Response
>```json
> {
> "id": `string`,
> "name": `string`,
> "data_type": `string`,
> "dataset": `string`,
> "assembly_ids": `[]string`,
> "metadata": {...},
> "schema": {...},
> }
> ```
<br />
<br />
Request
> &nbsp;&nbsp;**GET** `/tables/:id/summary`<br/>
> &nbsp;&nbsp;&nbsp;path params:
> - id : **string (UUID)** `(required)`
<br/>
Response
>```json
> {
> "count": `int`,
> "data_type_specific": {...},
> }
> ```
<br />
<br />
Request
> &nbsp;&nbsp;**DELETE** `/tables/:id`<br/>
> &nbsp;&nbsp;&nbsp;path params:
> - id : **string (UUID)** `(required)`
<br/>
Response
`Status Code:` **204**
<br />
## Releases
### **API :**
Expand Down
5 changes: 2 additions & 3 deletions src/api/Dockerfile
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Expand Up @@ -21,8 +21,7 @@ RUN apk update && \
RUN apk --update add ncurses-dev && \
apk add git build-base xz-dev zlib-dev bzip2-dev curl-dev && \
\
git config --global url."https://".insteadOf git:// && \
git clone git://github.com/samtools/htslib.git && \
git clone https://github.com/samtools/htslib.git && \
\
cd htslib && \
git submodule update --init --recursive && \
Expand All @@ -31,7 +30,7 @@ RUN apk --update add ncurses-dev && \
make install && \
\
cd .. && \
git clone git://github.com/samtools/samtools.git && \
git clone https://github.com/samtools/samtools.git && \
\
cd samtools && \
make && \
Expand Down
11 changes: 6 additions & 5 deletions src/api/go.mod
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Expand Up @@ -6,12 +6,13 @@ require (
github.com/Jeffail/gabs v1.4.0
github.com/cenkalti/backoff v2.2.1+incompatible
github.com/dgrijalva/jwt-go v3.2.0+incompatible // indirect
github.com/elastic/go-elasticsearch/v7 v7.15.0
github.com/elastic/go-elasticsearch v0.0.0
github.com/elastic/go-elasticsearch/v7 v7.17.1
github.com/google/uuid v1.3.0
github.com/kelseyhightower/envconfig v1.4.0
github.com/labstack/echo v3.3.10+incompatible
github.com/labstack/gommon v0.3.0 // indirect
github.com/mitchellh/mapstructure v1.4.2
github.com/valyala/fasttemplate v1.2.1 // indirect
golang.org/x/crypto v0.0.0-20210921155107-089bfa567519 // indirect
github.com/labstack/gommon v0.3.1 // indirect
github.com/mitchellh/mapstructure v1.4.3
github.com/stretchr/testify v1.7.1 // indirect
golang.org/x/crypto v0.0.0-20220411220226-7b82a4e95df4 // indirect
)
57 changes: 32 additions & 25 deletions src/api/go.sum
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Original file line number Diff line number Diff line change
@@ -1,51 +1,58 @@
github.com/Jeffail/gabs v1.4.0 h1://5fYRRTq1edjfIrQGvdkcd22pkYUrHZ5YC/H2GJVAo=
github.com/Jeffail/gabs v1.4.0/go.mod h1:6xMvQMK4k33lb7GUUpaAPh6nKMmemQeg5d4gn7/bOXc=
github.com/cenkalti/backoff v1.1.0 h1:QnvVp8ikKCDWOsFheytRCoYWYPO/ObCTBGxT19Hc+yE=
github.com/cenkalti/backoff v2.2.1+incompatible h1:tNowT99t7UNflLxfYYSlKYsBpXdEet03Pg2g16Swow4=
github.com/cenkalti/backoff v2.2.1+incompatible/go.mod h1:90ReRw6GdpyfrHakVjL/QHaoyV4aDUVVkXQJJJ3NXXM=
github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/dgrijalva/jwt-go v1.0.2 h1:KPldsxuKGsS2FPWsNeg9ZO18aCrGKujPoWXn2yo+KQM=
github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
github.com/dgrijalva/jwt-go v3.2.0+incompatible h1:7qlOGliEKZXTDg6OTjfoBKDXWrumCAMpl/TFQ4/5kLM=
github.com/dgrijalva/jwt-go v3.2.0+incompatible/go.mod h1:E3ru+11k8xSBh+hMPgOLZmtrrCbhqsmaPHjLKYnJCaQ=
github.com/elastic/go-elasticsearch v0.0.0 h1:Pd5fqOuBxKxv83b0+xOAJDAkziWYwFinWnBO0y+TZaA=
github.com/elastic/go-elasticsearch/v7 v7.15.0 h1:kMLoRAO97gAV97YKgn2z/5ExM8pVJeLoJPR0r33OREs=
github.com/elastic/go-elasticsearch/v7 v7.15.0/go.mod h1:OJ4wdbtDNk5g503kvlHLyErCgQwwzmDtaFC4XyOxXA4=
github.com/elastic/go-elasticsearch v0.0.0/go.mod h1:TkBSJBuTyFdBnrNqoPc54FN0vKf5c04IdM4zuStJ7xg=
github.com/elastic/go-elasticsearch/v7 v7.17.1 h1:49mHcHx7lpCL8cW1aioEwSEVKQF3s+Igi4Ye/QTWwmk=
github.com/elastic/go-elasticsearch/v7 v7.17.1/go.mod h1:OJ4wdbtDNk5g503kvlHLyErCgQwwzmDtaFC4XyOxXA4=
github.com/google/uuid v1.3.0 h1:t6JiXgmwXMjEs8VusXIJk2BXHsn+wx8BZdTaoZ5fu7I=
github.com/google/uuid v1.3.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
github.com/kelseyhightower/envconfig v1.4.0 h1:Im6hONhd3pLkfDFsbRgu68RDNkGF1r3dvMUtDTo2cv8=
github.com/kelseyhightower/envconfig v1.4.0/go.mod h1:cccZRl6mQpaq41TPp5QxidR+Sa3axMbJDNb//FQX6Gg=
github.com/labstack/echo v1.4.4 h1:1bEiBNeGSUKxcPDGfZ/7IgdhJJZx8wV/pICJh4W2NJI=
github.com/labstack/echo v3.3.10+incompatible h1:pGRcYk231ExFAyoAjAfD85kQzRJCRI8bbnE7CX5OEgg=
github.com/labstack/echo v3.3.10+incompatible/go.mod h1:0INS7j/VjnFxD4E2wkz67b8cVwCLbBmJyDaka6Cmk1s=
github.com/labstack/gommon v0.3.0 h1:JEeO0bvc78PKdyHxloTKiF8BD5iGrH8T6MSeGvSgob0=
github.com/labstack/gommon v0.3.0/go.mod h1:MULnywXg0yavhxWKc+lOruYdAhDwPK9wf0OL7NoOu+k=
github.com/mattn/go-colorable v0.1.2 h1:/bC9yWikZXAL9uJdulbSfyVNIR3n3trXl+v8+1sx8mU=
github.com/mattn/go-colorable v0.1.2/go.mod h1:U0ppj6V5qS13XJ6of8GYAs25YV2eR4EVcfRqFIhoBtE=
github.com/mattn/go-isatty v0.0.8/go.mod h1:Iq45c/XA43vh69/j3iqttzPXn0bhXyGjM0Hdxcsrc5s=
github.com/mattn/go-isatty v0.0.9 h1:d5US/mDsogSGW37IV293h//ZFaeajb69h+EHFsv2xGg=
github.com/mattn/go-isatty v0.0.9/go.mod h1:YNRxwqDuOph6SZLI9vUUz6OYw3QyUt7WiY2yME+cCiQ=
github.com/mitchellh/mapstructure v1.4.2 h1:6h7AQ0yhTcIsmFmnAwQls75jp2Gzs4iB8W7pjMO+rqo=
github.com/mitchellh/mapstructure v1.4.2/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RRV2QTWOzhPopBRo=
github.com/labstack/gommon v0.3.1 h1:OomWaJXm7xR6L1HmEtGyQf26TEn7V6X88mktX9kee9o=
github.com/labstack/gommon v0.3.1/go.mod h1:uW6kP17uPlLJsD3ijUYn3/M5bAxtlZhMI6m3MFxTMTM=
github.com/mattn/go-colorable v0.1.11 h1:nQ+aFkoE2TMGc0b68U2OKSexC+eq46+XwZzWXHRmPYs=
github.com/mattn/go-colorable v0.1.11/go.mod h1:u5H1YNBxpqRaxsYJYSkiCWKzEfiAb1Gb520KVy5xxl4=
github.com/mattn/go-isatty v0.0.14 h1:yVuAays6BHfxijgZPzw+3Zlu5yQgKGP2/hcQbHb7S9Y=
github.com/mattn/go-isatty v0.0.14/go.mod h1:7GGIvUiUoEMVVmxf/4nioHXj79iQHKdU27kJ6hsGG94=
github.com/mitchellh/mapstructure v1.4.3 h1:OVowDSCllw/YjdLkam3/sm7wEtOy59d8ndGgCcyj8cs=
github.com/mitchellh/mapstructure v1.4.3/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RRV2QTWOzhPopBRo=
github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM=
github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
github.com/stretchr/testify v1.7.1 h1:5TQK59W5E3v0r2duFAb7P95B6hEeOyEnHRa8MjYSMTY=
github.com/stretchr/testify v1.7.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
github.com/valyala/bytebufferpool v1.0.0 h1:GqA5TC/0021Y/b9FG4Oi9Mr3q7XYx6KllzawFIhcdPw=
github.com/valyala/bytebufferpool v1.0.0/go.mod h1:6bBcMArwyJ5K/AmCkWv1jt77kVWyCJ6HpOuEn7z0Csc=
github.com/valyala/fasttemplate v1.0.1/go.mod h1:UQGH1tvbgY+Nz5t2n7tXsz52dQxojPUpymEIMZ47gx8=
github.com/valyala/fasttemplate v1.2.1 h1:TVEnxayobAdVkhQfrfes2IzOB6o+z4roRkPF52WA1u4=
github.com/valyala/fasttemplate v1.2.1/go.mod h1:KHLXt3tVN2HBp8eijSv/kGJopbvo7S+qRAEEKiv+SiQ=
golang.org/x/crypto v0.0.0-20210921155107-089bfa567519 h1:7I4JAnoQBe7ZtJcBaYHi5UtiO8tQHbUSXxL+pnGRANg=
golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
golang.org/x/net v0.0.0-20210226172049-e18ecbb05110 h1:qWPm9rbaAMKs8Bq/9LRpbMqxWRVUAQwMI9fVrssnTfw=
golang.org/x/net v0.0.0-20210226172049-e18ecbb05110/go.mod h1:m0MpNAwzfU5UDzcl9v0D8zg8gWTRqZa9RBIspLL5mdg=
golang.org/x/sys v0.0.0-20190222072716-a9d3bda3a223/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
golang.org/x/sys v0.0.0-20190813064441-fde4db37ae7a/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/crypto v0.0.0-20220411220226-7b82a4e95df4 h1:kUhD7nTDoI3fVd9G4ORWrbV5NY0liEs/Jg2pv5f+bBA=
golang.org/x/crypto v0.0.0-20220411220226-7b82a4e95df4/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2 h1:CIJ76btIcR3eFI5EgSo6k1qKw9KJexJuRLI9G7Hp5wE=
golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2/go.mod h1:9nx3DQGgdP8bBQD5qxJ1jj9UTztislL4KSBs9R2vV5Y=
golang.org/x/sys v0.0.0-20201119102817-f84b799fce68/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20210423082822-04245dca01da/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1 h1:SrN+KX8Art/Sf4HNj6Zcz06G7VEz+7w9tdXTPOZ7+l4=
golang.org/x/sys v0.0.0-20210615035016-665e8c7367d1/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20210630005230-0f9fa26af87c/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20210927094055-39ccf1dd6fa6/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/sys v0.0.0-20211103235746-7861aae1554b h1:1VkfZQv42XQlA/jchYumAnv1UPo6RgF9rJFkTgZIxO4=
golang.org/x/sys v0.0.0-20211103235746-7861aae1554b/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
golang.org/x/text v0.3.3 h1:cokOdA+Jmi5PJGXLlLllQSgYigAEfHXJAERHVMaCc2k=
golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
golang.org/x/text v0.3.6 h1:aRYxNxv6iGQlyVaZmk6ZgYEDa+Jg18DxebPSrd6bg1M=
golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM=
gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI=
gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b h1:h8qDotaEPuJATrMmW04NCwg7v22aHH28wwpauUhK9Oo=
gopkg.in/yaml.v3 v3.0.0-20210107192922-496545a6307b/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM=
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