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View Code? Open in Web Editor NEWA Framework for Large Scale Phylogenetic Analysis
License: GNU General Public License v3.0
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Stargazers
Watchers
phylodb's Issues
Algorithms
Implementation of algorithms
API - Analyses
API implementation of the analyses
Authorization
Implementation of Authorization
Graph Model
Definition of the data model
Documentation
Code documentation;
API documentation.
API - Projects
API implementation of projects
API - Profiles
API implementation of the profiles
Authentication
Implementation of authentication
API - Visualizations
API implementation of the visualizations
API - Schemas
API implementation of the schemas
API Definition
Definition of the API
Unit tests
Site access
Hi, the site "http://192.92.147.36:8080/" specified in the README.md is not accessible (timeout).
API - Datasets
API implementation of the datasets
API - Isolates
API implementation of the isolates
API - Alleles
API implementation of alleles
Difficulty fully reproducing example.sh
Working to reproduce example.sh. I've gotten part way but seem to be running into some kind of server error. I've made some minor modifications along the way to allow example.sh to be run without hardcoding and to provide specific troubleshooting instructions where I've been able to figure them out. I've opened the work I've done on example.sh so far as PR #32.
Here is my log when trying to run example.sh, with private information redacted.
----------------------------------------------------------------------------------------------
Check server status:
----------------------------------------------------------------------------------------------
ok
ok TOKEN is defined.
ok USER_ID defined as XXXXXXXXXXXXXXXX
----------------------------------------------------------------------------------------------
List all users:
----------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, GET is already inferred.
* processing: http://localhost:8080/users?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> GET /users?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:46:52 GMT
< Connection: close
<
{ [36 bytes data]
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all taxa
----------------------------------------------------------------------------------------------
Taxa: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Create taxon:
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 68
>
} [68 bytes data]
100 68 0 0 100 68 0 56 0:00:01 0:00:01 --:--:-- 56
100 68 0 0 100 68 0 30 0:00:02 0:00:02 --:--:-- 30< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:46:57 GMT
< Connection: close
<
{ [36 bytes data]
100 98 0 30 100 68 12 28 0:00:02 0:00:02 --:--:-- 41
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all loci:
----------------------------------------------------------------------------------------------
Loci: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Delete locus (mark deprecated):
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis/loci/ftsZ?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> DELETE /taxa/bbacilliformis/loci/ftsZ?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
>
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:02 GMT
< Connection: close
<
{ [36 bytes data]
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Create locus:
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus1?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus1?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 55
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:04 GMT
< Connection: close
<
{ [36 bytes data]
100 96 0 30 100 66 12 27 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus2?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus2?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 54
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:07 GMT
< Connection: close
<
{ [36 bytes data]
100 96 0 30 100 66 12 27 0:00:02 0:00:02 --:--:-- 40
100 96 0 30 100 66 12 27 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus3?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus3?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 54
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:09 GMT
< Connection: close
<
{ [36 bytes data]
100 96 0 30 100 66 12 27 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus4?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus4?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 54
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:11 GMT
< Connection: close
<
{ [36 bytes data]
100 96 0 30 100 66 12 28 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus5?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus5?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 54
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:14 GMT
< Connection: close
<
{ [36 bytes data]
100 96 0 30 100 66 12 28 0:00:02 0:00:02 --:--:-- 40
100 96 0 30 100 66 12 28 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus6?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus6?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 54
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:16 GMT
< Connection: close
<
{ [41 bytes data]
100 96 0 30 100 66 12 27 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus7?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/loci/locus7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 66
>
} [66 bytes data]
100 66 0 0 100 66 0 54 0:00:01 0:00:01 --:--:-- 55
100 66 0 0 100 66 0 29 0:00:02 0:00:02 --:--:-- 29< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:18 GMT
< Connection: close
<
{ [36 bytes data]
100 96 0 30 100 66 12 28 0:00:02 0:00:02 --:--:-- 40
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Load alleles:
----------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus1/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus1/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 234
> Content-Type: multipart/form-data; boundary=------------------------c738321f324ad367
>
} [234 bytes data]
* We are completely uploaded and fine
100 234 0 0 100 234 0 1166 --:--:-- --:--:-- --:--:-- 1164
100 234 0 0 100 234 0 194 0:00:01 0:00:01 --:--:-- 194
100 234 0 0 100 234 0 106 0:00:02 0:00:02 --:--:-- 106< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:21 GMT
< Connection: close
<
{ [36 bytes data]
100 264 0 30 100 234 12 99 0:00:02 0:00:02 --:--:-- 111
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus2/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus2/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 276
> Content-Type: multipart/form-data; boundary=------------------------70b2c8ef1cf50a56
>
} [276 bytes data]
* We are completely uploaded and fine
100 276 0 0 100 276 0 229 0:00:01 0:00:01 --:--:-- 229
100 276 0 0 100 276 0 125 0:00:02 0:00:02 --:--:-- 125< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:23 GMT
< Connection: close
<
{ [36 bytes data]
100 306 0 30 100 276 12 117 0:00:02 0:00:02 --:--:-- 129
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus3/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus3/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 318
> Content-Type: multipart/form-data; boundary=------------------------c86ed064a617e4e0
>
} [318 bytes data]
* We are completely uploaded and fine
100 318 0 0 100 318 0 264 0:00:01 0:00:01 --:--:-- 264
100 318 0 0 100 318 0 144 0:00:02 0:00:02 --:--:-- 144< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:26 GMT
< Connection: close
<
{ [36 bytes data]
100 348 0 30 100 318 12 134 0:00:02 0:00:02 --:--:-- 147
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus4/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus4/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 404
> Content-Type: multipart/form-data; boundary=------------------------bf0637ad20dc1fcc
>
} [404 bytes data]
* We are completely uploaded and fine
100 404 0 0 100 404 0 2013 --:--:-- --:--:-- --:--:-- 2009
100 404 0 0 100 404 0 336 0:00:01 0:00:01 --:--:-- 336
100 404 0 0 100 404 0 183 0:00:02 0:00:02 --:--:-- 183< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:28 GMT
< Connection: close
<
{ [36 bytes data]
100 434 0 30 100 404 12 170 0:00:02 0:00:02 --:--:-- 183
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus5/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus5/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 447
> Content-Type: multipart/form-data; boundary=------------------------7a9201d078966e11
>
} [447 bytes data]
* We are completely uploaded and fine
100 447 0 0 100 447 0 372 0:00:01 0:00:01 --:--:-- 372
100 447 0 0 100 447 0 202 0:00:02 0:00:02 --:--:-- 202< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:30 GMT
< Connection: close
<
{ [36 bytes data]
100 477 0 30 100 447 12 189 0:00:02 0:00:02 --:--:-- 202
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus6/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus6/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 362
> Content-Type: multipart/form-data; boundary=------------------------8b536850a85edf27
>
} [362 bytes data]
* We are completely uploaded and fine
100 362 0 0 100 362 0 301 0:00:01 0:00:01 --:--:-- 301
100 362 0 0 100 362 0 164 0:00:02 0:00:02 --:--:-- 164< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:33 GMT
< Connection: close
<
{ [41 bytes data]
100 392 0 30 100 362 12 153 0:00:02 0:00:02 --:--:-- 166
100 392 0 30 100 362 12 153 0:00:02 0:00:02 --:--:-- 166
* Closing connection
{"message":"/problems/server"}Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/taxa/bbacilliformis/loci/locus7/alleles/files?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /taxa/bbacilliformis/loci/locus7/alleles/files?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 491
> Content-Type: multipart/form-data; boundary=------------------------b3ffd1349a1ccd95
>
} [491 bytes data]
* We are completely uploaded and fine
100 491 0 0 100 491 0 408 0:00:01 0:00:01 --:--:-- 408
100 491 0 0 100 491 0 222 0:00:02 0:00:02 --:--:-- 222< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:47:35 GMT
< Connection: close
<
{ [36 bytes data]
100 521 0 30 100 491 12 208 0:00:02 0:00:02 --:--:-- 221
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List alleles:
----------------------------------------------------------------------------------------------
Alleles[locus1]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Alleles[locus2]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Alleles[locus3]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Alleles[locus4]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Alleles[locus5]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Alleles[locus6]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Alleles[locus7]: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
An allele: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all schemas:
----------------------------------------------------------------------------------------------
Schemas: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
Schema: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Create schema:
----------------------------------------------------------------------------------------------
* processing: http://localhost:8080/taxa/bbacilliformis/schemas/mlst7?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> PUT /taxa/bbacilliformis/schemas/mlst7?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 199
>
} [199 bytes data]
100 199 0 0 100 199 0 165 0:00:01 0:00:01 --:--:-- 165
100 199 0 0 100 199 0 90 0:00:02 0:00:02 --:--:-- 90< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:48:01 GMT
< Connection: close
<
{ [36 bytes data]
100 229 0 30 100 199 12 84 0:00:02 0:00:02 --:--:-- 96
* Closing connection
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
List all projects:
----------------------------------------------------------------------------------------------
Projects: % Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0
0 0 0 0 0 0 0 0 --:--:-- 0:00:02 --:--:-- 0
100 30 0 30 0 0 12 0 --:--:-- 0:00:02 --:--:-- 12
{"message":"/problems/server"}
----------------------------------------------------------------------------------------------
Create project:
----------------------------------------------------------------------------------------------
Note: Unnecessary use of -X or --request, POST is already inferred.
* processing: http://localhost:8080/projects?provider=google
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0* Trying [::1]:8080...
* Connected to localhost (::1) port 8080
> POST /projects?provider=google HTTP/1.1
> Host: localhost:8080
> User-Agent: curl/8.2.1
> Accept: */*
> Content-Type: application/json
> Authorization: Bearer XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
> Content-Length: 152
>
} [152 bytes data]
100 152 0 0 100 152 0 757 --:--:-- --:--:-- --:--:-- 756
100 152 0 0 100 152 0 126 0:00:01 0:00:01 --:--:-- 126
100 152 0 0 100 152 0 69 0:00:02 0:00:02 --:--:-- 68< HTTP/1.1 500
< Content-Type: application/problem+json
< Transfer-Encoding: chunked
< Date: Sun, 31 Dec 2023 05:48:06 GMT
< Connection: close
<
{ [36 bytes data]
100 182 0 30 100 152 12 64 0:00:02 0:00:02 --:--:-- 77
* Closing connection
{"message":"/problems/server"}Error: PROJECT is not defined. Please follow these steps:
# TODO
#
# Then, execute
#
# > export PROJECT="YOUR_PROJECT_ID"
#
# and run this script again.
API - Taxons
API implementation of the taxons
API - Jobs
API implementation of jobs
Benchmark tests
API - Users
API implementation of users
API - Loci
API implementation of the loci
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