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Replace HLA algorithm code with the new module #31

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127 changes: 88 additions & 39 deletions alldata/hla_class/hla.php
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Original file line number Diff line number Diff line change
@@ -1,6 +1,14 @@
<?php
ini_set("error_reporting","E_ALL & ~E_NOTICE");
session_start();
session_start();

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "----\n");
fwrite($myfile, date("h:i:sa Y-m-d") . " Opening HLA debugging log.\n");
$session_string_dump = print_r($_SESSION, true);
fwrite($myfile, "session: " . $_SESSION . "\n");
fwrite($myfile, "session results: " . $_SESSION["results"] . "\n");
fclose($myfile);

//hmmm
if ($_SESSION["results"]) {
Expand All @@ -9,52 +17,93 @@
unlink($_SESSION["tech_errors"]);
unlink($_SESSION["errors"]);
//posix_kill($_SESSION["pid"], 15); // SIGTERM, I hope.
}
}

if ($_SESSION["updates"]) {
unlink($_SESSION["updates"]);
}

$ruby = "ruby";
$script = dirname(__FILE__) . "/hla-easy.rb";
$_SESSION["results"] = dirname(__FILE__) . tempnam("/tmp", "");
$_SESSION["details"] = dirname(__FILE__) . tempnam("/tmp", "");
$_SESSION["tech_errors"] = dirname(__FILE__) . tempnam("/tmp", "");
$_SESSION["errors"] = dirname(__FILE__) . tempnam("/tmp", "");

$letter = $_POST["letter"];
if ($_SESSION["updates"]) {
unlink($_SESSION["updates"]);
}

$ruby = "/root/.rbenv/shims/ruby";
$script = dirname(__FILE__) . "/hla-easy.rb";
$_SESSION["results"] = dirname(__FILE__) . tempnam("/tmp", "");
$_SESSION["details"] = dirname(__FILE__) . tempnam("/tmp", "");
$_SESSION["tech_errors"] = dirname(__FILE__) . tempnam("/tmp", "");
$_SESSION["errors"] = dirname(__FILE__) . tempnam("/tmp", "");

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
$session_string_dump = print_r($_SESSION, true);
fwrite($myfile, "session (after setting some variables): " . $_SESSION . "\n");
fwrite($myfile, "session results: " . $_SESSION["results"] . "\n");
fwrite($myfile, "session details: " . $_SESSION["details"] . "\n");
fwrite($myfile, "session tech_errors: " . $_SESSION["tech_errors"] . "\n");
fwrite($myfile, "session errors: " . $_SESSION["errors"] . "\n");
fclose($myfile);

$letter = $_POST["letter"];
$threshold = $_POST["threshold"];
$fasta_text = $_POST["fasta_text"];

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "Parameters:\n");
fwrite($myfile, "letter: " . $letter . "\n");
fwrite($myfile, "threshold: " . $threshold . "\n");
fwrite($myfile, "fasta_text: " . $fasta_text . "\n");
fclose($myfile);


$descriptors = array (
0 => array("pipe", "r"),
1 => array("file", $_SESSION["results"], "a"),
2 => array("file", $_SESSION["tech_errors"], "a"),
7 => array("file", $_SESSION["errors"], "a"),
8 => array("file", $_SESSION["details"], "a")
);


$descriptors = array (
0 => array("pipe", "r"),
1 => array("file", $_SESSION["results"], "a"),
2 => array("file", $_SESSION["tech_errors"], "a"),
7 => array("file", $_SESSION["errors"], "a"),
8 => array("file", $_SESSION["details"], "a")
);



if ($threshold >= 0) {
$cmd = sprintf("echo \"%s\" | %s %s -t %s %s &", $fasta_text, $ruby,
$script, $threshold, $letter);
} else {
$cmd = sprintf("echo \"%s\" | %s %s --threshold=\"-1\" %s &", $fasta_text, $ruby,
$script, $letter);
}
if ($threshold >= 0) {
$cmd = sprintf("echo \"%s\" | %s %s -t %s %s &", $fasta_text, $ruby,
$script, $threshold, $letter);
} else {
$cmd = sprintf("echo \"%s\" | %s %s --threshold=\"-1\" %s &", $fasta_text, $ruby,
$script, $letter);
}

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "Invoking Ruby.\n");
fwrite($myfile, "Ruby executable: " . $ruby . "\n");
fwrite($myfile, "script: " . $script . "\n");
fwrite($myfile, "command: " . $cmd . "\n");
fclose($myfile);

$process = proc_open($cmd, $descriptors, $pipes);
$process = proc_open($cmd, $descriptors, $pipes);

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "process: " . $process . "\n");
fclose($myfile);

$pstatus = proc_get_status($process);

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "pstatus: " . $pstatus . "\n");
fclose($myfile);

$_SESSION["pid"] = $pstatus["pid"];
fclose($pipes[0]);
proc_close($process);
$_SESSION["pid"] = $pstatus["pid"];

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "pid (?): " . $pstatus["pid"] . "\n");
fclose($myfile);

fclose($pipes[0]);
proc_close($process);

$myfile = fopen("/alldata/bblab_site/logs/hla_debugging.log", "a");
fwrite($myfile, "Done with Ruby.\n");
fclose($myfile);

$resfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["results"]));
$detfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["details"]));
$techerrfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["tech_errors"]));
$errfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["errors"]));
printf("%s\n%s\n%s\n%s", $resfile, $detfile, $techerrfile, $errfile);
$resfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["results"]));
$detfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["details"]));
$techerrfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["tech_errors"]));
$errfile = "/django/tools/hla_class/tmp/" . array_pop(explode("/", $_SESSION["errors"]));
printf("%s\n%s\n%s\n%s", $resfile, $detfile, $techerrfile, $errfile);
?>
1 change: 1 addition & 0 deletions bblab.dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,7 @@ RUN wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc |
ENV R_BASE_VERSION 4.5.1

RUN apt-get install -q -y --no-install-recommends \
r-recommended=${R_BASE_VERSION}-* \
r-base=${R_BASE_VERSION}-* \
r-base-dev=${R_BASE_VERSION}-* \
r-base-core=${R_BASE_VERSION}-* \
Expand Down
8 changes: 8 additions & 0 deletions compose-template.env
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Original file line number Diff line number Diff line change
Expand Up @@ -50,3 +50,11 @@ BBLAB_TOOL_ROOT=/alldata/bblab_site/tools/
BBLAB_TEMPLATE_ROOT=/alldata/bblab_site/templates/

PYTHONPATH=/alldata/bblab_site/tools

# Mounts for generated data (these have sensible defaults in the compose file already):
# BBLAB_LOGS=/srv/bblab_site/logs
# BBLAB_MEDIA=/srv/bblab_site/media
# BBLAB_GUAVA_LAYOUT_OUTPUT=/srv/bblab_site/guava_layout/output
# BBLAB_SEQUENCING_LAYOUT_OUTPUT=/srv/bblab_site/sequencing_layout/output
# BBLAB_MYSQL=/srv/bblab_site/mysql
# BBLAB_DB_DUMP=/srv/bblab_site/db_dump
19 changes: 10 additions & 9 deletions docker-compose-bblab.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ services:
dockerfile: bblab.dockerfile
target: bblab-site
image: cfe-lab/bblab-site:${BBLAB_IMAGE_TAG:?no image tag set}
env_file: .env-bblab
# env_file: .env-bblab
environment:
- SMTP_MAIL_SERVER=${SMTP_MAIL_SERVER:?no smtp server set}
- SMTP_MAIL_PORT=${SMTP_MAIL_PORT:?no smtp port set}
Expand All @@ -41,6 +41,7 @@ services:
- BBLAB_OP_PATH=${BBLAB_OP_PATH:?no op path set}
- BBLAB_TOOL_ROOT=${BBLAB_TOOL_ROOT:?no tool root dir set}
- BBLAB_TEMPLATE_ROOT=${BBLAB_TEMPLATE_ROOT:?no template root dir set}
- PYTHONPATH=${BBLAB_PYTHONPATH:-/alldata/bblab_site/tools}
depends_on:
- db
networks:
Expand All @@ -51,8 +52,8 @@ services:
# in this container. Apache will set the URL from
# BBLAB_WEB_ADDRESS (use "localhost" or your DNS)
# and Django will accept requests to that address
# ports:
# - "80:80/tcp"
ports:
- "8000:80/tcp"
command: /bin/sh -c "/usr/sbin/apachectl -D FOREGROUND"
labels:
- "traefik.enable=true"
Expand All @@ -63,10 +64,10 @@ services:
- "traefik.http.routers.bblab-site.service=bblab-site"
- "traefik.http.services.bblab-site.loadbalancer.server.port=80"
volumes:
- /srv/bblab_site/logs:/alldata/bblab_site/logs:rw
- /srv/bblab_site/media:/alldata/bblab_site/media
- /srv/bblab_site/tools/guava_layout/output:/alldata/bblab_site/tools/guava_layout/output
- /srv/bblab_site/tools/sequencing_layout/output:/alldata/bblab_site/tools/sequencing_layout/output
- ${BBLAB_LOGS:-/srv/bblab_site/logs}:/alldata/bblab_site/logs:rw
- ${BBLAB_MEDIA:-/srv/bblab_site/media}:/alldata/bblab_site/media
- ${BBLAB_GUAVA_LAYOUT_OUTPUT:-/srv/bblab_site/tools/guava_layout/output}:/alldata/bblab_site/tools/guava_layout/output
- ${BBLAB_SEQUENCING_LAYOUT_OUTPUT:-/srv/bblab_site/tools/sequencing_layout/output}:/alldata/bblab_site/tools/sequencing_layout/output

db:
image: mariadb:11.6
Expand All @@ -82,8 +83,8 @@ services:
- MYSQL_PASSWORD=${BBLAB_DB_PASSWORD:?no password set}
- MYSQL_INITDB_SKIP_TZINFO=1
volumes:
- /srv/bblab_site/mysql:/var/lib/mysql
- /srv/bblab_site/db_dump:/docker-entrypoint-initdb.d
- ${BBLAB_MYSQL:-/srv/bblab_site/mysql}:/var/lib/mysql
- ${BBLAB_DB_DUMP:-/srv/bblab_site/db_dump}:/docker-entrypoint-initdb.d

# traefik:
# image: "traefik:${TRAEFIK_IMAGE_TAG:-latest}"
Expand Down