{"action":"created","comment":{"url":"https://api.github.com/repos/cylc/cylc/pulls/comments/99995768","pull_request_review_id":20686964,"id":99995768,"diff_hunk":"@@ -0,0 +1,188 @@\n+#!/bin/bash\n+\n+# THIS FILE IS PART OF THE CYLC SUITE ENGINE.\n+# Copyright (C) 2008-2017 NIWA\n+#\n+# This program is free software: you can redistribute it and/or modify\n+# it under the terms of the GNU General Public License as published by\n+# the Free Software Foundation, either version 3 of the License, or\n+# (at your option) any later version.\n+#\n+# This program is distributed in the hope that it will be useful,\n+# but WITHOUT ANY WARRANTY; without even the implied warranty of\n+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\n+# GNU General Public License for more details.\n+#\n+# You should have received a copy of the GNU General Public License\n+# along with this program.  If not, see <http://www.gnu.org/licenses/>.\n+\n+###############################################################################\n+# Shell functions for a cylc task job.\n+###############################################################################\n+\n+###############################################################################\n+# The main function for a cylc task job.\n+cylc::job::main() {\n+    # Turn on xtrace in debug mode\n+    if \"${CYLC_DEBUG:-false}\"; then\n+        PS4='+[\\D{%Y%m%dT%H%M%S%z}]\\u@\\h '\n+        set -x\n+    fi\n+    # Prelude\n+    local NAME=\n+    for NAME in \\\n+        \"${HOME}/.cylc/job-init-env.sh\" \\\n+        \"${CYLC_DIR}/conf/job-init-env.sh\" \\\n+        \"${CYLC_DIR}/conf/job-init-env-default.sh\"\n+    do\n+        if [[ -f \"${NAME}\" ]]; then\n+            . \"${NAME}\" 1>'/dev/null' 2>&1\n+            break\n+        fi\n+    done\n+    # Init-Script\n+    cylc::job::run_inst_func 'global-init-script'\n+    cylc::job::run_inst_func 'init-script'\n+    # Start error and vacation traps\n+    local S=\n+    for S in ${CYLC_FAIL_SIGNALS}; do\n+        trap \"cylc::job::trap_err ${S}\" \"${S}\"\n+    done\n+    for S in ${CYLC_VACATION_SIGNALS:-}; do\n+        trap \"cylc::job::trap_vacation ${S}\" \"${S}\"\n+    done\n+    set -u\n+    set -o pipefail\n+    # Export CYLC_ suite and task environment variables\n+    cylc::job::inst::cylc-env\n+    # Write task job self-identify\n+    USER=\"${USER:-$(whoami)}\"\n+    if [[ \"$(uname)\" == 'AIX' ]]; then\n+        # On AIX the hostname command has no '-f' option\n+        local HOSTNAME=\"$(hostname).$(namerslv -sn 2>'/dev/null' | awk '{print $2}')\"\n+    else\n+        local HOSTNAME=\"$(hostname -f)\"\n+    fi\n+    cat <<__OUT__\n+Suite    : ${CYLC_SUITE_NAME}\n+Task Job : ${CYLC_TASK_JOB} (try ${CYLC_TASK_TRY_NUMBER})\n+User@Host: ${USER}@${HOSTNAME}\n+\n+__OUT__\n+    # Derived environment variables\n+    export CYLC_SUITE_LOG_DIR=\"${CYLC_SUITE_RUN_DIR}/log/suite\"\n+    CYLC_SUITE_WORK_DIR_ROOT=\"${CYLC_SUITE_WORK_DIR_ROOT:-${CYLC_SUITE_RUN_DIR}}\"\n+    export CYLC_SUITE_SHARE_DIR=\"${CYLC_SUITE_WORK_DIR_ROOT}/share\"\n+    export CYLC_SUITE_WORK_DIR=\"${CYLC_SUITE_WORK_DIR_ROOT}/work\"\n+    export CYLC_TASK_CYCLE_POINT=\"$(cut -d '/' -f 1 <<<\"${CYLC_TASK_JOB}\")\"\n+    export CYLC_TASK_NAME=\"$(cut -d '/' -f 2 <<<\"${CYLC_TASK_JOB}\")\"\n+    # The \"10#\" part ensures that the submit number is interpretted in base 10.\n+    # Otherwise, a zero padded number will be interpretted as an octal.\n+    export CYLC_TASK_SUBMIT_NUMBER=$((10#$(cut -d '/' -f 3 <<<\"${CYLC_TASK_JOB}\")))\n+    export CYLC_TASK_ID=\"${CYLC_TASK_NAME}.${CYLC_TASK_CYCLE_POINT}\"\n+    export CYLC_TASK_LOG_ROOT=\"${CYLC_SUITE_RUN_DIR}/log/job/${CYLC_TASK_JOB}/job\"\n+    if [[ -n \"${CYLC_TASK_WORK_DIR_BASE:-}\" ]]; then\n+        # Note: value of CYLC_TASK_WORK_DIR_BASE may contain variable\n+        # substitution syntax including some of the derived variables above, so\n+        # it can only be derived at point of use.\n+        CYLC_TASK_WORK_DIR_BASE=\"$(eval echo \"${CYLC_TASK_WORK_DIR_BASE}\")\"\n+    else\n+        CYLC_TASK_WORK_DIR_BASE=\"${CYLC_TASK_CYCLE_POINT}/${CYLC_TASK_NAME}\"\n+    fi\n+    export CYLC_TASK_WORK_DIR=\"${CYLC_SUITE_WORK_DIR}/${CYLC_TASK_WORK_DIR_BASE}\"\n+    # DEPRECATED environment variables\n+    export CYLC_SUITE_SHARE_PATH=\"${CYLC_SUITE_SHARE_DIR}\"\n+    export CYLC_SUITE_INITIAL_CYCLE_TIME=\"${CYLC_SUITE_INITIAL_CYCLE_POINT}\"\n+    export CYLC_SUITE_FINAL_CYCLE_TIME=\"${CYLC_SUITE_FINAL_CYCLE_POINT}\"\n+    export CYLC_TASK_CYCLE_TIME=\"${CYLC_TASK_CYCLE_POINT}\"\n+    export CYLC_TASK_WORK_PATH=\"${CYLC_TASK_WORK_DIR}\"\n+    # Env-Script\n+    cylc::job::run_inst_func 'env-script'\n+    # Send task started message\n+    cylc task message 'started' &\n+    CYLC_TASK_MESSAGE_STARTED_PID=$!\n+    # Access to the suite bin directory\n+    if [[ -n \"${CYLC_SUITE_DEF_PATH:-}\" && -d \"${CYLC_SUITE_DEF_PATH}/bin\" ]]\n+    then\n+        export PATH=\"${CYLC_SUITE_DEF_PATH}/bin:${PATH}\"\n+    fi\n+    # Create share and work directories\n+    mkdir -p \"${CYLC_SUITE_SHARE_DIR}\" || true\n+    mkdir -p \"$(dirname \"${CYLC_TASK_WORK_DIR}\")\" || true\n+    mkdir -p \"${CYLC_TASK_WORK_DIR}\"\n+    cd \"${CYLC_TASK_WORK_DIR}\"\n+    # User Environment, Pre-Script, Script and Post-Script\n+    for NAME in 'user-env' 'pre-script' 'script' 'post-script'; do\n+        cylc::job::run_inst_func \"${NAME}\"\n+    done\n+    # Empty work directory remove\n+    cd\n+    rmdir \"${CYLC_TASK_WORK_DIR}\" 2>'/dev/null' || true\n+    # Send task succeeded message\n+    wait \"${CYLC_TASK_MESSAGE_STARTED_PID}\" 2>'/dev/null' || true\n+    cylc task message 'succeeded' || true\n+    trap '' EXIT\n+    exit 0\n+}\n+\n+###############################################################################\n+# Run a function in the task job instant file, if possible.\n+# Arguments:\n+#   NAME - name of function without the \"cylc::job::inst::\" prefix\n+# Returns:\n+#   return 0, or the return code of the function if called\n+cylc::job::run_inst_func() {\n+    local NAME=\"$1\"\n+    if declare -F \"cylc::job::inst::${NAME}\" 1>'/dev/null' 2>&1; then\n+        \"cylc::job::inst::${NAME}\"\n+    fi\n+}","path":"lib/cylc/job.sh","position":139,"original_position":139,"commit_id":"5f60d7b6f6732f119b0237163737c140ef366719","original_commit_id":"5f60d7b6f6732f119b0237163737c140ef366719","user":{"login":"hjoliver","id":2362137,"avatar_url":"https://avatars.githubusercontent.com/u/2362137?v=3","gravatar_id":"","url":"https://api.github.com/users/hjoliver","html_url":"https://github.com/hjoliver","followers_url":"https://api.github.com/users/hjoliver/followers","following_url":"https://api.github.com/users/hjoliver/following{/other_user}","gists_url":"https://api.github.com/users/hjoliver/gists{/gist_id}","starred_url":"https://api.github.com/users/hjoliver/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hjoliver/subscriptions","organizations_url":"https://api.github.com/users/hjoliver/orgs","repos_url":"https://api.github.com/users/hjoliver/repos","events_url":"https://api.github.com/users/hjoliver/events{/privacy}","received_events_url":"https://api.github.com/users/hjoliver/received_events","type":"User","site_admin":false},"body":"Insert blank line, for consistency?","created_at":"2017-02-08T05:48:50Z","updated_at":"2017-02-08T05:50:36Z","html_url":"https://github.com/cylc/cylc/pull/2141#discussion_r99995768","pull_request_url":"https://api.github.com/repos/cylc/cylc/pulls/2141","_links":{"self":{"href":"https://api.github.com/repos/cylc/cylc/pulls/comments/99995768"},"html":{"href":"https://github.com/cylc/cylc/pull/2141#discussion_r99995768"},"pull_request":{"href":"https://api.github.com/repos/cylc/cylc/pulls/2141"}}},"pull_request":{"url":"https://api.github.com/repos/cylc/cylc/pulls/2141","id":104372244,"html_url":"https://github.com/cylc/cylc/pull/2141","diff_url":"https://github.com/cylc/cylc/pull/2141.diff","patch_url":"https://github.com/cylc/cylc/pull/2141.patch","issue_url":"https://api.github.com/repos/cylc/cylc/issues/2141","number":2141,"state":"open","locked":false,"title":"job file: improve style","user":{"login":"matthewrmshin","id":908613,"avatar_url":"https://avatars.githubusercontent.com/u/908613?v=3","gravatar_id":"","url":"https://api.github.com/users/matthewrmshin","html_url":"https://github.com/matthewrmshin","followers_url":"https://api.github.com/users/matthewrmshin/followers","following_url":"https://api.github.com/users/matthewrmshin/following{/other_user}","gists_url":"https://api.github.com/users/matthewrmshin/gists{/gist_id}","starred_url":"https://api.github.com/users/matthewrmshin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthewrmshin/subscriptions","organizations_url":"https://api.github.com/users/matthewrmshin/orgs","repos_url":"https://api.github.com/users/matthewrmshin/repos","events_url":"https://api.github.com/users/matthewrmshin/events{/privacy}","received_events_url":"https://api.github.com/users/matthewrmshin/received_events","type":"User","site_admin":false},"body":"Separate the job script into static part and generated part.\r\n* Static part now lives in `lib/cylc/job.sh`, which will be loaded by the job file in run time.\r\n* Generated part will continue to be generated by `cylc.job_file`. It is now quite small and contains:\r\n  * The header, unchanged.\r\n  * Essential environment variables to provide an initial environment, at the top.\r\n  * Logic fragments in shell functions for cylc environment, user environment, user script, etc.\r\n  * A line to load the static job script library, and a line to call its main function.\r\n  * The footer, unchanged.\r\n\r\nReduce number of environment variables in job file.\r\n* Mark old variables as duplicates.\r\n* Move communication related variables to contact file.\r\n* Remove variables that should not be needed by anything.\r\n\r\nImprove diagnostics.\r\n* Job script and `cylc message` no longer repeat one another.\r\n* Report only relevant items for jobs. E.g. don't report suite host, port, etc.\r\n\r\nQuote and brace shell and environment variable values.\r\n* Safer - in case there are spaces and other special characters in file system paths.\r\n* Logic easier to read.\r\n\r\nRemove space from keys in \"job_conf\".\r\n\r\n(Rationale behind this change is that I want to review the logic for job script generation before I move on to look at #2043.)","created_at":"2017-02-02T16:26:06Z","updated_at":"2017-02-08T05:50:36Z","closed_at":null,"merged_at":null,"merge_commit_sha":"291c6902b592eb34a98d16010d7e476b98c60887","assignee":{"login":"matthewrmshin","id":908613,"avatar_url":"https://avatars.githubusercontent.com/u/908613?v=3","gravatar_id":"","url":"https://api.github.com/users/matthewrmshin","html_url":"https://github.com/matthewrmshin","followers_url":"https://api.github.com/users/matthewrmshin/followers","following_url":"https://api.github.com/users/matthewrmshin/following{/other_user}","gists_url":"https://api.github.com/users/matthewrmshin/gists{/gist_id}","starred_url":"https://api.github.com/users/matthewrmshin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthewrmshin/subscriptions","organizations_url":"https://api.github.com/users/matthewrmshin/orgs","repos_url":"https://api.github.com/users/matthewrmshin/repos","events_url":"https://api.github.com/users/matthewrmshin/events{/privacy}","received_events_url":"https://api.github.com/users/matthewrmshin/received_events","type":"User","site_admin":false},"assignees":[{"login":"matthewrmshin","id":908613,"avatar_url":"https://avatars.githubusercontent.com/u/908613?v=3","gravatar_id":"","url":"https://api.github.com/users/matthewrmshin","html_url":"https://github.com/matthewrmshin","followers_url":"https://api.github.com/users/matthewrmshin/followers","following_url":"https://api.github.com/users/matthewrmshin/following{/other_user}","gists_url":"https://api.github.com/users/matthewrmshin/gists{/gist_id}","starred_url":"https://api.github.com/users/matthewrmshin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/matthewrmshin/subscriptions","organizations_url":"https://api.github.com/users/matthewrmshin/orgs","repos_url":"https://api.github.com/users/matthewrmshin/repos","events_url":"https://api.github.com/users/matthewrmshin/events{/privacy}","received_events_url":"https://api.github.com/users/matthewrmshin/received_events","type":"User","site_admin":false},{"login":"hjoliver","id":2362137,"avatar_url":"https://avatars.githubusercontent.com/u/2362137?v=3","gravatar_id":"","url":"https://api.github.com/users/hjoliver","html_url":"https://github.com/hjoliver","followers_url":"https://api.github.com/users/hjoliver/followers","following_url":"https://api.github.com/users/hjoliver/following{/other_user}","gists_url":"https://api.github.com/users/hjoliver/gists{/gist_id}","starred_url":"https://api.github.com/users/hjoliver/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hjoliver/subscriptions","organizations_url":"https://api.github.com/users/hjoliver/orgs","repos_url":"https://api.github.com/users/hjoliver/repos","events_url":"https://api.github.com/users/hjoliver/events{/privacy}","received_events_url":"https://api.github.com/users/hjoliver/received_events","type":"User","site_admin":false},{"login":"oliver-sanders","id":16705946,"avatar_url":"https://avatars.githubusercontent.com/u/16705946?v=3","gravatar_id":"","url":"https://api.github.com/users/oliver-sanders","html_url":"https://github.com/oliver-sanders","followers_url":"https://api.github.com/users/oliver-sanders/followers","following_url":"https://api.github.com/users/oliver-sanders/following{/other_user}","gists_url":"https://api.github.com/users/oliver-sanders/gists{/gist_id}","starred_url":"https://api.github.com/users/oliver-sanders/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oliver-sanders/subscriptions","organizations_url":"https://api.github.com/users/oliver-sanders/orgs","repos_url":"https://api.github.com/users/oliver-sanders/repos","events_url":"https://api.github.com/users/oliver-sanders/events{/privacy}","received_events_url":"https://api.github.com/users/oliver-sanders/received_events","type":"User","site_admin":false}],"milestone":{"url":"https://api.github.com/repos/cylc/cylc/milestones/5","html_url":"https://github.com/cylc/cylc/milestone/5","labels_url":"https://api.github.com/repos/cylc/cylc/milestones/5/labels","id":262614,"number":5,"title":"soon","description":"A few months in the future. Top priority issues and easy fixes should initially be marked against this milestone, and then moved to *next-release* if work progresses quickly 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