Merge branch 'okta-oidc-auth' of github.com:selten/galaxy into okta-oidc-auth

.ci/jenkins/api-py3

@@ -0,0 +1 @@
+api

.ci/jenkins/api-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails -api "$@"

.ci/jenkins/framework-py3

@@ -0,0 +1 @@
+framework

.ci/jenkins/framework-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --framework "$@"

.ci/jenkins/integration-py3

@@ -0,0 +1 @@
+integration

.ci/jenkins/integration-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-DOCKER_RUN_EXTRA_ARGS="--privileged" ./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --integration "$@"

.ci/jenkins/main-tools-py3

@@ -0,0 +1 @@
+main-tools

.ci/jenkins/main-tools-py3/run_tests.sh

@@ -1,3 +0,0 @@
-#!/bin/bash
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc -main "$@"

.ci/jenkins/selenium-compose/run_galaxy.bash

@@ -20,8 +20,7 @@ virtualenv "$GALAXY_VIRTUAL_ENV"
 chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
 
 cd /galaxy
-HOME=/galaxy
-sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
+sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
 
 echo "Waiting for postgres to become available"
 while ! nc -z postgres 5432;
@@ -34,7 +33,7 @@ echo "Creating postgres database for Galaxy"
 createdb -w -U postgres -h postgres galaxy
 
 echo "Starting and waiting for Galaxy daemon(s)"
-sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
+sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
 
 echo "Galaxy daemon ready, monitoring Galaxy logs"
 tail -f "$GALAXY_ROOT/main.log"

.ci/jenkins/selenium-py3

@@ -0,0 +1 @@
+selenium

.ci/jenkins/selenium-py3/run_tests.sh

@@ -1,26 +0,0 @@
-#!/bin/bash
-
-# Enable retries on tests to reduce chances of transient failures.
-: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
-
-# If in Jenkins environment, use it for artifacts.
-if [ -n "$BUILD_NUMBER" ];
-then
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
-else
-    : ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
-    : ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
-fi
-
-mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
-mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
-
-mkdir -p ~/.jenkins-yarn-cache
-YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
-
-# Start Selenium server in the test Docker container.
-DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} --shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY}"
-export DOCKER_RUN_EXTRA_ARGS
-
-./run_tests.sh --dockerize --python3 --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"

.circleci/config.yml

@@ -81,23 +81,6 @@ jobs:
           key: v1-repo-{{ .Environment.CIRCLE_SHA1 }}
           paths:
             - ~/repo
-  py27_lint:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py27-lint
-  py27_unit:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      # Ensure minimum virtualenv version due to https://github.com/pypa/virtualenv/issues/1670
-      - run: sudo pip install tox 'virtualenv>=20.0.8'
-      - run: tox -e py27-unit
   py35_docstring:
     docker:
       - image: circleci/python:3.5
@@ -106,14 +89,6 @@ jobs:
       - *restore_repo_cache
       - *install_tox
       - run: tox -e py35-lint_docstring_include_list
-  py27_first_startup:
-    docker:
-      - image: circleci/python:2.7
-    <<: *set_workdir
-    steps:
-      - *restore_repo_cache
-      - *install_tox
-      - run: tox -e py27-first_startup
   py35_lint:
     docker:
       - image: circleci/python:3.5
@@ -136,10 +111,9 @@ jobs:
     <<: *set_workdir
     steps:
       - *restore_repo_cache
-      - run: sh scripts/common_startup.sh
-      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite
-      - run: mv db_gx_rev_0127.sqlite database/universe.sqlite
-      - run: sh manage_db.sh -c ./config/galaxy.yml.sample upgrade
+      # Use this job to test the latest migrations
+      - run: wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
+      - run: mv db_gx_rev_0141.sqlite database/universe.sqlite
       - *install_tox
       - run: tox -e py35-first_startup
   validate_test_tools:
@@ -195,12 +169,6 @@ workflows:
   get_code_and_test:
     jobs:
       - get_code
-      - py27_lint:
-          <<: *requires_get_code
-      - py27_unit:
-          <<: *requires_get_code
-      - py27_first_startup:
-          <<: *requires_get_code
       - py35_docstring:
           <<: *requires_get_code
       - py35_lint:

.github/workflows/integration.yaml

@@ -27,10 +27,15 @@ jobs:
     steps:
     - name: Prune unused docker image, volumes and containers
       run: docker system prune -a -f
+    - name: Clean dotnet folder for space
+      if: matrix.subset == 'kubernetes'
+      run: rm -Rf /usr/share/dotnet
     - name: Setup Minikube
       if: matrix.subset == 'kubernetes'
       id: minikube
-      uses: CodingNagger/minikube-setup-action@v1.0.2
+      uses: CodingNagger/minikube-setup-action@v1.0.3
+      with:
+        minikube-version: "1.9.0-0_amd64"
     - name: Launch Minikube
       if: matrix.subset == 'kubernetes'
       run: eval ${{ steps.minikube.outputs.launcher }}

.github/workflows/osx_startup.yaml

@@ -0,0 +1,28 @@
+name: OSX
+on: [push, pull_request]
+jobs:
+
+  test:
+    name: Startup test
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/Library/Caches/pip
+        # scripts/common_startup.sh creates a conda env for Galaxy containing Python 3.6
+        key: pip-cache-3.6-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Install tox
+      run: pip install tox
+    - name: Install and activate miniconda  # use this job to test using Python from a conda environment
+      uses: goanpeca/setup-miniconda@v1
+      with:
+        activate-environment: ''
+    - name: run tests
+      run: tox -e first_startup
+      shell: bash -l {0}  # need this to have CONDA_EXE set
+      working-directory: 'galaxy root'

.github/workflows/toolshed.yaml

@@ -0,0 +1,37 @@
+name: Toolshed
+on: [push, pull_request]
+env:
+  GALAXY_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/galaxy?client_encoding=utf8'
+  TOOL_SHED_TEST_DBURI: 'postgres://postgres:postgres@localhost:5432/toolshed?client_encoding=utf8'
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-18.04
+    strategy:
+      matrix:
+        python-version: [3.7]
+    services:
+      postgres:
+        image: postgres:11
+        env:
+          POSTGRES_USER: postgres
+          POSTGRES_PASSWORD: postgres
+          POSTGRES_DB: postgres
+        ports:
+          - 5432:5432
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        path: 'galaxy root'
+    - uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Cache pip dir
+      uses: actions/cache@v1
+      id: pip-cache
+      with:
+        path: ~/.cache/pip
+        key: pip-cache-${{ matrix.python-version }}-${{ hashFiles('galaxy root/requirements.txt') }}
+    - name: Run tests
+      run: './run_tests.sh -toolshed'
+      working-directory: 'galaxy root'

.travis.yml

@@ -1,29 +0,0 @@
-os: osx
-# No version of Python is available via virtualenv on OS X workers, see https://github.com/travis-ci/travis-ci/issues/2312
-language: generic
-
-env:
-  - TOX_ENV=py27-first_startup
-  - TOX_ENV=py37-first_startup
-
-install:
-  - set -e
-  - pip install tox
-  - |
-    if [ "$TOX_ENV" == "py27-first_startup" ]; then
-        # Use this job to test the latest migrations
-        wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0141.sqlite
-        mv db_gx_rev_0141.sqlite database/universe.sqlite
-    elif [ "$TOX_ENV" == "py37-first_startup" ]; then
-        # There is now a pre-installed python3 on osx Travis workers, but use this job to test using a conda environment
-        MINICONDA_URL="https://repo.anaconda.com/miniconda"
-        MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh"
-        curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}"
-        bash $MINICONDA_FILE -b
-        . ~/miniconda3/bin/activate
-    fi
-
-script: tox -e $TOX_ENV
-
-notifications:
-  email: false

CONTRIBUTORS.md

@@ -86,6 +86,7 @@ The following individuals have contributed code to Galaxy:
 * Joachim Jacob <joachim.jacob@gmail.com>
 * Xiaoqian Jiang <jxq198409@hotmail.com>
 * Jim Johnson <jj@umn.edu> <jj@msi.umn.edu>
+* Kaivan Kamali <kxk302@gmail.com>
 * Radhesh Kamath <radhesh@bx.psu.edu>
 * Iyad Kandalaft <ik@iyadk.com>
 * Jan Kanis <jan.code@jankanis.nl>

client/galaxy/scripts/bundleEntries.js

@@ -95,6 +95,7 @@ export { mountJobMetrics } from "components/JobMetrics";
 export { mountJobParameters } from "components/JobParameters";
 export { mountWorkflowEditor } from "components/Workflow/Editor/mount";
 export { mountPageDisplay } from "components/PageDisplay";
+export { mountDestinationParams } from "components/JobDestinationParams";
 
 // Used in common.mako
 export { default as store } from "storemodern";

client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.test.js

@@ -0,0 +1,67 @@
+import Vuex from "vuex";
+import axios from "axios";
+import MockAdapter from "axios-mock-adapter";
+import { mount, createLocalVue } from "@vue/test-utils";
+import { createStore } from "../../store";
+import flushPromises from "flush-promises";
+import JobDestinationParams from "./JobDestinationParams";
+import jobDestinationResponse from "./testData/jobDestinationResponse";
+
+const JOB_ID = "foo_job_id";
+
+describe("JobDestinationParams/JobDestinationParams.vue", () => {
+    const localVue = createLocalVue();
+    localVue.use(Vuex);
+
+    const responseKeys = Object.keys(jobDestinationResponse);
+
+    let testStore, axiosMock, wrapper;
+
+    beforeEach(async () => {
+        axiosMock = new MockAdapter(axios);
+        testStore = createStore();
+        const propsData = {
+            jobId: JOB_ID,
+        };
+        axiosMock.onGet(`/api/jobs/${JOB_ID}/destination_params`).reply(200, jobDestinationResponse);
+        wrapper = mount(JobDestinationParams, {
+            store: testStore,
+            propsData,
+            localVue,
+        });
+        await flushPromises();
+        assert(responseKeys.length > 0, "test data is invalid!");
+    });
+
+    afterEach(() => {
+        axiosMock.restore();
+    });
+
+    it("destination parameters should exist", async () => {
+        expect(Object.keys(wrapper.vm.jobDestinationParams).length).to.equals(responseKeys.length);
+        expect(wrapper.vm.jobId).to.equals(JOB_ID);
+        expect(wrapper.vm.jobDestinationParams["docker_net"]).to.equals("bridge");
+        expect(wrapper.vm.jobDestinationParams["docker_set_user"]).to.equals(null);
+    });
+
+    it("destination parameters should be rendered", async () => {
+        console.log(wrapper.html());
+        const paramsTable = wrapper.find("#destination_parameters");
+        expect(paramsTable.isVisible()).to.equals(true);
+        const params = paramsTable.findAll("tbody > tr");
+        expect(params.length).to.equals(responseKeys.length);
+
+        for (let counter = 0; counter < responseKeys.length - 1; counter++) {
+            const parameter = params.at(counter).findAll("td");
+            const parameterTitle = parameter.at(0).text();
+            const parameterValue = parameter.at(1).text();
+
+            assert(responseKeys.includes(parameterTitle), "rendered parameter should exist in test data!");
+            // since we render null as an empty string, rendered empty string should always equal null in test data
+            assert(
+                jobDestinationResponse[parameterTitle] === (parameterValue === "" ? null : parameterValue),
+                "parameter value is not equal to test data!"
+            );
+        }
+    });
+});

client/galaxy/scripts/components/JobDestinationParams/JobDestinationParams.vue

@@ -0,0 +1,36 @@
+<template>
+    <div>
+        <table id="destination_parameters" class="tabletip info_data_table">
+            <tbody>
+                <tr v-for="(value, title) in jobDestinationParams" :key="title">
+                    <td>{{ title }}</td>
+                    <td>{{ value }}</td>
+                </tr>
+            </tbody>
+        </table>
+    </div>
+</template>
+
+<script>
+import { mapCacheActions } from "vuex-cache";
+
+export default {
+    props: {
+        jobId: {
+            type: String,
+            required: true,
+        },
+    },
+    created: function () {
+        this.fetchJobDestinationParams(this.jobId);
+    },
+    computed: {
+        jobDestinationParams: function () {
+            return this.$store.getters.jobDestinationParams(this.jobId);
+        },
+    },
+    methods: {
+        ...mapCacheActions(["fetchJobDestinationParams"]),
+    },
+};
+</script>

client/galaxy/scripts/components/JobDestinationParams/index.js

@@ -0,0 +1,3 @@
+export { default as JobDestinationParams } from "./JobDestinationParams";
+
+export { mountDestinationParams } from "./mount";

client/galaxy/scripts/components/JobDestinationParams/mount.js

@@ -0,0 +1,13 @@
+/**
+ * Endpoint for mounting job metrics from non-Vue environment.
+ */
+import $ from "jquery";
+import JobDestinationParams from "./JobDestinationParams.vue";
+import { mountVueComponent } from "utils/mountVueComponent";
+
+export const mountDestinationParams = (propsData = {}) => {
+    $(".job-destination-parameters").each((index, el) => {
+        propsData.jobId = $(el).attr("job_id");
+        mountVueComponent(JobDestinationParams)(propsData, el);
+    });
+};

client/galaxy/scripts/components/JobDestinationParams/testData/jobDestinationResponse.json

@@ -0,0 +1,12 @@
+{
+  "Runner": "local",
+  "Runner Job ID": "23027",
+  "Handler": "main.web.1",
+  "docker_auto_rm": "true",
+  "docker_enabled": "true",
+  "docker_net": "bridge",
+  "docker_set_user": null,
+  "docker_sudo": "false",
+  "docker_volumes": "$galaxy_root:ro,$tool_directory:ro,$job_directory:rw,$working_directory:rw,$default_file_path:ro",
+  "require_container": "true"
+}

client/galaxy/scripts/components/Panels/ToolBoxWorkflow.vue

@@ -77,12 +77,15 @@ export default {
         },
         workflows: {
             type: Array,
+            required: true,
         },
         dataManagers: {
             type: Array,
+            required: true,
         },
         moduleSections: {
             type: Array,
+            required: true,
         },
     },
     computed: {

client/galaxy/scripts/components/ToolRecommendation.vue

@@ -1,6 +1,6 @@
 <template>
-    <div id="tool-recommendation" class="tool-recommendation-view">
-        <div v-if="!deprecated" class="infomessagelarge">
+    <div>
+        <div v-if="!deprecated && showMessage" class="infomessagelarge">
             <h4>Tool recommendation</h4>
             You have used {{ getToolId }} tool. For further analysis, you could try using the following/recommended
             tools. The recommended tools are shown in the decreasing order of their scores predicted using machine
@@ -8,14 +8,17 @@
             tool than a tool with a lower score. Please click on one of the following/recommended tools to open its
             definition.
         </div>
-        <div v-else class="warningmessagelarge">You have used {{ getToolId }} tool. {{ deprecatedMessage }}</div>
+        <div v-else-if="deprecated" class="warningmessagelarge">
+            You have used {{ getToolId }} tool. {{ deprecatedMessage }}
+        </div>
+        <div id="tool-recommendation" class="tool-recommendation-view"></div>
     </div>
 </template>
 
 <script>
 import * as d3 from "d3";
 import { getAppRoot } from "onload/loadConfig";
-import axios from "axios";
+import { getDatatypeMapping, getToolPredictions } from "components/Workflow/Editor/services";
 
 export default {
     props: {
@@ -26,8 +29,9 @@ export default {
     },
     data() {
         return {
-            deprecated: null,
+            deprecated: false,
             deprecatedMessage: "",
+            showMessage: false,
         };
     },
     created() {
@@ -46,86 +50,75 @@ export default {
     methods: {
         loadRecommendations() {
             const toolId = this.getToolId;
-            const url = `${getAppRoot()}api/workflows/get_tool_predictions`;
-            axios
-                .post(url, {
-                    tool_sequence: toolId,
-                })
-                .then((response) => {
-                    axios.get(`${getAppRoot()}api/datatypes/mapping`).then((responseMapping) => {
-                        const predData = response.data.predicted_data;
-                        const datatypesMapping = responseMapping.data;
-                        const extToType = datatypesMapping.ext_to_class_name;
-                        const typeToType = datatypesMapping.class_to_classes;
-                        this.deprecated = predData.is_deprecated;
-
-                        if (response.data !== null && predData.children.length > 0) {
-                            const filteredData = {};
-                            const compatibleTools = {};
-                            const filteredChildren = [];
-                            const outputDatatypes = predData.o_extensions;
-                            const children = predData.children;
-                            for (const nameObj of children.entries()) {
-                                const inputDatatypes = nameObj[1].i_extensions;
-                                for (const out_t of outputDatatypes.entries()) {
-                                    for (const in_t of inputDatatypes.entries()) {
-                                        const child = extToType[out_t[1]];
-                                        const parent = extToType[in_t[1]];
-                                        if (
-                                            (typeToType[child] && parent in typeToType[child]) === true ||
-                                            out_t[1] === "input" ||
-                                            out_t[1] === "_sniff_" ||
-                                            out_t[1] === "input_collection"
-                                        ) {
-                                            compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
-                                            break;
-                                        }
-                                    }
-                                }
-                            }
-                            for (const id in compatibleTools) {
-                                for (const nameObj of children.entries()) {
-                                    if (nameObj[1].tool_id === id) {
-                                        filteredChildren.push(nameObj[1]);
+            const requestData = {
+                tool_sequence: toolId,
+            };
+            getToolPredictions(requestData).then((responsePred) => {
+                getDatatypeMapping().then((datatypesMapping) => {
+                    const predData = responsePred.predicted_data;
+                    const extToType = datatypesMapping.ext_to_class_name;
+                    const typeToType = datatypesMapping.class_to_classes;
+                    this.deprecated = predData.is_deprecated;
+                    this.deprecatedMessage = predData.message;
+                    if (responsePred !== null && predData.children.length > 0) {
+                        const filteredData = {};
+                        const compatibleTools = {};
+                        const filteredChildren = [];
+                        const outputDatatypes = predData.o_extensions;
+                        const children = predData.children;
+                        for (const nameObj of children.entries()) {
+                            const inputDatatypes = nameObj[1].i_extensions;
+                            for (const outT of outputDatatypes.entries()) {
+                                for (const inTool of inputDatatypes.entries()) {
+                                    const child = extToType[outT[1]];
+                                    const parent = extToType[inTool[1]];
+                                    if (
+                                        (typeToType[child] && parent in typeToType[child]) === true ||
+                                        outT[1] === "input" ||
+                                        outT[1] === "_sniff_" ||
+                                        outT[1] === "input_collection"
+                                    ) {
+                                        compatibleTools[nameObj[1].tool_id] = nameObj[1].name;
                                         break;
                                     }
                                 }
                             }
-                            filteredData.o_extensions = predData.o_extensions;
-                            filteredData.name = predData.name;
-                            filteredData.children = filteredChildren;
-                            if (filteredChildren.length > 0 && this.deprecated === false) {
-                                this.renderD3Tree(filteredData);
-                            } else if (this.deprecated === true) {
-                                this.deprecatedMessage = predData.message;
+                        }
+                        for (const id in compatibleTools) {
+                            for (const nameObj of children.entries()) {
+                                if (nameObj[1].tool_id === id) {
+                                    filteredChildren.push(nameObj[1]);
+                                    break;
+                                }
                             }
                         }
-                    });
+                        filteredData.o_extensions = predData.o_extensions;
+                        filteredData.name = predData.name;
+                        filteredData.children = filteredChildren;
+                        if (filteredChildren.length > 0 && this.deprecated === false) {
+                            this.showMessage = true;
+                            this.renderD3Tree(filteredData);
+                        }
+                    }
                 });
+            });
         },
         renderD3Tree(predictedTools) {
-            const duration = 750;
-            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
             let i = 0;
             let root = null;
-            let x = 0;
-            let y = 0;
-            let translateX = 0;
-
+            const duration = 750;
+            const maxTextLength = 20;
+            const svg = d3.select("#tool-recommendation").append("svg").attr("class", "tree-size").append("g");
             const gElem = svg[0][0];
             const svgElem = gElem.parentNode;
             const clientH = svgElem.clientHeight;
             const clientW = svgElem.clientWidth;
-            y = parseInt(clientH * 0.9);
-            x = parseInt(clientW * 0.6);
-            translateX = parseInt(clientW * 0.15);
+            const translateX = parseInt(clientW * 0.15);
 
-            svgElem.setAttribute("viewBox", "0 0 " + x + " " + clientH);
-            svgElem.setAttribute("preserveAspectRatio", "xMinYMin");
-            gElem.setAttribute("transform", "translate(" + translateX + ", 5)");
-
-            const tree = d3.layout.tree().size([y, x]);
+            svgElem.setAttribute("viewBox", -translateX + " 0 " + 0.5 * clientW + " " + clientH);
+            svgElem.setAttribute("preserveAspectRatio", "xMidYMid meet");
 
+            const tree = d3.layout.tree().size([clientH, clientW]);
             const diagonal = d3.svg.diagonal().projection((d) => {
                 return [d.y, d.x];
             });
@@ -135,9 +128,9 @@ export default {
                 const links = tree.links(nodes);
                 // Normalize for fixed-depth.
                 nodes.forEach((d) => {
-                    d.y = d.depth * 180;
+                    d.y = d.depth * (clientW / 10);
                 });
-                // Update the nodes…
+                // Update the nodes
                 const node = svg.selectAll("g.node").data(nodes, (d) => {
                     return d.id || (d.id = ++i);
                 });
@@ -161,11 +154,14 @@ export default {
                         return d.children || d._children ? "end" : "start";
                     })
                     .text((d) => {
+                        const tName = d.name;
+                        if (tName.length > maxTextLength) {
+                            return tName.slice(0, maxTextLength) + "...";
+                        }
                         return d.name;
-                    })
-                    .attr("class", "node-enter");
+                    });
                 nodeEnter.append("title").text((d) => {
-                    return d.children || d._children ? "Click to collapse" : "Click to open tool definition";
+                    return d.children || d._children ? d.name : "Open tool - " + d.name;
                 });
                 // Transition nodes to their new position.
                 const nodeUpdate = node
@@ -174,19 +170,15 @@ export default {
                     .attr("transform", (d) => {
                         return "translate(" + d.y + "," + d.x + ")";
                     });
-                nodeUpdate.select("circle").attr("r", 4.5);
-                nodeUpdate.select("text").attr("class", "node-update");
+                nodeUpdate.select("circle").attr("r", 2.5);
                 // Transition exiting nodes to the parent's new position.
-                const nodeExit = node
-                    .exit()
+                node.exit()
                     .transition()
                     .duration(duration)
                     .attr("transform", (d) => {
                         return "translate(" + source.y + "," + source.x + ")";
                     })
                     .remove();
-                nodeExit.select("circle").attr("r", 1e-6);
-                nodeExit.select("text").attr("class", "node-enter");
                 // Update the links
                 const link = svg.selectAll("path.link").data(links, (d) => {
                     return d.target.id;
@@ -239,7 +231,7 @@ export default {
                 }
             };
             root = predictedTools;
-            root.x0 = y / 2;
+            root.x0 = parseInt(clientH / 2);
             root.y0 = 0;
             root.children.forEach(collapse);
             update(root);

client/galaxy/scripts/components/Toolshed/Index.vue

@@ -4,6 +4,7 @@
         <div v-else>
             <b-input-group class="mb-3">
                 <b-input
+                    id="toolshed-repo-search"
                     placeholder="Search Repositories"
                     v-model="queryInput"
                     @input="delayQuery"

client/galaxy/scripts/components/Toolshed/RepositoryDetails/InstallationSettings.vue

@@ -1,5 +1,5 @@
 <template>
-    <b-modal :static="modalStatic" v-model="modalShow" @ok="onOk" @hide="onHide">
+    <b-modal id="repo-install-settings" :static="modalStatic" v-model="modalShow" @ok="onOk" @hide="onHide">
         <template v-slot:modal-header>
             <h4 class="title m-0">
                 {{ modalTitle }}

client/galaxy/scripts/components/Toolshed/SearchList/Repositories.vue

@@ -1,6 +1,6 @@
 <template>
     <div>
-        <b-table striped :items="repositories" :fields="fields">
+        <b-table striped id="shed-search-results" :items="repositories" :fields="fields">
             <template v-slot:cell(name)="row">
                 <b-link href="javascript:void(0)" role="button" class="font-weight-bold" @click="row.toggleDetails">
                     {{ row.item.name }}

client/galaxy/scripts/components/User/UserPreferencesModel.js

@@ -83,7 +83,7 @@ export const getUserPreferencesModel = () => {
         },
         logout: {
             title: _l("Sign Out"),
-            id: "edit-preferences-custom-builds",
+            id: "edit-preferences-sign-out",
             description: _l("Click here to sign out of all sessions."),
             icon: "fa-sign-out",
             shouldRender: !!Galaxy.session_csrf_token,

client/galaxy/scripts/components/Workflow/Editor/Attributes.vue

@@ -68,15 +68,19 @@ export default {
         },
         annotation: {
             type: String,
+            default: "",
         },
         version: {
             type: Number,
+            default: null,
         },
         versions: {
             type: Array,
+            default: null,
         },
         parameters: {
             type: Array,
+            default: null,
         },
     },
     data() {

client/galaxy/scripts/components/Workflow/Editor/EditorPanel.vue

@@ -6,11 +6,11 @@
             </div>
         </div>
         <div class="unified-panel-body workflow-right">
-            <div v-if="canvas" class="m-1">
+            <div class="m-1" v-show="canvas">
                 <slot name="attributes" />
                 <div id="right-content" class="right-content" />
             </div>
-            <ReportHelp v-else />
+            <ReportHelp v-show="!canvas" />
         </div>
     </div>
 </template>

client/galaxy/scripts/components/Workflow/Editor/Index.vue

@@ -4,8 +4,8 @@
             <template v-slot:panel>
                 <ToolBoxWorkflow
                     :toolbox="toolbox"
-                    :module-sections="module_sections"
-                    :data-managers="data_managers"
+                    :module-sections="moduleSections"
+                    :data-managers="dataManagers"
                     :workflows="workflows"
                     @onInsertTool="onInsertTool"
                     @onInsertModule="onInsertModule"
@@ -110,30 +110,39 @@ export default {
     props: {
         id: {
             type: String,
+            required: true,
         },
         version: {
             type: Number,
+            required: true,
         },
         name: {
             type: String,
+            required: true,
         },
         tags: {
             type: Array,
+            required: true,
         },
         annotation: {
             type: String,
+            required: true,
         },
-        module_sections: {
+        moduleSections: {
             type: Array,
+            required: true,
         },
-        data_managers: {
+        dataManagers: {
             type: Array,
+            required: true,
         },
         workflows: {
             type: Array,
+            required: true,
         },
         toolbox: {
             type: Array,
+            required: true,
         },
     },
     data() {

client/galaxy/scripts/components/Workflow/Editor/Node.vue

@@ -10,6 +10,19 @@
             >
                 <i class="fa fa-times" />
             </b-button>
+            <b-button
+                :id="popoverId"
+                v-if="isEnabled"
+                class="node-recommendations py-0 float-right"
+                variant="primary"
+                size="sm"
+                aria-label="tool recommendations"
+            >
+                <i class="fa fa-arrow-right" />
+            </b-button>
+            <b-popover :target="popoverId" triggers="hover" placement="bottom" :show.sync="popoverShow">
+                <WorkflowRecommendations :node="node" @onCreate="onCreate" />
+            </b-popover>
             <b-button
                 v-if="canClone"
                 class="node-clone py-0 float-right"
@@ -35,17 +48,27 @@
 import Vue from "vue";
 import BootstrapVue from "bootstrap-vue";
 import WorkflowIcons from "components/Workflow/icons";
+import { getModule } from "./services";
 import LoadingSpan from "components/LoadingSpan";
+import { getGalaxyInstance } from "app";
+import WorkflowRecommendations from "components/Workflow/Editor/Recommendations";
 
 Vue.use(BootstrapVue);
 
 export default {
     components: {
         LoadingSpan,
+        WorkflowRecommendations,
+    },
+    data() {
+        return {
+            popoverShow: false,
+        };
     },
     props: {
         id: {
             type: String,
+            default: "",
         },
         title: {
             type: String,
@@ -57,6 +80,11 @@ export default {
         },
         node: {
             type: Object,
+            default: null,
+        },
+        nodeId: {
+            type: String,
+            default: "",
         },
     },
     computed: {
@@ -67,9 +95,15 @@ export default {
             }
             return null;
         },
+        popoverId() {
+            return `popover-${this.nodeId}`;
+        },
         canClone() {
             return this.type != "subworkflow";
         },
+        isEnabled() {
+            return getGalaxyInstance().config.enable_tool_recommendations;
+        },
     },
     methods: {
         onDestroy() {
@@ -78,6 +112,18 @@ export default {
         onClone() {
             this.node.clone();
         },
+        onCreate(toolId, event) {
+            const requestData = {
+                tool_id: toolId,
+                type: "tool",
+                _: "true",
+            };
+            getModule(requestData).then((response) => {
+                var node = this.node.app.create_node("tool", response.name, toolId);
+                this.node.app.set_node(node, response);
+                this.popoverShow = false;
+            });
+        },
     },
 };
 </script>

client/galaxy/scripts/components/Workflow/Editor/Recommendations.vue

@@ -0,0 +1,145 @@
+<template>
+    <div class="workflow-recommendations">
+        <div class="header-background">
+            <h4>{{ popoverHeaderText }}</h4>
+        </div>
+        <LoadingSpan v-if="showLoading" message="Loading recommendations" />
+        <div v-if="compatibleTools.length > 0 && !isDeprecated">
+            <div v-for="tool in compatibleTools" :key="tool.id">
+                <i class="fa mr-1 fa-wrench"></i>
+                <a href="#" title="Open tool" :id="tool.id" @click="$emit('onCreate', tool.id, $event)">
+                    {{ tool.name }}
+                </a>
+            </div>
+        </div>
+        <div v-else-if="isDeprecated">
+            {{ deprecatedMessage }}
+        </div>
+        <div v-if="compatibleTools.length === 0 && !showLoading">
+            {{ noRecommendationsMessage }}
+        </div>
+    </div>
+</template>
+
+<script>
+import { getToolPredictions } from "./services";
+import LoadingSpan from "components/LoadingSpan";
+import _l from "utils/localization";
+
+export default {
+    components: {
+        LoadingSpan,
+    },
+    props: {
+        node: {
+            type: Object,
+            required: true,
+        },
+    },
+    data() {
+        return {
+            compatibleTools: [],
+            isDeprecated: false,
+            popoverHeaderText: _l("Tool recommendations"),
+            noRecommendationsMessage: _l("No tool recommendations"),
+            deprecatedMessage: "",
+            showLoading: true,
+        };
+    },
+    created() {
+        this.loadRecommendations();
+    },
+    methods: {
+        getToolId(toolId) {
+            if (toolId !== undefined && toolId !== null && toolId.indexOf("/") > -1) {
+                const toolIdSlash = toolId.split("/");
+                toolId = toolIdSlash[toolIdSlash.length - 2];
+            }
+            return toolId;
+        },
+        getWorkflowPath(wfSteps, currentNodeId) {
+            const steps = {};
+            const stepNames = {};
+            for (const stpIdx in wfSteps.steps) {
+                const step = wfSteps.steps[stpIdx];
+                const inputConnections = step.input_connections;
+                stepNames[step.id] = this.getToolId(step.content_id);
+                for (const icIdx in inputConnections) {
+                    const ic = inputConnections[icIdx];
+                    if (ic !== null && ic !== undefined) {
+                        const prevConn = [];
+                        for (const conn of ic) {
+                            prevConn.push(conn.id.toString());
+                        }
+                        steps[step.id.toString()] = prevConn;
+                    }
+                }
+            }
+            // recursive call to determine path
+            function readPaths(nodeId, ph) {
+                for (const st in steps) {
+                    if (parseInt(st) === parseInt(nodeId)) {
+                        const parentId = parseInt(steps[st][0]);
+                        if (parentId !== undefined && parentId !== null) {
+                            ph.push(parentId);
+                            if (steps[parentId] !== undefined && steps[parentId] !== null) {
+                                readPaths(parentId, ph);
+                            }
+                        }
+                    }
+                }
+                return ph;
+            }
+            let ph = [];
+            const stepNameList = [];
+            ph.push(currentNodeId);
+            ph = readPaths(currentNodeId, ph);
+            for (const sIdx of ph) {
+                const sName = stepNames[sIdx.toString()];
+                if (sName !== undefined && sName !== null) {
+                    stepNameList.push(sName);
+                }
+            }
+            return stepNameList.join(",");
+        },
+        loadRecommendations() {
+            const workflowSimple = this.node.app.to_simple();
+            const node = this.node;
+            const toolSequence = this.getWorkflowPath(workflowSimple, node.id);
+            const requestData = { tool_sequence: toolSequence };
+            getToolPredictions(requestData).then((responsePred) => {
+                const predictedData = responsePred.predicted_data;
+                const outputDatatypes = predictedData.o_extensions;
+                const predictedDataChildren = predictedData.children;
+                const app = this.node.app;
+                this.isDeprecated = predictedData.is_deprecated;
+                this.deprecatedMessage = predictedData.message;
+                if (predictedDataChildren.length > 0) {
+                    const cTools = [];
+                    for (const nameObj of predictedDataChildren.entries()) {
+                        const t = {};
+                        const inputDatatypes = nameObj[1].i_extensions;
+                        for (const outT of outputDatatypes.entries()) {
+                            for (const inTool of inputDatatypes.entries()) {
+                                if (
+                                    app.isSubType(outT[1], inTool[1]) === true ||
+                                    outT[1] === "input" ||
+                                    outT[1] === "_sniff_" ||
+                                    outT[1] === "input_collection"
+                                ) {
+                                    t.id = nameObj[1].tool_id;
+                                    t.name = nameObj[1].name;
+                                    cTools.push(t);
+                                    break;
+                                }
+                            }
+                        }
+                    }
+                    this.compatibleTools = cTools;
+                }
+                this.showLoading = false;
+            });
+        },
+    },
+};
+</script>

client/galaxy/scripts/components/Workflow/Editor/services.js

@@ -67,3 +67,21 @@ export async function saveWorkflow(workflow, id) {
     }
     return {};
 }
+
+export async function getDatatypeMapping() {
+    try {
+        const mappingRequest = await axios.get(`${getAppRoot()}api/datatypes/mapping`);
+        return mappingRequest.data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}
+
+export async function getToolPredictions(requestData) {
+    try {
+        const response = await axios.post(`${getAppRoot()}api/workflows/get_tool_predictions`, requestData);
+        return response.data;
+    } catch (e) {
+        rethrowSimple(e);
+    }
+}

client/galaxy/scripts/components/Workflow/Editor/utilities.js

@@ -144,9 +144,9 @@ export function getWorkflowParameters(nodes) {
             });
         }
         if (node.post_job_actions) {
-            Object.entries(node.post_job_actions).forEach(([k, pja]) => {
+            Object.values(node.post_job_actions).forEach((pja) => {
                 if (pja.action_arguments) {
-                    Object.entries(pja.action_arguments).forEach(([k, action_argument]) => {
+                    Object.values(pja.action_arguments).forEach((action_argument) => {
                         if (typeof action_argument === "string") {
                             const arg_matches = action_argument.match(parameter_re);
                             if (arg_matches) {
@@ -198,7 +198,8 @@ export function saveAs(workflow) {
                     window.location = `${getAppRoot()}workflow/editor?id=${id}`;
                     hide_modal();
                 })
-                .fail(() => {
+                .fail((err) => {
+                    console.debug(err);
                     hide_modal();
                     alert("Saving this workflow failed. Please contact this site's administrator.");
                 });

client/galaxy/scripts/entry/panels/admin-panel.js

@@ -87,6 +87,7 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Forms"),
                         url: "admin/forms",
                         target: "__use_router__",
+                        id: "admin-link-forms",
                     },
                 ],
             },
@@ -97,17 +98,20 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("Install and Uninstall"),
                         url: "admin/toolshed",
                         target: "__use_router__",
+                        id: "admin-link-toolshed",
                         enabled: this.settings.is_tool_shed_installed,
                     },
                     {
                         title: _l("Manage Metadata"),
                         url: "admin/reset_metadata",
+                        id: "admin-link-metadata",
                         enabled: this.settings.is_repo_installed,
                         target: "__use_router__",
                     },
                     {
                         title: _l("Manage Whitelist"),
                         url: "admin/sanitize_whitelist",
+                        id: "admin-link-whitelist",
                     },
                     {
                         title: _l("Manage Dependencies"),
@@ -123,14 +127,17 @@ const AdminPanel = Backbone.View.extend({
                         title: _l("View Lineage"),
                         url: "admin/tool_versions",
                         target: "__use_router__",
+                        id: "admin-link-tool-versions",
                     },
                     {
                         title: _l("View Migration Stages"),
                         url: "admin/review_tool_migration_stages",
+                        id: "admin-link-migrations",
                     },
                     {
                         title: _l("View Error Logs"),
                         url: "admin/error_stack",
+                        id: "admin-link-error-stack",
                         target: "__use_router__",
                     },
                 ],

client/galaxy/scripts/mvc/tool/tool-form-base.js

@@ -24,7 +24,7 @@ export default FormBase.extend({
         FormBase.prototype.initialize.call(this, options);
 
         // optional model update
-        this._update(this.model.get("initialmodel"));
+        this._update();
 
         // listen to history panel
         if (this.model.get("listen_to_history") && Galaxy.currHistoryPanel) {
@@ -39,9 +39,9 @@ export default FormBase.extend({
     },
 
     /** Allows tool form variation to update tool model */
-    _update: function (callback) {
+    _update: function () {
         var self = this;
-        callback = callback || this.model.get("buildmodel");
+        var callback = this.model.get("buildmodel");
         if (callback) {
             this.deferred.reset();
             this.deferred.execute((process) => {

client/galaxy/scripts/mvc/workflow/workflow-forms.js

@@ -1,4 +1,4 @@
-import $ from "jquery";
+import axios from "axios";
 import { getAppRoot } from "onload/loadConfig";
 import { getGalaxyInstance } from "app";
 import _l from "utils/localization";
@@ -11,95 +11,85 @@ export class DefaultForm {
     constructor(options) {
         var self = this;
         var node = options.node;
-        this.form = new Form(
-            Utils.merge(options, {
-                onchange: function () {
-                    Utils.request({
-                        type: "POST",
-                        url: `${getAppRoot()}api/workflows/build_module`,
-                        data: {
-                            id: node.id,
-                            type: node.type,
-                            content_id: node.content_id,
-                            inputs: self.form.data.create(),
-                        },
-                        success: function (data) {
-                            node.update_field_data(data);
-                        },
+        this.workflow = options.workflow;
+        _addLabelAnnotation(this, node);
+        this.form = new Form({
+            ...options,
+            onchange() {
+                axios
+                    .post(`${getAppRoot()}api/workflows/build_module`, {
+                        id: node.id,
+                        type: node.type,
+                        content_id: node.content_id,
+                        inputs: self.form.data.create(),
+                    })
+                    .then((response) => {
+                        const data = response.data;
+                        node.update_field_data(data);
                     });
-                },
-            })
-        );
-        _addLabelAnnotation(this.form);
-        this.form.render();
+            },
+        });
     }
 }
 
 /** Tool form wrapper for the workflow editor. */
 export class ToolForm {
     constructor(options) {
-        var self = this;
-        var node = options.node;
-        this.form = new ToolFormBase(
-            Utils.merge(options, {
-                text_enable: "Set in Advance",
-                text_disable: "Set at Runtime",
-                narrow: true,
-                initial_errors: true,
-                cls: "ui-portlet-section",
-                initialmodel: function (process, form) {
-                    self._customize(form);
-                    process.resolve();
-                },
-                buildmodel: function (process, form) {
-                    form.model.get("postchange")(process, form);
-                },
-                postchange: function (process, form) {
-                    const Galaxy = getGalaxyInstance();
-                    var options = form.model.attributes;
-                    var current_state = {
-                        tool_id: options.id,
-                        tool_version: options.version,
-                        type: "tool",
-                        inputs: $.extend(true, {}, form.data.create()),
-                    };
-                    Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
-                    Utils.request({
-                        type: "POST",
-                        url: `${getAppRoot()}api/workflows/build_module`,
-                        data: current_state,
-                        success: function (data) {
-                            form.model.set(data.config_form);
-                            self._customize(form);
-                            form.update(data.config_form);
-                            form.errors(data.config_form);
-                            // This hasn't modified the workflow, just returned
-                            // module information for the tool to update the workflow
-                            // state stored on the client with. User needs to save
-                            // for this to take effect.
-                            node.update_field_data(data);
-                            Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
-                            process.resolve();
-                        },
-                        error: function (response) {
-                            Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
-                            process.reject();
-                        },
+        const self = this;
+        const node = options.node;
+        this.workflow = options.workflow;
+        this.datatypes = options.datatypes;
+        this._customize(node);
+        this.form = new ToolFormBase({
+            ...node.config_form,
+            text_enable: "Set in Advance",
+            text_disable: "Set at Runtime",
+            narrow: true,
+            initial_errors: true,
+            cls: "ui-portlet-section",
+            postchange(process, form) {
+                const Galaxy = getGalaxyInstance();
+                const options = form.model.attributes;
+                const current_state = {
+                    tool_id: options.id,
+                    tool_version: options.version,
+                    type: "tool",
+                    inputs: Object.assign({}, form.data.create()),
+                };
+                Galaxy.emit.debug("tool-form-workflow::postchange()", "Sending current state.", current_state);
+                axios
+                    .post(`${getAppRoot()}api/workflows/build_module`, current_state)
+                    .then((response) => {
+                        const data = response.data;
+                        self._customize(data);
+                        self.form.model.set(data.config_form);
+                        self.form.update(data.config_form);
+                        self.form.errors(data.config_form);
+                        // This hasn't modified the workflow, just returned
+                        // module information for the tool to update the workflow
+                        // state stored on the client with. User needs to save
+                        // for this to take effect.
+                        node.update_field_data(data);
+                        Galaxy.emit.debug("tool-form-workflow::postchange()", "Received new model.", data);
+                        process.resolve();
+                    })
+                    .catch((response) => {
+                        Galaxy.emit.debug("tool-form-workflow::postchange()", "Refresh request failed.", response);
+                        process.reject();
                     });
-                },
-            })
-        );
+            },
+        });
     }
-    _customize(form) {
-        var options = form.model.attributes;
-        Utils.deepeach(options.inputs, (input) => {
+    _customize(node) {
+        const inputs = node.config_form.inputs;
+        Utils.deepeach(inputs, (input) => {
             if (input.type) {
-                input.connectable = true;
                 if (["data", "data_collection"].indexOf(input.type) != -1) {
                     input.type = "hidden";
                     input.info = `Data input '${input.name}' (${Utils.textify(input.extensions)})`;
                     input.value = { __class__: "RuntimeValue" };
                 } else if (!input.fixed) {
+                    input.connectable = true;
                     input.collapsible_value = {
                         __class__: "RuntimeValue",
                     };
@@ -108,23 +98,22 @@ export class ToolForm {
                 }
             }
         });
-        Utils.deepeach(options.inputs, (input) => {
+        Utils.deepeach(inputs, (input) => {
             if (input.type === "conditional") {
                 input.connectable = false;
                 input.test_param.collapsible_value = undefined;
             }
         });
-        _addSections(form);
-        _addLabelAnnotation(form);
+        _addSections(this, node);
+        _addLabelAnnotation(this, node);
     }
 }
 
 /** Augments the module form definition by adding label and annotation fields */
-function _addLabelAnnotation(form) {
-    var options = form.model.attributes;
-    var workflow = options.workflow;
-    var node = options.node;
-    options.inputs.unshift({
+function _addLabelAnnotation(self, node) {
+    var workflow = self.workflow;
+    const inputs = node.config_form.inputs;
+    inputs.unshift({
         type: "text",
         name: "__annotation",
         label: "Annotation",
@@ -133,7 +122,7 @@ function _addLabelAnnotation(form) {
         area: true,
         help: "Add an annotation or notes to this step. Annotations are available when a workflow is viewed.",
     });
-    options.inputs.unshift({
+    inputs.unshift({
         type: "text",
         name: "__label",
         label: "Label",
@@ -149,20 +138,20 @@ function _addLabelAnnotation(form) {
                     break;
                 }
             }
-            var input_id = form.data.match("__label");
-            var input_element = form.element_list[input_id];
+            var input_id = self.form.data.match("__label");
+            var input_element = self.form.element_list[input_id];
             input_element.model.set(
                 "error_text",
                 duplicate && "Duplicate label. Please fix this before saving the workflow."
             );
-            form.trigger("change");
+            self.form.trigger("change");
         },
     });
 }
 
 /** Visit input nodes and enrich by name/value pairs from server data */
-function _visit(head, head_list, output_id, options) {
-    var post_job_actions = options.node.post_job_actions;
+function _visit(head, head_list, output_id, node) {
+    var post_job_actions = node.post_job_actions;
     head_list = head_list || [];
     head_list.push(head);
     for (var i in head.inputs) {
@@ -192,7 +181,7 @@ function _visit(head, head_list, output_id, options) {
             }
         }
         if (input.inputs) {
-            _visit(input, head_list.slice(0), output_id, options);
+            _visit(input, head_list.slice(0), output_id, node);
         }
     }
 }
@@ -215,13 +204,11 @@ function _makeRenameHelp(name_labels) {
 }
 
 /** Builds sub section with step actions/annotation */
-function _makeSection(output_id, label, options) {
+function _makeSection(self, output_id, label, node) {
     var extensions = [];
     var name_label_map = [];
-    var datatypes = options.datatypes;
-    var node = options.node;
-    var workflow = options.workflow;
-
+    var datatypes = self.datatypes;
+    var workflow = self.workflow;
     for (const key in datatypes) {
         extensions.push({ 0: datatypes[key], 1: datatypes[key] });
     }
@@ -350,18 +337,15 @@ function _makeSection(output_id, label, options) {
             },
         ],
     };
-    _visit(input_config, [], output_id, options);
+    _visit(input_config, [], output_id, node);
     return input_config;
 }
 
 /** Builds all sub sections */
-function _addSections(form) {
-    var options = form.model.attributes;
-    var inputs = options.inputs;
-    var node = options.node;
+function _addSections(self, node) {
+    var inputs = node.config_form.inputs;
     var post_job_actions = node.post_job_actions;
     var output_id = node.output_terminals && Object.keys(node.output_terminals)[0];
-
     if (output_id) {
         inputs.push({
             name: `pja__${output_id}__EmailAction`,
@@ -385,7 +369,7 @@ function _addSections(form) {
         });
         for (const output_id in node.output_terminals) {
             const label = node.output_terminals[output_id].label || output_id;
-            inputs.push(_makeSection(output_id, label, options));
+            inputs.push(_makeSection(self, output_id, label, node));
         }
     }
 }

client/galaxy/scripts/mvc/workflow/workflow-manager.js

@@ -18,6 +18,7 @@ class Workflow extends EventEmitter {
         this.has_changes = false;
         this.workflowOutputLabels = {};
         this.workflow_version = 0;
+        this.popover_counter = 0;
 
         // Canvas overview management
         this.canvas_manager = new WorkflowCanvas(this, $("#canvas-viewport"), $("#overview-container"));
@@ -49,7 +50,7 @@ class Workflow extends EventEmitter {
     set_node(node, data) {
         node.init_field_data(data);
         node.update_field_data(data);
-        $.each(node.output_terminals, (ot_id, ot) => {
+        Object.values(node.output_terminals).forEach((ot) => {
             node.addWorkflowOutput(ot.name);
             node.markWorkflowOutput(ot.name);
         });
@@ -142,8 +143,10 @@ class Workflow extends EventEmitter {
             type: type,
             title: title_text,
             node: node,
+            nodeId: this.popover_counter,
         });
 
+        this.popover_counter++;
         // Set initial scroll position
         $f.css("left", $(window).scrollLeft() + 20);
         $f.css("top", $(window).scrollTop() + 20);
@@ -195,20 +198,20 @@ class Workflow extends EventEmitter {
     }
     remove_all() {
         var wf = this;
-        $.each(this.nodes, (k, v) => {
-            v.destroy();
-            wf.remove_node(v);
+        Object.values(this.nodes).forEach((node) => {
+            node.destroy();
+            wf.remove_node(node);
         });
     }
     rectify_workflow_outputs() {
         // Find out if we're using workflow_outputs or not.
         var using_workflow_outputs = false;
         var has_existing_pjas = false;
-        $.each(this.nodes, (k, node) => {
+        Object.values(this.nodes).forEach((node) => {
             if (node.type === "tool" && node.workflow_outputs && node.workflow_outputs.length > 0) {
                 using_workflow_outputs = true;
             }
-            $.each(node.post_job_actions, (pja_id, pja) => {
+            Object.values(node.post_job_actions).forEach((pja) => {
                 if (pja.action_type === "HideDatasetAction") {
                     has_existing_pjas = true;
                 }
@@ -216,26 +219,26 @@ class Workflow extends EventEmitter {
         });
         if (using_workflow_outputs !== false || has_existing_pjas !== false) {
             // Using workflow outputs, or has existing pjas.  Remove all PJAs and recreate based on outputs.
-            $.each(this.nodes, (k, node) => {
+            Object.values(this.nodes).forEach((node) => {
                 var node_changed = false;
                 if (node.post_job_actions === null) {
                     node.post_job_actions = {};
                     node_changed = true;
                 }
                 var pjas_to_rem = [];
-                $.each(node.post_job_actions, (pja_id, pja) => {
+                Object.entries(node.post_job_actions).forEach(([pja_id, pja]) => {
                     if (pja.action_type == "HideDatasetAction") {
                         pjas_to_rem.push(pja_id);
                     }
                 });
                 if (pjas_to_rem.length > 0) {
-                    $.each(pjas_to_rem, (i, pja_name) => {
+                    pjas_to_rem.forEach((pja_name) => {
                         node_changed = true;
                         delete node.post_job_actions[pja_name];
                     });
                 }
                 if (using_workflow_outputs) {
-                    $.each(node.output_terminals, (ot_id, ot) => {
+                    Object.values(node.output_terminals).forEach((ot) => {
                         var create_pja = !node.isWorkflowOutput(ot.name);
                         if (create_pja === true) {
                             node_changed = true;
@@ -258,14 +261,14 @@ class Workflow extends EventEmitter {
     }
     to_simple() {
         var nodes = {};
-        $.each(this.nodes, (i, node) => {
+        Object.values(this.nodes).forEach((node) => {
             var input_connections = {};
-            $.each(node.input_terminals, (k, t) => {
+            Object.values(node.input_terminals).forEach((t) => {
                 input_connections[t.name] = null;
                 // There should only be 0 or 1 connectors, so this is
                 // really a sneaky if statement
                 var cons = [];
-                $.each(t.connectors, (i, c) => {
+                t.connectors.forEach((c, i) => {
                     if (c.handle1) {
                         var con_dict = {
                             id: c.handle1.node.id,
@@ -282,8 +285,8 @@ class Workflow extends EventEmitter {
             });
             var post_job_actions = {};
             if (node.post_job_actions) {
-                $.each(node.post_job_actions, (i, act) => {
-                    var pja = {
+                Object.values(node.post_job_actions).forEach((act) => {
+                    const pja = {
                         action_type: act.action_type,
                         output_name: act.output_name,
                         action_arguments: act.action_arguments,
@@ -316,8 +319,7 @@ class Workflow extends EventEmitter {
         const report = this.report;
         return { steps: nodes, report: report };
     }
-    from_simple(data, initialImport_) {
-        var initialImport = initialImport_ === undefined ? true : initialImport_;
+    from_simple(data, initialImport = true) {
         var wf = this;
         var offset = 0;
         if (initialImport) {
@@ -330,13 +332,13 @@ class Workflow extends EventEmitter {
         var using_workflow_outputs = false;
         wf.workflow_version = data.version;
         wf.report = data.report || {};
-        $.each(data.steps, (id, step) => {
+        Object.entries(data.steps).forEach(([id, step]) => {
             var node = wf.prebuildNode(step.type, step.name, step.content_id);
             // If workflow being copied into another, wipe UUID and let
             // Galaxy assign new ones.
             if (!initialImport) {
                 step.uuid = null;
-                $.each(step.workflow_outputs, (name, workflow_output) => {
+                step.workflow_outputs.forEach((workflow_output) => {
                     workflow_output.uuid = null;
                 });
             }
@@ -358,7 +360,7 @@ class Workflow extends EventEmitter {
                 if (node.workflow_outputs.length > 0) {
                     using_workflow_outputs = true;
                 } else {
-                    $.each(node.post_job_actions || [], (pja_id, pja) => {
+                    Object.values(node.post_job_actions).forEach((pja) => {
                         if (pja.action_type === "HideDatasetAction") {
                             using_workflow_outputs = true;
                         }
@@ -368,14 +370,14 @@ class Workflow extends EventEmitter {
         });
         wf.id_counter = max_id + 1;
         // Second pass, connections
-        $.each(data.steps, (id, step) => {
+        Object.entries(data.steps).forEach(([id, step]) => {
             const node = wf.nodes[parseInt(id) + offset];
-            $.each(step.input_connections, (k, v) => {
+            Object.entries(step.input_connections).forEach(([k, v]) => {
                 if (v) {
-                    if (!$.isArray(v)) {
+                    if (!Array.isArray(v)) {
                         v = [v];
                     }
-                    $.each(v, (l, x) => {
+                    v.forEach((x) => {
                         const other_node = wf.nodes[parseInt(x.id) + offset];
                         const c = new Connector(this.canvas_manager);
                         c.connect(other_node.output_terminals[x.output_name], node.input_terminals[k]);
@@ -385,7 +387,7 @@ class Workflow extends EventEmitter {
             });
             if (using_workflow_outputs) {
                 // Ensure that every output terminal has a WorkflowOutput or HideDatasetAction.
-                $.each(node.output_terminals, (ot_id, ot) => {
+                Object.values(node.output_terminals).forEach((ot) => {
                     if (node.post_job_actions[`HideDatasetAction${ot.name}`] === undefined) {
                         node.addWorkflowOutput(ot.name);
                         node.markWorkflowOutput(ot.name);
@@ -451,7 +453,7 @@ class Workflow extends EventEmitter {
         var n_pred = {};
         var successors = {};
         // First pass to initialize arrays even for nodes with no connections
-        $.each(this.nodes, (id, node) => {
+        Object.keys(this.nodes).forEach((id) => {
             if (n_pred[id] === undefined) {
                 n_pred[id] = 0;
             }
@@ -460,9 +462,9 @@ class Workflow extends EventEmitter {
             }
         });
         // Second pass to count predecessors and successors
-        $.each(this.nodes, (id, node) => {
-            $.each(node.input_terminals, (j, t) => {
-                $.each(t.connectors, (k, c) => {
+        Object.values(this.nodes).forEach((node) => {
+            Object.values(node.input_terminals).forEach((t) => {
+                t.connectors.forEach((c) => {
                     // A connection exists from `other` to `node`
                     var other = c.handle1.node;
                     // node gains a predecessor
@@ -505,14 +507,14 @@ class Workflow extends EventEmitter {
         var h_pad = 80;
         var v_pad = 30;
         var left = h_pad;
-        $.each(node_ids_by_level, (i, ids) => {
+        node_ids_by_level.forEach((ids) => {
             // We keep nodes in the same order in a level to give the user
             // some control over ordering
             ids.sort((a, b) => $(all_nodes[a].element).position().top - $(all_nodes[b].element).position().top);
             // Position each node
             var max_width = 0;
             var top = v_pad;
-            $.each(ids, (j, id) => {
+            ids.forEach((id) => {
                 var node = all_nodes[id];
                 var element = $(node.element);
                 $(element).css({ top: top, left: left });
@@ -522,7 +524,7 @@ class Workflow extends EventEmitter {
             left += max_width + h_pad;
         });
         // Need to redraw all connectors
-        $.each(all_nodes, (_, node) => {
+        Object.values(all_nodes).forEach((node) => {
             node.redraw();
         });
     }
@@ -532,7 +534,7 @@ class Workflow extends EventEmitter {
         var ymin = Infinity;
         var ymax = -Infinity;
         var p;
-        $.each(this.nodes, (id, node) => {
+        Object.values(this.nodes).forEach((node) => {
             var e = $(node.element);
             p = e.position();
             xmin = Math.min(xmin, p.left);

client/galaxy/scripts/mvc/workflow/workflow-node.js

@@ -274,7 +274,7 @@ export class Node {
                     x.destroy(); // Removes the noodle connectors
                 }
             });
-            nodeView.outputViews[unused_output].remove(); // removes the rendered output
+            nodeView.outputViews[unused_output].$el.remove(); // removes the rendered output
             delete nodeView.outputViews[unused_output]; // removes the reference to the output
             delete node.output_terminals[unused_output]; // removes the output terminal
         });

client/galaxy/scripts/store/index.js

@@ -9,6 +9,7 @@ import createCache from "vuex-cache";
 import { gridSearchStore } from "./gridSearchStore";
 import { tagStore } from "./tagStore";
 import { jobMetricsStore } from "./jobMetricsStore";
+import { jobDestinationParametersStore } from "./jobDestinationParametersStore";
 import { invocationStore } from "./invocationStore";
 import { historyStore } from "./historyStore";
 import { userStore } from "./userStore";
@@ -31,6 +32,7 @@ export function createStore() {
             histories: historyStore,
             tags: tagStore,
             jobMetrics: jobMetricsStore,
+            destinationParameters: jobDestinationParametersStore,
             invocations: invocationStore,
             user: userStore,
             config: configStore,

client/galaxy/scripts/store/jobDestinationParametersStore.js

@@ -0,0 +1,33 @@
+export const state = {
+    jobDestinationParametersByJobId: {},
+};
+
+import Vue from "vue";
+import { getAppRoot } from "onload/loadConfig";
+import axios from "axios";
+
+const getters = {
+    jobDestinationParams: (state) => (jobId) => {
+        return state.jobDestinationParametersByJobId[jobId] || [];
+    },
+};
+
+const actions = {
+    fetchJobDestinationParams: async ({ commit }, jobId) => {
+        const { data } = await axios.get(`${getAppRoot()}api/jobs/${jobId}/destination_params`);
+        commit("saveJobDestinationParamsForJobId", { jobId, jobDestinationParams: data });
+    },
+};
+
+const mutations = {
+    saveJobDestinationParamsForJobId: (state, { jobId, jobDestinationParams }) => {
+        Vue.set(state.jobDestinationParametersByJobId, jobId, jobDestinationParams);
+    },
+};
+
+export const jobDestinationParametersStore = {
+    state,
+    getters,
+    actions,
+    mutations,
+};

client/galaxy/scripts/utils/simple-error.js

@@ -9,5 +9,6 @@ export function errorMessageAsString(e) {
 }
 
 export function rethrowSimple(e) {
+    console.debug(e);
     throw errorMessageAsString(e);
 }

client/galaxy/style/scss/base.scss

@@ -1656,31 +1656,29 @@ body.reports {
     .node {
         cursor: pointer;
         circle {
-            fill: lighten($brand-primary, 20%);
-            stroke: lighten($brand-primary, 20%);
-            stroke-width: 0.1rem;
+            fill: $brand-primary;
+            stroke: $brand-primary;
         }
         text {
-            font: 0.4rem sans-serif;
+            font-size: 0.4rem;
         }
     }
 
-    .node-enter {
-        fill-opacity: 1e-6;
-    }
-
-    .node-update {
-        fill-opacity: 1;
-    }
-
     .tree-size {
         width: 100%;
-        height: 50%;
     }
 
     .link {
         fill: none;
-        stroke: lighten($brand-primary, 20%);
-        stroke-width: 0.2rem;
+        stroke: $brand-primary;
+        stroke-width: 1;
+    }
+}
+
+.workflow-recommendations {
+    display: block;
+    .header-background {
+        border-bottom: solid 1px $brand-primary;
+        margin-bottom: 0.5rem;
     }
 }

client/galaxy/style/scss/workflow.scss

@@ -7,6 +7,9 @@
         display: flex;
         flex-direction: column;
         flex-grow: 1;
+        .workflow-recommendations {
+            height: 30rem;
+        }
         .workflow-node {
             @extend .card;
             @extend .position-absolute;

client/gulpfile.js

@@ -21,7 +21,7 @@ const paths = {
     //    "../config/plugins/{visualizations,interactive_environments}/*/*/package.json"
     //],
     plugin_build_dirs: [
-        "../config/plugins/visualizations/{annotate_image,hyphyvision,openlayers}/package.json",
+        "../config/plugins/visualizations/{annotate_image,hyphyvision,openlayers,editor}/package.json",
     ],
     lib_locs: {
         // This is a stepping stone towards having all this staged

config/plugins/visualizations/editor/config/editor.xml

@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
+<visualization name="Editor">
+    <description>Manually edit text</description>
+    <data_sources>
+        <data_source>
+            <model_class>HistoryDatasetAssociation</model_class>
+            <test type="isinstance" test_attr="datatype" result_type="datatype">data.Data</test>
+            <to_param param_attr="id">dataset_id</to_param>
+        </data_source>
+    </data_sources>
+    <params>
+        <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
+    </params>
+    <entry_point entry_point_type="mako">editor.mako</entry_point>
+</visualization>

config/plugins/visualizations/editor/package.json

@@ -0,0 +1,21 @@
+{
+  "devDependencies": {
+    "css-loader": "^3.4.2",
+    "file-loader": "^5.0.2",
+    "mini-css-extract-plugin": "^0.9.0",
+    "style-loader": "^1.1.3",
+    "webpack": "^4.41.6",
+    "webpack-cli": "^3.3.11",
+    "extract-text-webpack-plugin": "^3.0.2"
+  },
+  "dependencies": {
+    "ace-builds": "^1.4.8"
+  },
+  "name": "galaxy-vis-editor",
+  "version": "1.1.0",
+  "main": "index.js",
+  "license": "MIT",
+  "scripts": {
+    "build": "webpack --mode production"
+  }
+}

config/plugins/visualizations/editor/src/index.js

@@ -0,0 +1,4 @@
+import './styles/style.css';
+import "ace-builds/src-noconflict/ace";
+import "ace-builds/src-noconflict/mode-powershell";
+import "ace-builds/src-noconflict/theme-textmate";

config/plugins/visualizations/editor/src/styles/style.css

@@ -0,0 +1,41 @@
+#editor {
+    position: absolute;
+    top: 0;
+    right: 0;
+    bottom: 0;
+    left: 0;
+}
+
+#export-btn {
+    position: relative;
+    z-index: 3;
+    left: 90%;
+}
+
+.transparent_btn {
+    display: inline-block;
+    padding: 10px 14px;
+    color: #FFF;
+    border: 1px solid #FFF;
+    text-decoration: none;
+    font-size: 14px;
+    line-height: 120%;
+    background-color: rgba(255, 255, 255, 0);
+    -webkit-border-radius: 4px;
+    -moz-border-radius: 4px;
+    border-radius: 4px;
+    -webkit-transition: 300ms ease;
+    -moz-transition:  300ms ease;
+    transition: 300ms ease;
+    cursor: pointer;
+}
+
+.transparent_btn.blue {
+    color: #aeddf5;
+    border-color: #aeddf5;
+}
+
+.transparent_btn.blue:hover {
+    color: #0062ff;
+    background-color: rgba(174, 221, 245, 0.3);
+}

config/plugins/visualizations/editor/templates/editor.mako

@@ -0,0 +1,72 @@
+<%
+    default_title = "JS Editor"
+
+    # Use root for resource loading.
+    root = h.url_for( '/static/' )
+    app_root    = root + "plugins/visualizations/editor/static/"
+%>
+## ----------------------------------------------------------------------------
+
+<!DOCTYPE HTML>
+<html>
+<head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
+    <title> ${visualization_name}</title>
+    ${h.javascript_link( app_root + "script.js" )}
+    ${h.stylesheet_link( app_root + "main.css" )}
+</head>
+
+<body>
+<div id="editor">
+</div>
+<button onclick="exportData()" class="transparent_btn blue" id="export-btn">export</button>
+<script>
+    function httpGet(theUrl) {
+        var xmlHttp = new XMLHttpRequest();
+        xmlHttp.open("GET", theUrl, false);
+        xmlHttp.send(null);
+        return xmlHttp.responseText;
+    }
+
+    function exportData() {
+        ## Prepare data for export
+        const upload_data = {
+            tool_id: "upload1",
+            history_id: "${trans.security.encode_id(hda.history_id)}",
+            inputs: {
+                "file_count": 1,
+                "file_type": "auto",
+                "files_0|file_type": "auto",
+                "files_0|url_paste": editor.getValue(),
+                "files_0|NAME": "${ hda.name } (modified)"
+            }
+        };
+        ## upload data
+        const request = new XMLHttpRequest();
+        request.open("POST", "/api/tools");
+        request.setRequestHeader("Content-Type", "application/json");
+        request.send(JSON.stringify(upload_data));
+        request.onreadystatechange = function () {
+            if (request.readyState === XMLHttpRequest.DONE) {
+                var status = request.status;
+                if (status === 0 || (200 >= status && status < 400)) {
+                    top.location = "/"
+                } else {
+                    alert("something went wrong, please contact us!");
+                }
+            }
+        };
+    }
+
+    const hda_id = '${ trans.security.encode_id( hda.id ) }';
+
+    const ajax_url = "${h.url_for( controller='/datasets', action='index')}/" + hda_id + "/display";
+    const data = httpGet(ajax_url);
+    document.getElementById("editor").innerHTML = data;
+    var editor = ace.edit("editor", {
+        mode: "ace/mode/powershell",
+        theme: "ace/theme/textmate"
+    });
+</script>
+</body>
+</html>

config/plugins/visualizations/editor/webpack.config.js

@@ -0,0 +1,39 @@
+const webpack = require("webpack");
+const path = require("path");
+const MiniCssExtractPlugin = require("mini-css-extract-plugin");
+
+module.exports = {
+    mode: 'production',
+    entry: path.resolve(__dirname, "src/index.js"),
+    output: {
+        filename: "script.js",
+        path: path.resolve(__dirname, "static")
+    },
+    plugins: [
+        new MiniCssExtractPlugin(),
+    ],
+    module: {
+        rules: [
+            {
+                test: /\.css$/i,
+                use: [MiniCssExtractPlugin.loader, 'css-loader'],
+            },
+            {
+                test: /\.(woff|woff2)(\?v=\d+\.\d+\.\d+)?$/,
+                loader: "url-loader",
+                options: {limit: 10000, mimetype: "application/font-woff"}
+            },
+            {
+                test: /\.ttf(\?v=\d+\.\d+\.\d+)?$/,
+                loader: "url-loader",
+                options: {limit: 10000, mimetype: "application/octet-stream"}
+            },
+            {test: /\.eot(\?v=\d+\.\d+\.\d+)?$/, loaders: "file-loader"},
+            {
+                test: /\.svg(\?v=\d+\.\d+\.\d+)?$/,
+                loaders: "url-loader",
+                options: {limit: 10000, mimetype: "image/svg+xml"}
+            }
+        ]
+    },
+};

doc/source/admin/galaxy_options.rst

@@ -1376,6 +1376,27 @@
 :Type: bool
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``interactivetools_proxy_host``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Proxy host - assumed to just be hosted on the same hostname and
+    port as Galaxy by default.
+:Default: ``None``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~
+``interactivetools_map``
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Map for interactivetool proxy.
+:Default: ``interactivetools_map.sqlite``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 ``visualizations_visible``
 ~~~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/authnz/psa_authnz.py

@@ -116,9 +116,9 @@ class PSAAuthnz(IdentityProvider):
 
         # Secondary AuthZ with Google identities is currently supported
         if provider != "google":
-            if "SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER" in self.config:
+            if 'SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER' in self.config:
                 del self.config["SOCIAL_AUTH_SECONDARY_AUTH_PROVIDER"]
-            if "SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT" in self.config:
+            if 'SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT' in self.config:
                 del self.config["SOCIAL_AUTH_SECONDARY_AUTH_ENDPOINT"]
 
     def _setup_idp(self, oidc_backend_config):

lib/galaxy/config/__init__.py

@@ -118,6 +118,10 @@ class BaseAppConfiguration(object):
         self._create_attributes_from_raw_config()  # Create attributes based on raw_config
         self._resolve_paths()  # Overwrite attribute values with resolved paths
 
+    def resolve_path(self, path):
+        """Resolve a path relative to Galaxy's root."""
+        return self._in_root_dir(path)
+
     def _set_config_base(self, config_kwargs):
 
         def _set_global_conf():
@@ -245,17 +249,23 @@ class BaseAppConfiguration(object):
         for key in self.schema.paths_to_resolve:
             resolve(key)
 
+    def _in_root_dir(self, path):
+        return self._in_dir(self.root, path)
+
     def _in_managed_config_dir(self, path):
-        return os.path.join(self.managed_config_dir, path)
+        return self._in_dir(self.managed_config_dir, path)
 
     def _in_config_dir(self, path):
-        return os.path.join(self.config_dir, path)
+        return self._in_dir(self.config_dir, path)
 
     def _in_sample_dir(self, path):
-        return os.path.join(self.sample_config_dir, path)
+        return self._in_dir(self.sample_config_dir, path)
 
     def _in_data_dir(self, path):
-        return os.path.join(self.data_dir, path)
+        return self._in_dir(self.data_dir, path)
+
+    def _in_dir(self, _dir, path):
+        return os.path.join(_dir, path) if path else None
 
     def _parse_config_file_options(self, defaults, listify_defaults, config_kwargs):
         for var, values in defaults.items():
@@ -291,7 +301,47 @@ class BaseAppConfiguration(object):
             setattr(self, var, [os.path.join(self.root, x) for x in paths])
 
 
-class GalaxyAppConfiguration(BaseAppConfiguration):
+class CommonConfigurationMixin(object):
+    """Shared configuration settings code for Galaxy and ToolShed."""
+
+    @property
+    def admin_users(self):
+        return self._admin_users
+
+    @admin_users.setter
+    def admin_users(self, value):
+        self._admin_users = value
+        if value:
+            self.admin_users_list = [u.strip() for u in value.split(',') if u]
+        else:  # provide empty list for convenience (check membership, etc.)
+            self.admin_users_list = []
+
+    def is_admin_user(self, user):
+        """Determine if the provided user is listed in `admin_users`."""
+        return user is not None and user.email in self.admin_users_list
+
+    @property
+    def sentry_dsn_public(self):
+        """
+        Sentry URL with private key removed for use in client side scripts,
+        sentry server will need to be configured to accept events
+        """
+        if self.sentry_dsn:
+            return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
+
+    def get_bool(self, key, default):
+        # Warning: the value of self.config_dict['foo'] may be different from self.foo
+        if key in self.config_dict:
+            return string_as_bool(self.config_dict[key])
+        else:
+            return default
+
+    def get(self, key, default=None):
+        # Warning: the value of self.config_dict['foo'] may be different from self.foo
+        return self.config_dict.get(key, default)
+
+
+class GalaxyAppConfiguration(BaseAppConfiguration, CommonConfigurationMixin):
     deprecated_options = ('database_file', 'track_jobs_in_database')
     default_config_file_name = 'galaxy.yml'
     deprecated_dirs = {'config_dir': 'config', 'data_dir': 'database'}
@@ -317,12 +367,11 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         # Database related configuration
         self.check_migrate_databases = kwargs.get('check_migrate_databases', True)
         if not self.database_connection:  # Provide default if not supplied by user
-            db_path = os.path.join(self.data_dir, 'universe.sqlite')
+            db_path = self._in_data_dir('universe.sqlite')
             self.database_connection = 'sqlite:///%s?isolation_level=IMMEDIATE' % db_path
         self.database_engine_options = get_database_engine_options(kwargs)
         self.database_create_tables = string_as_bool(kwargs.get('database_create_tables', 'True'))
         self.database_encoding = kwargs.get('database_encoding')  # Create new databases with this encoding
-        self.database_log_query_counts = string_as_bool(kwargs.get("database_log_query_counts", 'False'))
         self.thread_local_log = None
         if self.enable_per_request_sql_debugging:
             self.thread_local_log = threading.local()
@@ -334,10 +383,10 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             tempfile.tempdir = self.new_file_path
         self.shared_home_dir = kwargs.get("shared_home_dir")
         self.cookie_path = kwargs.get("cookie_path")
-        self.tool_path = os.path.join(self.root, self.tool_path)
-        self.tool_data_path = os.path.join(self.root, self.tool_data_path)
+        self.tool_path = self._in_root_dir(self.tool_path)
+        self.tool_data_path = self._in_root_dir(self.tool_data_path)
         if not running_from_source and kwargs.get("tool_data_path") is None:
-            self.tool_data_path = os.path.join(self.data_dir, "tool-data")
+            self.tool_data_path = self._in_data_dir(self.schema.defaults['tool_data_path'])
         self.builds_file_path = os.path.join(self.tool_data_path, self.builds_file_path)
         self.len_file_path = os.path.join(self.tool_data_path, self.len_file_path)
         # Galaxy OIDC settings.
@@ -347,7 +396,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         self.integrated_tool_panel_config = self._in_managed_config_dir(self.integrated_tool_panel_config)
         integrated_tool_panel_tracking_directory = kwargs.get('integrated_tool_panel_tracking_directory')
         if integrated_tool_panel_tracking_directory:
-            self.integrated_tool_panel_tracking_directory = os.path.join(self.root, integrated_tool_panel_tracking_directory)
+            self.integrated_tool_panel_tracking_directory = self._in_root_dir(integrated_tool_panel_tracking_directory)
         else:
             self.integrated_tool_panel_tracking_directory = None
         self.toolbox_filter_base_modules = listify(self.toolbox_filter_base_modules)
@@ -363,7 +412,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         self.password_expiration_period = timedelta(days=int(self.password_expiration_period))
 
         if self.shed_tool_data_path:
-            self.shed_tool_data_path = os.path.join(self.root, self.shed_tool_data_path)
+            self.shed_tool_data_path = self._in_root_dir(self.shed_tool_data_path)
         else:
             self.shed_tool_data_path = self.tool_data_path
 
@@ -398,21 +447,21 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             for ip in kwargs.get("fetch_url_whitelist", "").split(',')
             if len(ip.strip()) > 0
         ]
-        self.template_path = os.path.join(self.root, kwargs.get("template_path", "templates"))
+        self.template_path = self._in_root_dir(kwargs.get("template_path", "templates"))
         self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5"))
-        self.cluster_files_directory = self.resolve_path(self.cluster_files_directory)
+        self.cluster_files_directory = self._in_root_dir(self.cluster_files_directory)
 
         # Fall back to legacy job_working_directory config variable if set.
-        self.jobs_directory = os.path.join(self.data_dir, kwargs.get("jobs_directory", self.job_working_directory))
+        self.jobs_directory = self._in_data_dir(kwargs.get("jobs_directory", self.job_working_directory))
         if self.preserve_python_environment not in ["legacy_only", "legacy_and_local", "always"]:
             log.warning("preserve_python_environment set to unknown value [%s], defaulting to legacy_only")
             self.preserve_python_environment = "legacy_only"
         self.nodejs_path = kwargs.get("nodejs_path")
         # Older default container cache path, I don't think anyone is using it anymore and it wasn't documented - we
         # should probably drop the backward compatiblity to save the path check.
-        self.container_image_cache_path = os.path.join(self.data_dir, kwargs.get("container_image_cache_path", "container_images"))
+        self.container_image_cache_path = self._in_data_dir(kwargs.get("container_image_cache_path", "container_images"))
         if not os.path.exists(self.container_image_cache_path):
-            self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", os.path.join(self.data_dir, "container_cache")))
+            self.container_image_cache_path = self._in_root_dir(kwargs.get("container_image_cache_path", self._in_data_dir("container_cache")))
         self.output_size_limit = int(kwargs.get('output_size_limit', 0))
         # activation_email was used until release_15.03
         activation_email = kwargs.get('activation_email')
@@ -421,7 +470,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         #  Get the disposable email domains blacklist file and its contents
         self.blacklist_content = None
         if self.blacklist_file:
-            self.blacklist_file = os.path.join(self.root, self.blacklist_file)
+            self.blacklist_file = self._in_root_dir(self.blacklist_file)
             try:
                 with open(self.blacklist_file) as f:
                     self.blacklist_content = [line.rstrip() for line in f]
@@ -449,7 +498,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             workflow_resource_params_mapper = None
         elif ":" not in workflow_resource_params_mapper:
             # Assume it is not a Python function, so a file
-            workflow_resource_params_mapper = self.resolve_path(workflow_resource_params_mapper)
+            workflow_resource_params_mapper = self._in_root_dir(workflow_resource_params_mapper)
         # else: a Python a function!
         self.workflow_resource_params_mapper = workflow_resource_params_mapper
 
@@ -460,7 +509,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
 
         _sanitize_whitelist_path = self._in_managed_config_dir(self.sanitize_whitelist_file)
         if not os.path.isfile(_sanitize_whitelist_path):  # then check old default location
-            deprecated = os.path.join(self.root, 'config/sanitize_whitelist.txt')
+            deprecated = self._in_root_dir('config/sanitize_whitelist.txt')
             if os.path.isfile(deprecated):
                 log.warning("The path '%s' for the 'sanitize_whitelist_file' config option is "
                     "deprecated and will be no longer checked in a future release. Please consult "
@@ -488,29 +537,26 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         # not needed on production systems but useful if running many functional tests.
         self.index_tool_help = string_as_bool(kwargs.get("index_tool_help", True))
         self.tool_labels_boost = kwargs.get("tool_labels_boost", 1)
-        default_tool_test_data_directories = os.environ.get("GALAXY_TEST_FILE_DIR", os.path.join(self.root, "test-data"))
+        default_tool_test_data_directories = os.environ.get("GALAXY_TEST_FILE_DIR", self._in_root_dir("test-data"))
         self.tool_test_data_directories = kwargs.get("tool_test_data_directories", default_tool_test_data_directories)
         # Deployers may either specify a complete list of mapping files or get the default for free and just
         # specify a local mapping file to adapt and extend the default one.
         if "conda_mapping_files" not in kwargs:
-            conda_mapping_files = [
-                self.local_conda_mapping_file,
-                os.path.join(self.root, "lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"),
-            ]
+            _default_mapping = self._in_root_dir(os.path.join("lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"))
             # dependency resolution options are consumed via config_dict - so don't populate
             # self, populate config_dict
-            self.config_dict["conda_mapping_files"] = conda_mapping_files
+            self.config_dict["conda_mapping_files"] = [self.local_conda_mapping_file, _default_mapping]
 
         if self.containers_resolvers_config_file:
-            self.containers_resolvers_config_file = os.path.join(self.config_dir, self.containers_resolvers_config_file)
+            self.containers_resolvers_config_file = self._in_config_dir(self.containers_resolvers_config_file)
 
         # tool_dependency_dir can be "none" (in old configs). If so, set it to None
         if self.tool_dependency_dir and self.tool_dependency_dir.lower() == 'none':
             self.tool_dependency_dir = None
         if self.involucro_path is None:
             target_dir = self.tool_dependency_dir or self.schema.defaults['tool_dependency_dir']
-            self.involucro_path = os.path.join(self.data_dir, target_dir, "involucro")
-        self.involucro_path = os.path.join(self.root, self.involucro_path)
+            self.involucro_path = self._in_data_dir(os.path.join(target_dir, "involucro"))
+        self.involucro_path = self._in_root_dir(self.involucro_path)
         if self.mulled_channels:
             self.mulled_channels = [c.strip() for c in self.mulled_channels.split(',')]
 
@@ -524,18 +570,12 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             self.nginx_upload_store = os.path.abspath(self.nginx_upload_store)
         self.object_store = kwargs.get('object_store', 'disk')
         self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False))
-        self.object_store_cache_path = self.resolve_path(kwargs.get("object_store_cache_path", os.path.join(self.data_dir, "object_store_cache")))
-        object_store_store_by = kwargs.get('object_store_store_by', None)
-        if object_store_store_by is None:
-            if not self.file_path_set:
-                if self.file_path.endswith('objects'):
-                    object_store_store_by = 'uuid'
-                else:
-                    object_store_store_by = 'id'
-            else:
-                object_store_store_by = 'id'
-        assert object_store_store_by in ['id', 'uuid'], "Invalid value for object_store_store_by [%s]" % object_store_store_by
-        self.object_store_store_by = object_store_store_by
+        self.object_store_cache_path = self._in_root_dir(kwargs.get("object_store_cache_path", self._in_data_dir("object_store_cache")))
+        if self.object_store_store_by is None:
+            self.object_store_store_by = 'id'
+            if not self.file_path_set and self.file_path.endswith('objects'):
+                self.object_store_store_by = 'uuid'
+        assert self.object_store_store_by in ['id', 'uuid'], "Invalid value for object_store_store_by [%s]" % self.object_store_store_by
         # Handle AWS-specific config options for backward compatibility
         if kwargs.get('aws_access_key') is not None:
             self.os_access_key = kwargs.get('aws_access_key')
@@ -554,7 +594,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         self.object_store_cache_size = float(kwargs.get('object_store_cache_size', -1))
         self.distributed_object_store_config_file = kwargs.get('distributed_object_store_config_file')
         if self.distributed_object_store_config_file is not None:
-            self.distributed_object_store_config_file = os.path.join(self.root, self.distributed_object_store_config_file)
+            self.distributed_object_store_config_file = self._in_root_dir(self.distributed_object_store_config_file)
         self.irods_root_collection_path = kwargs.get('irods_root_collection_path')
         self.irods_default_resource = kwargs.get('irods_default_resource')
         # Heartbeat log file name override
@@ -600,7 +640,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         elif 'database_connection' in kwargs:
             self.amqp_internal_connection = "sqlalchemy+" + self.database_connection
         else:
-            self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % os.path.join(self.data_dir, "control.sqlite")
+            self.amqp_internal_connection = "sqlalchemy+sqlite:///%s?isolation_level=IMMEDIATE" % self._in_data_dir("control.sqlite")
         self.pretty_datetime_format = expand_pretty_datetime_format(self.pretty_datetime_format)
         try:
             with open(self.user_preferences_extra_conf_path, 'r') as stream:
@@ -617,7 +657,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         # This is for testing new library browsing capabilities.
         self.new_lib_browse = string_as_bool(kwargs.get('new_lib_browse', False))
         # Logging configuration with logging.config.configDict:
-        self.logging = kwargs.get('logging')
         # Statistics and profiling with statsd
         self.statsd_host = kwargs.get('statsd_host', '')
 
@@ -630,8 +669,9 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
         self.manage_dynamic_proxy = self.dynamic_proxy_manage  # Set to false if being launched externally
 
         # InteractiveTools propagator mapping file
-        self.interactivetool_map = self.resolve_path(kwargs.get("interactivetools_map", os.path.join(self.data_dir, "interactivetools_map.sqlite")))
+        self.interactivetools_map = self._in_root_dir(kwargs.get("interactivetools_map", self._in_data_dir("interactivetools_map.sqlite")))
         self.interactivetool_prefix = kwargs.get("interactivetools_prefix", "interactivetool")
+        self.interactivetool_proxy_host = kwargs.get("interactivetool_proxy_host", None)
 
         self.containers_conf = parse_containers_config(self.containers_config_file)
 
@@ -708,33 +748,8 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
                 'UWSGI_PORT': port
             })
 
-    @property
-    def admin_users(self):
-        return self._admin_users
-
-    @admin_users.setter
-    def admin_users(self, value):
-        self._admin_users = value
-        if value:
-            self.admin_users_list = [u.strip() for u in value.split(',') if u]
-        else:  # provide empty list for convenience (check membership, etc.)
-            self.admin_users_list = []
-
-    @property
-    def sentry_dsn_public(self):
-        """
-        Sentry URL with private key removed for use in client side scripts,
-        sentry server will need to be configured to accept events
-        """
-        if self.sentry_dsn:
-            return re.sub(r"^([^:/?#]+:)?//(\w+):(\w+)", r"\1//\2", self.sentry_dsn)
-        else:
-            return None
-
     def parse_config_file_options(self, kwargs):
-        """
-        Backwards compatibility for config files moved to the config/ dir.
-        """
+        """Backwards compatibility for config files moved to the config/ dir."""
         defaults = dict(
             auth_config_file=[self._in_config_dir('auth_conf.xml')],
             build_sites_config_file=[self._in_config_dir('build_sites.yml'), self._in_sample_dir('build_sites.yml.sample')],
@@ -792,15 +807,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             if explicit:
                 log.warning("Sanitize log file explicitly specified as '%s' but does not exist, continuing with no tools whitelisted.", self.sanitize_whitelist_file)
 
-    def get(self, key, default=None):
-        return self.config_dict.get(key, default)
-
-    def get_bool(self, key, default):
-        if key in self.config_dict:
-            return string_as_bool(self.config_dict[key])
-        else:
-            return default
-
     def ensure_tempdir(self):
         self._ensure_directory(self.new_file_path)
 
@@ -838,20 +844,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration):
             if key in self.deprecated_options:
                 log.warning("Config option '%s' is deprecated and will be removed in a future release.  Please consult the latest version of the sample configuration file." % key)
 
-    def is_admin_user(self, user):
-        """
-        Determine if the provided user is listed in `admin_users`.
-
-        NOTE: This is temporary, admin users will likely be specified in the
-              database in the future.
-        """
-        return user is not None and user.email in self.admin_users_list
-
-    def resolve_path(self, path):
-        """ Resolve a path relative to Galaxy's root.
-        """
-        return os.path.join(self.root, path)
-
     @staticmethod
     def _parse_allowed_origin_hostnames(kwargs):
         """
@@ -877,7 +869,7 @@ Configuration = GalaxyAppConfiguration
 
 
 def reload_config_options(current_config):
-    """ Reload modified reloadable config options """
+    """Reload modified reloadable config options."""
     modified_config = read_properties_from_file(current_config.config_file)
     for option in current_config.schema.reloadable_options:
         if option in modified_config:
@@ -978,8 +970,7 @@ def configure_logging(config):
 
 
 class ConfiguresGalaxyMixin(object):
-    """ Shared code for configuring Galaxy-like app objects.
-    """
+    """Shared code for configuring Galaxy-like app objects."""
 
     def _configure_genome_builds(self, data_table_name="__dbkeys__", load_old_style=True):
         self.genome_builds = GenomeBuilds(self, data_table_name=data_table_name, load_old_style=load_old_style)
@@ -1116,9 +1107,7 @@ class ConfiguresGalaxyMixin(object):
             self.tool_shed_registry = galaxy.tool_shed.tool_shed_registry.Registry()
 
     def _configure_models(self, check_migrate_databases=False, check_migrate_tools=False, config_file=None):
-        """
-        Preconditions: object_store must be set on self.
-        """
+        """Preconditions: object_store must be set on self."""
         db_url = get_database_url(self.config)
         install_db_url = self.config.install_database_connection
         # TODO: Consider more aggressive check here that this is not the same

lib/galaxy/config/sample/datatypes_conf.xml.sample

@@ -17,6 +17,8 @@
     <datatype extension="anvio_structure_db" type="galaxy.datatypes.anvio:AnvioStructureDB" display_in_upload="false" />
     <datatype extension="anvio_variability" type="galaxy.datatypes.tabular:TSV" display_in_upload="false" subclass="true" />
     <datatype extension="arff" type="galaxy.datatypes.text:Arff" mimetype="text/plain" display_in_upload="true"/>
+    <datatype extension="paf" type="galaxy.datatypes.text:Paf" mimetype="text/plain" display_in_upload="true"/>
+    <datatype extension="gfa1" type="galaxy.datatypes.text:Gfa1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1" type="galaxy.datatypes.data:GenericAsn1" mimetype="text/plain" display_in_upload="true"/>
     <datatype extension="asn1-binary" type="galaxy.datatypes.binary:GenericAsn1Binary" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format.  Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines.  Blocks are separated from one another by blank lines.  The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
@@ -228,19 +230,27 @@
     <datatype extension="directory" type="galaxy.datatypes.data:Directory">
     </datatype>
     <!-- Proteomics Datatypes -->
+    <datatype extension="mrm" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true" subclass="true"/>
+    <datatype extension="dta" type="galaxy.datatypes.proteomics:Dta" display_in_upload="true" />
+    <datatype extension="dta2d" type="galaxy.datatypes.proteomics:Dta2d" display_in_upload="true" />
+    <datatype extension="edta" type="galaxy.datatypes.proteomics:Edta" display_in_upload="true" />
     <datatype extension="pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="raw_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="peptideprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="interprophet_pepxml" type="galaxy.datatypes.proteomics:PepXml" mimetype="application/xml" subclass="true"/>
     <datatype extension="protxml" type="galaxy.datatypes.proteomics:ProtXML" mimetype="application/xml" display_in_upload="true"/>
-    <datatype extension="trafoxml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Transformation of retention times"/>
+    <datatype extension="paramxml" type="galaxy.datatypes.proteomics:ParamXml" mimetype="application/xml" subclass="true" display_in_upload="true" />
     <datatype extension="qcml" type="galaxy.datatypes.xml:GenericXml" mimetype="application/xml" subclass="true" display_in_upload="true" description="Quality control data in XML format (https://code.google.com/p/qcml/)."/>
+    <datatype extension="kroenik" type="galaxy.datatypes.proteomics:Kroenik" display_in_upload="true"/>
+    <datatype extension="peplist" type="galaxy.datatypes.proteomics:PepList" display_in_upload="true"/>
+    <datatype extension="psms" type="galaxy.datatypes.proteomics:PSMS" display_in_upload="true"/>
     <datatype extension="pepxml.tsv" type="galaxy.datatypes.proteomics:PepXmlReport" display_in_upload="true"/>
     <datatype extension="protxml.tsv" type="galaxy.datatypes.proteomics:ProtXmlReport" display_in_upload="true"/>
     <datatype extension="mascotdat" type="galaxy.datatypes.proteomics:MascotDat" display_in_upload="false"/>
     <datatype extension="mzid" type="galaxy.datatypes.proteomics:MzIdentML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="idxml" type="galaxy.datatypes.proteomics:IdXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="tandem" type="galaxy.datatypes.proteomics:TandemXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="sirius.ms" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="false"/>
     <datatype extension="thermo.raw" type="galaxy.datatypes.proteomics:ThermoRAW" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="brukerbaf.d.tar" type="galaxy.datatypes.binary:BafTar" display_in_upload="true"/>
     <datatype extension="agilentbrukeryep.d.tar" type="galaxy.datatypes.binary:YepTar" display_in_upload="true"/>
@@ -248,6 +258,9 @@
     <datatype extension="agilentmasshunter.d.tar" type="galaxy.datatypes.binary:MassHunterTar" display_in_upload="true"/>
     <datatype extension="watersmasslynx.raw.tar" type="galaxy.datatypes.binary:MassLynxTar" display_in_upload="true"/>
     <datatype extension="wiff.tar" type="galaxy.datatypes.binary:WiffTar" display_in_upload="true"/>
+    <datatype extension="mascotxml" type="galaxy.datatypes.proteomics:MascotXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="mztab" type="galaxy.datatypes.proteomics:MzTab" display_in_upload="true"/>
+    <datatype extension="mztab2" type="galaxy.datatypes.proteomics:MzTab2" display_in_upload="true"/>
     <datatype extension="mzml" type="galaxy.datatypes.proteomics:MzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="nmrml" type="galaxy.datatypes.proteomics:NmrML" mimetype="application/xml" display_in_upload="true" description="nmrML is an open mark-up language for NMR data." description_url="http://nmrml.org/schema/"/>
     <datatype extension="mgf" type="galaxy.datatypes.proteomics:Mgf" display_in_upload="true"/>
@@ -256,11 +269,18 @@
     <datatype extension="mzdata" type="galaxy.datatypes.proteomics:MzData" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true"/>
     <datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="mz.sqlite" type="galaxy.datatypes.binary:MzSQlite" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="osw" type="galaxy.datatypes.binary:OSW" mimetype="application/octet-stream" display_in_upload="true"/>
+    <datatype extension="pqp" type="galaxy.datatypes.binary:PQP" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="trafoxml" type="galaxy.datatypes.proteomics:TrafoXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="uniprotxml" type="galaxy.datatypes.proteomics:UniProtXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="xquest.xml" type="galaxy.datatypes.proteomics:XquestXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="spec.xml" type="galaxy.datatypes.proteomics:XquestSpecXML" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="qcml" type="galaxy.datatypes.proteomics:QCML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true"/>
     <datatype extension="splib_noindex" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true"/>
     <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true"/>
@@ -284,6 +304,7 @@
     <datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>
     <datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
     <datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
+    <datatype extension="peff" type="galaxy.datatypes.proteomics:PEFF" display_in_upload="true"/>
     <!-- End Proteomics Datatypes -->
     <datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
@@ -341,9 +362,7 @@
       <converter file="tabular_to_csv.xml" target_datatype="csv"/>
     </datatype>
     <datatype extension="twobit" type="galaxy.datatypes.binary:TwoBit" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="sqlite" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true"/>
-    <datatype extension="pqp" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
-    <datatype extension="osw" type="galaxy.datatypes.binary:SQlite" mimetype="application/octet-stream" display_in_upload="true" subclass="true"/>
+    <datatype extension="sqmass" type="galaxy.datatypes.binary:SQmass" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="gemini.sqlite" type="galaxy.datatypes.binary:GeminiSQLite" mimetype="application/octet-stream" display_in_upload="true"/>
     <datatype extension="cuffdiff.sqlite" type="galaxy.datatypes.binary:CuffDiffSQlite" display_in_upload="true"/>
     <datatype extension="gafa.sqlite" type="galaxy.datatypes.binary:GAFASQLite" mimetype="application/octet-stream" display_in_upload="true"/>
@@ -379,6 +398,7 @@
       <display file="igb/wig.xml"/>
     </datatype>
     <datatype extension="interval_index" type="galaxy.datatypes.binary:Binary" subclass="true"/>
+    <datatype extension="odgi" type="galaxy.datatypes.binary:Binary" subclass="true" description="Genomic variation graphs self index used by odgi."/>
     <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="bgzip" type="galaxy.datatypes.binary:Binary" subclass="true"/>
     <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">
@@ -798,7 +818,10 @@
     <sniffer type="galaxy.datatypes.tabular:Vcf"/>
     <sniffer type="galaxy.datatypes.binary:TwoBit"/>
     <sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
+    <sniffer type="galaxy.datatypes.binary:SQmass"/>
     <sniffer type="galaxy.datatypes.binary:MzSQlite"/>
+    <sniffer type="galaxy.datatypes.binary:OSW"/>
+    <sniffer type="galaxy.datatypes.binary:PQP"/>
     <sniffer type="galaxy.datatypes.binary:IdpDB"/>
     <sniffer type="galaxy.datatypes.binary:ElibSQlite"/>
     <sniffer type="galaxy.datatypes.binary:DlibSQlite"/>
@@ -840,27 +863,48 @@
     <sniffer type="galaxy.datatypes.binary:Cpt"/>
     <sniffer type="galaxy.datatypes.binary:Edr"/>
     <sniffer type="galaxy.datatypes.binary:Vel"/>
+    <sniffer type="galaxy.datatypes.binary:Xlsx"/>
+    <sniffer type="galaxy.datatypes.binary:CompressedZipArchive"/>
     <sniffer type="galaxy.datatypes.annotation:Augustus"/>
     <sniffer type="galaxy.datatypes.triples:Rdf"/>
     <sniffer type="galaxy.datatypes.blast:BlastXml"/>
     <sniffer type="galaxy.datatypes.xml:Phyloxml"/>
     <sniffer type="galaxy.datatypes.xml:Owl"/>
     <sniffer type="galaxy.datatypes.xml:Sbml"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzML"/>
-    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
-    <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:Dta2d"/>
+    <sniffer type="galaxy.datatypes.proteomics:Edta"/>
+    <sniffer type="galaxy.datatypes.proteomics:ConsensusXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:IdXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:FeatureXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MascotXML"/>
     <sniffer type="galaxy.datatypes.proteomics:Mgf"/>
-    <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzData"/>
-    <sniffer type="galaxy.datatypes.proteomics:TraML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
-    <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
-    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Ms2"/>
     <sniffer type="galaxy.datatypes.proteomics:Msp"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzData"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzIdentML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzQuantML"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzTab"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzTab2"/>
+    <sniffer type="galaxy.datatypes.proteomics:ParamXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:MzXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:NmrML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Kroenik"/>
+    <sniffer type="galaxy.datatypes.proteomics:PepList"/>
+    <sniffer type="galaxy.datatypes.proteomics:PSMS"/>
+    <sniffer type="galaxy.datatypes.proteomics:PepXml"/>
+    <sniffer type="galaxy.datatypes.proteomics:ProtXML"/>
     <sniffer type="galaxy.datatypes.proteomics:SPLib"/>
+    <sniffer type="galaxy.datatypes.proteomics:TandemXML"/>
     <sniffer type="galaxy.datatypes.proteomics:ThermoRAW"/>
+    <sniffer type="galaxy.datatypes.proteomics:TraML"/>
+    <sniffer type="galaxy.datatypes.proteomics:TrafoXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:UniProtXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:XquestXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:XquestSpecXML"/>
+    <sniffer type="galaxy.datatypes.proteomics:QCML"/>
+    <sniffer type="galaxy.datatypes.proteomics:Wiff"/>
+    <sniffer type="galaxy.datatypes.proteomics:PEFF"/>
     <sniffer type="galaxy.datatypes.molecules:CML"/>
     <sniffer type="galaxy.datatypes.xml:GenericXml"/>
     <sniffer type="galaxy.datatypes.triples:HDT"/>
@@ -897,6 +941,7 @@
     <sniffer type="galaxy.datatypes.interval:Gff"/>
     <sniffer type="galaxy.datatypes.interval:Gff3"/>
     <sniffer type="galaxy.datatypes.tabular:Pileup"/>
+    <sniffer type="galaxy.datatypes.text:Paf"/>
     <sniffer type="galaxy.datatypes.interval:Interval"/>
     <sniffer type="galaxy.datatypes.tabular:Sam"/>
     <sniffer type="galaxy.datatypes.data:Newick"/>

lib/galaxy/config/sample/galaxy.yml.sample

@@ -761,6 +761,13 @@ galaxy:
   # Enable InteractiveTools.
   #interactivetools_enable: false
 
+  # Proxy host - assumed to just be hosted on the same hostname and port
+  # as Galaxy by default.
+  #interactivetools_proxy_host: null
+
+  # Map for interactivetool proxy.
+  #interactivetools_map: interactivetools_map.sqlite
+
   # Show visualization tab and list in masthead.
   #visualizations_visible: true
 

lib/galaxy/config/sample/tool_conf.xml.sample

@@ -5,6 +5,7 @@
     <tool file="data_source/ucsc_tablebrowser.xml" />
     <!-- <tool file="data_source/ucsc_tablebrowser_test.xml" /> -->
     <tool file="data_source/ucsc_tablebrowser_archaea.xml" />
+    <tool file="data_source/sra.xml" />
     <tool file="data_source/ebi_sra.xml" />
     <tool file="data_source/fly_modencode.xml" />
     <tool file="data_source/intermine.xml" />

lib/galaxy/datatypes/binary.py

@@ -249,6 +249,16 @@ class CompressedZipArchive(CompressedArchive):
         except Exception:
             return "Compressed zip file (%s)" % (nice_size(dataset.get_size()))
 
+    def sniff(self, filename):
+        with zipfile.ZipFile(filename) as zf:
+            zf_files = zf.infolist()
+            count = 0
+            for f in zf_files:
+                if f.file_size > 0 and not f.filename.startswith('__MACOSX/') and not f.filename.endswith('.DS_Store'):
+                    count += 1
+                if count > 1:
+                    return True
+
 
 class GenericAsn1Binary(Binary):
     """Class for generic ASN.1 binary format"""
@@ -1571,6 +1581,91 @@ class MzSQlite(SQlite):
         return False
 
 
+class PQP(SQlite):
+    """
+    Class describing a Peptide query parameters file
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.pqp')
+    >>> PQP().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.osw')
+    >>> PQP().sniff(fname)
+    False
+    """
+    file_ext = "pqp"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(PQP, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        """
+        table definition according to https://github.com/grosenberger/OpenMS/blob/develop/src/openms/source/ANALYSIS/OPENSWATH/TransitionPQPFile.cpp#L264
+        for now VERSION GENE PEPTIDE_GENE_MAPPING are excluded, since
+        there is test data wo these tables, see also here https://github.com/OpenMS/OpenMS/issues/4365
+        """
+        if not super(PQP, self).sniff(filename):
+            return False
+        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
+                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
+                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING']
+        osw_table_names = ['FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return self.sniff_table_names(filename, table_names) and not self.sniff_table_names(filename, osw_table_names)
+
+
+class OSW(SQlite):
+    """
+    Class describing OpenSwath output
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.osw')
+    >>> OSW().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.sqmass')
+    >>> OSW().sniff(fname)
+    False
+    """
+    file_ext = "osw"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(OSW, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        # osw seems to be an extension of pqp (few tables are added)
+        # see also here https://github.com/OpenMS/OpenMS/issues/4365
+        if not super(OSW, self).sniff(filename):
+            return False
+        table_names = ['COMPOUND', 'PEPTIDE', 'PEPTIDE_PROTEIN_MAPPING', 'PRECURSOR',
+                       'PRECURSOR_COMPOUND_MAPPING', 'PRECURSOR_PEPTIDE_MAPPING', 'PROTEIN',
+                       'TRANSITION', 'TRANSITION_PEPTIDE_MAPPING', 'TRANSITION_PRECURSOR_MAPPING',
+                       'FEATURE', 'FEATURE_MS1', 'FEATURE_MS2', 'FEATURE_TRANSITION', 'RUN']
+        return self.sniff_table_names(filename, table_names)
+
+
+class SQmass(SQlite):
+    """
+    Class describing a Sqmass database
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.sqmass')
+    >>> SQmass().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.pqp')
+    >>> SQmass().sniff(fname)
+    False
+    """
+    file_ext = "sqmass"
+
+    def set_meta(self, dataset, overwrite=True, **kwd):
+        super(SQmass, self).set_meta(dataset, overwrite=overwrite, **kwd)
+
+    def sniff(self, filename):
+        if super(SQmass, self).sniff(filename):
+            table_names = ["CHROMATOGRAM", "PRECURSOR", "RUN", "SPECTRUM", "DATA", "PRODUCT", "RUN_EXTRA"]
+            return self.sniff_table_names(filename, table_names)
+        return False
+
+
 class BlibSQlite(SQlite):
     """Class describing a Proteomics Spectral Library Sqlite database """
     MetadataElement(name="blib_version", default='1.8', param=MetadataParameter, desc="Blib Version",

lib/galaxy/datatypes/proteomics.py

@@ -7,8 +7,9 @@ import re
 from galaxy.datatypes import data
 from galaxy.datatypes.binary import Binary
 from galaxy.datatypes.data import Text
+from galaxy.datatypes.sequence import Sequence
 from galaxy.datatypes.sniff import build_sniff_from_prefix
-from galaxy.datatypes.tabular import Tabular
+from galaxy.datatypes.tabular import Tabular, TabularData
 from galaxy.datatypes.xml import GenericXml
 from galaxy.util import nice_size
 
@@ -53,6 +54,221 @@ class Wiff(Binary):
         return "\n".join(rval)
 
 
+@build_sniff_from_prefix
+class MzTab(Text):
+    """
+    exchange format for proteomics and metabolomics results
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.mztab')
+    >>> MzTab().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.mztab2')
+    >>> MzTab().sniff(fname)
+    False
+    """
+    edam_data = "data_3681"
+    file_ext = "mztab"
+    # section names (except MTD)
+    _sections = ["PRH", "PRT", "PEH", "PEP", "PSH", "PSM", "SMH", "SML", "COM"]
+    # mandatory metadata fields and list of allowed entries (in lower case)
+    # (or None if everything is allowed)
+    _man_mtd = {"mzTab-mode": ["complete", "summary"],
+                "mzTab-type": ['quantification', 'identification'],
+                "description": None}
+    _version_re = r"(1)(\.[0-9])?(\.[0-9])?"
+
+    def __init__(self, **kwd):
+        super(MzTab, self).__init__(**kwd)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            dataset.blurb = 'mzTab Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff_prefix(self, file_prefix):
+        """ Determines whether the file is the correct type. """
+        has_version = False
+        found_man_mtd = set()
+        contents = file_prefix.string_io()
+        for line in contents:
+            if re.match(r"^\s*$", line):
+                continue
+            line = line.strip("\r\n").split("\t")
+            if line[0] == "MTD":
+                if line[1] == "mzTab-version" and re.match(self._version_re, line[2]) is not None:
+                    has_version = True
+                elif line[1] in self._man_mtd and (self._man_mtd[line[1]] is None or line[2].lower() in self._man_mtd[line[1]]):
+                    found_man_mtd.add(line[1])
+            elif not line[0] in self._sections:
+                return False
+        return has_version and found_man_mtd == set(self._man_mtd.keys())
+
+
+class MzTab2(MzTab):
+    """
+    exchange format for proteomics and metabolomics results
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.mztab2')
+    >>> MzTab2().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.mztab')
+    >>> MzTab2().sniff(fname)
+    False
+    """
+    file_ext = "mztab2"
+    _sections = ["SMH", "SML", "SFH", "SMF", "SEH", "SME", "COM"]
+    _version_re = r"(2)(\.[0-9])?(\.[0-9])?-M$"
+    _man_mtd = {"mzTab-ID": None}
+
+    def __init__(self, **kwd):
+        super(MzTab2, self).__init__(**kwd)
+
+    def set_peek(self, dataset, is_multi_byte=False):
+        """Set the peek and blurb text"""
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek(dataset.file_name)
+            dataset.blurb = 'mzTab2 Format'
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+
+@build_sniff_from_prefix
+class Kroenik(Tabular):
+    """
+    Kroenik (HardKloer sibling) files
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.kroenik')
+    >>> Kroenik().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.peplist')
+    >>> Kroenik().sniff(fname)
+    False
+    """
+    file_ext = "kroenik"
+
+    def __init__(self, **kwd):
+        super(Kroenik, self).__init__(**kwd)
+        self.column_names = ["File", "First Scan", "Last Scan", "Num of Scans", "Charge", "Monoisotopic Mass", "Base Isotope Peak", "Best Intensity", "Summed Intensity", "First RTime", "Last RTime", "Best RTime", "Best Correlation", "Modifications"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if line != self.column_names:
+            return False
+        line = fh.readline().split("\t")
+        try:
+            [int(_) for _ in line[1:5]]
+            [float(_) for _ in line[5:13]]
+        except ValueError:
+            return False
+        return True
+
+
+@build_sniff_from_prefix
+class PepList(Tabular):
+    """
+    Peplist file as used in OpenMS
+    https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L432
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.peplist')
+    >>> PepList().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.psms')
+    >>> PepList().sniff(fname)
+    False
+    """
+    file_ext = "peplist"
+
+    def __init__(self, **kwd):
+        super(PepList, self).__init__(**kwd)
+        self.column_names = ["m/z", "rt(min)", "snr", "charge", "intensity"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if line == self.column_names:
+            return True
+        return False
+
+
+@build_sniff_from_prefix
+class PSMS(Tabular):
+    """
+    Percolator tab-delimited output (PSM level, .psms) as used in OpenMS
+    https://github.com/OpenMS/OpenMS/blob/0fc8765670a0ad625c883f328de60f738f7325a4/src/openms/source/FORMAT/FileHandler.cpp#L453
+    see also http://www.kojak-ms.org/docs/percresults.html
+
+    Note that the data rows can have more columns than the header line
+    since ProteinIds are listed tab-separated.
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.psms')
+    >>> PSMS().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.kroenik')
+    >>> PSMS().sniff(fname)
+    False
+    """
+    file_ext = "psms"
+
+    def __init__(self, **kwd):
+        super(PSMS, self).__init__(**kwd)
+        self.column_names = ["PSMId", "score", "q-value", "posterior_error_prob", "peptide", "proteinIds"]
+
+    def display_peek(self, dataset):
+        """Returns formated html of peek"""
+        return self.make_html_table(dataset, column_names=self.column_names)
+
+    def sniff_prefix(self, file_prefix):
+        fh = file_prefix.string_io()
+        line = [_.strip() for _ in fh.readline().split("\t")]
+        if line == self.column_names:
+            return True
+        return False
+
+
+@build_sniff_from_prefix
+class PEFF(Sequence):
+    """
+    PSI Extended FASTA Format
+    https://github.com/HUPO-PSI/PEFF
+    """
+    file_ext = "peff"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname( 'test.peff' )
+        >>> PEFF().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'sequence.fasta' )
+        >>> PEFF().sniff( fname )
+        False
+        """
+        fh = file_prefix.string_io()
+        if re.match(r"# PEFF \d+.\d+", fh.readline()):
+            return True
+        else:
+            return False
+
+
 class PepXmlReport(Tabular):
     """pepxml converted to tabular report"""
     edam_data = "data_2536"
@@ -92,6 +308,277 @@ class ProtXmlReport(Tabular):
         return self.make_html_table(dataset, column_names=self.column_names)
 
 
+class Dta(TabularData):
+    """dta
+    The first line contains the singly protonated peptide mass (MH+) and the
+    peptide charge state separated by a space. Subsequent lines contain space
+    separated pairs of fragment ion m/z and intensity values.
+    """
+    file_ext = "dta"
+    comment_lines = 0
+
+    def set_meta(self, dataset, **kwd):
+        column_types = []
+        data_row = []
+        data_lines = 0
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for line in dtafile:
+                    data_lines += 1
+
+        # Guess column types
+        for cell in data_row:
+            column_types.append(self.guess_type(cell))
+
+        # Set metadata
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.column_types = ['float', 'float']
+        dataset.metadata.columns = 2
+        dataset.metadata.column_names = ['m/z', 'intensity']
+        dataset.metadata.delimiter = " "
+
+
+@build_sniff_from_prefix
+class Dta2d(TabularData):
+    """
+    dta2d: files with three tab/space-separated columns.
+    The default format is: retention time (seconds) , m/z , intensity.
+    If the first line starts with '#', a different order is defined by the the
+    order of the keywords 'MIN' (retention time in minutes) or 'SEC' (retention
+    time in seconds), 'MZ', and 'INT'.
+    Example: '#MZ MIN INT'
+    The peaks of one retention time have to be in subsequent lines.
+
+    Note: sniffer detects (tab or space separated) dta2d files with correct
+    header, wo header seems to generic
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.dta2d')
+    >>> Dta2d().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.edta')
+    >>> Dta2d().sniff(fname)
+    False
+    """
+    file_ext = "dta2d"
+    comment_lines = 0
+
+    def _parse_header(self, line):
+        if len(line) != 3 or len(line[0]) < 3 or not line[0].startswith("#"):
+            return None
+        line[0] = line[0].lstrip("#")
+        line = [_.strip() for _ in line]
+        if 'MZ' not in line or 'INT' not in line or ('MIN' not in line and 'SEC' not in line):
+            return None
+        return line
+
+    def _parse_delimiter(self, line):
+        if len(line.split(" ")) == 3:
+            return " "
+        elif len(line.split("\t")) == 3:
+            return "\t"
+        return None
+
+    def _parse_dataline(self, line):
+        try:
+            line = [float(_) for _ in line]
+        except ValueError:
+            return False
+        if not all(_ >= 0 for _ in line):
+            return False
+        return True
+
+    def set_meta(self, dataset, **kwd):
+        data_lines = 0
+        delim = None
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for line in dtafile:
+                    if delim is None:
+                        delim = self._parse_delimiter(line)
+                        dataset.metadata.column_names = self._parse_header(line.split(delim))
+                    data_lines += 1
+
+        # Set metadata
+        if delim is not None:
+            dataset.metadata.delimiter = delim
+
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.column_types = ['float', 'float', 'float']
+        dataset.metadata.columns = 3
+        if dataset.metadata.column_names is None or dataset.metadata.column_names == []:
+            dataset.metadata.comment_lines += 1
+            dataset.metadata.data_lines -= 1
+            dataset.metadata.column_names = ['SEC', 'MZ', 'INT']
+
+    def sniff_prefix(self, file_prefix):
+        sep = None
+        header = None
+        for idx, line in enumerate(file_prefix.line_iterator()):
+            line = line.strip()
+            if sep is None:
+                sep = self._parse_delimiter(line)
+                if sep is None:
+                    return False
+            line = line.split(sep)
+            if len(line) != 3:
+                return False
+            if idx == 0:
+                header = self._parse_header(line)
+                if (header is None) and not self._parse_dataline(line):
+                    return False
+            elif not self._parse_dataline(line):
+                return False
+        if sep is None or header is None:
+            return False
+        return True
+
+
+@build_sniff_from_prefix
+class Edta(TabularData):
+    """
+    Input text file containing tab, space or comma separated columns.
+    The separator between columns is checked in the first line in this order.
+
+    It supports three variants of this format.
+
+    1. Columns are: RT, MZ, Intensity A header is optional.
+    2. Columns are: RT, MZ, Intensity, Charge, <Meta-Data> columns{0,} A header is mandatory.
+    3. Columns are: (RT, MZ, Intensity, Charge){1,}, <Meta-Data> columns{0,}
+       Header is mandatory. First quadruplet is the consensus. All following
+       quadruplets describe the sub-features. This variant is discerned from
+       variant #2 by the name of the fifth column, which is required to be RT1
+       (or rt1). All other column names for sub-features are faithfully ignored.
+
+    Note the sniffer only detects files with header.
+
+    >>> from galaxy.datatypes.sniff import get_test_fname
+    >>> fname = get_test_fname('test.edta')
+    >>> Edta().sniff(fname)
+    True
+    >>> fname = get_test_fname('test.dta2d')
+    >>> Edta().sniff(fname)
+    False
+    """
+    file_ext = "edta"
+    comment_lines = 0
+
+    def _parse_delimiter(self, line):
+        if len(line.split(" ")) >= 3:
+            return " "
+        elif len(line.split("\t")) >= 3:
+            return "\t"
+        elif len(line.split(",")) >= 3:
+            return "\t"
+        return None
+
+    def _parse_type(self, line):
+        """
+        parse the type from the header line
+        types 1-3 as in the class docs, 0: type 1 wo/wrong header
+        """
+        if len(line) < 3:
+            return None
+        line = [_.lower().replace("/", "") for _ in line]
+        if len(line) == 3:
+            if line[0] == "rt" and line[1] == "mz" and (line[2] == "int" or line[2] == "intensity"):
+                return 1
+            else:
+                return None
+        if line[0] != "rt" or line[1] != "mz" or (line[2] != "int" and line[2] != "intensity") or line[3] != "charge":
+            return None
+        if not line[4].startswith("rt"):
+            return 2
+        else:
+            return 3
+
+    def _parse_dataline(self, line, tpe):
+        if tpe == 2 or tpe == 3:
+            idx = 4
+        else:
+            idx = 3
+        try:
+            line = [float(_) for _ in line[:idx]]
+        except ValueError:
+            return False
+        if not all(_ >= 0 for _ in line[:idx]):
+            return False
+        return True
+
+    def _clean_header(self, line):
+        for idx, el in enumerate(line):
+            el = el.lower()
+            if el.startswith("rt"):
+                line[idx] = "RT"
+            elif el.startswith("int"):
+                line[idx] = "intensity"
+            elif el.startswith("mz"):
+                line[idx] = "m/z"
+            elif el.startswith("charge"):
+                line[idx] = "charge"
+            else:
+                break
+            if idx // 4 > 0:
+                line[idx] += str(idx // 4)
+        return line
+
+    def set_meta(self, dataset, **kwd):
+        data_lines = 0
+        delim = None
+        if dataset.has_data():
+            with open(dataset.file_name, 'r') as dtafile:
+                for idx, line in enumerate(dtafile):
+                    if idx == 0:
+                        delim = self._parse_delimiter(line)
+                        tpe = self._parse_type(line.split(delim))
+                        if tpe == 0:
+                            dataset.metadata.column_names = ["RT", "m/z", "intensity"]
+                        else:
+                            dataset.metadata.column_names = self._clean_header(line.split(delim))
+                    data_lines += 1
+
+        # Set metadata
+        if delim is not None:
+            dataset.metadata.delimiter = delim
+        for c in dataset.metadata.column_names:
+            if any(c.startswith(_) for _ in ["RT", "m/z", "intensity", "charge"]):
+                dataset.metadata.column_types.append("float")
+            else:
+                dataset.metadata.column_types.append("str")
+
+        dataset.metadata.data_lines = data_lines
+        dataset.metadata.comment_lines = 0
+        dataset.metadata.columns = len(dataset.metadata.column_names)
+        if tpe > 0:
+            dataset.metadata.comment_lines += 1
+            dataset.metadata.data_lines -= 1
+
+    def sniff_prefix(self, file_prefix):
+        sep = None
+        tpe = None
+        for idx, line in enumerate(file_prefix.line_iterator()):
+            line = line.strip("\r\n")
+            if sep is None:
+                sep = self._parse_delimiter(line)
+                if sep is None:
+                    return False
+            line = line.split(sep)
+
+            if idx == 0:
+                tpe = self._parse_type(line)
+                if tpe is None:
+                    return False
+                elif tpe == 0 and not self._parse_dataline(line, tpe):
+                    return False
+            elif not self._parse_dataline(line, tpe):
+                return False
+        if tpe is None:
+            return False
+        return True
+
+
 class ProteomicsXml(GenericXml):
     """ An enhanced XML datatype used to reuse code across several
     proteomic/mass-spec datatypes. """
@@ -102,12 +589,12 @@ class ProteomicsXml(GenericXml):
         """ Determines whether the file is the correct XML type. """
         contents = file_prefix.string_io()
         while True:
-            line = contents.readline()
+            line = contents.readline().strip()
             if line is None or not line.startswith('<?'):
                 break
         # pattern match <root or <ns:root for any ns string
-        pattern = r'^<(\w*:)?%s' % self.root
-        return line is not None and re.match(pattern, line) is not None
+        pattern = r'<(\w*:)?%s' % self.root
+        return line is not None and re.search(pattern, line) is not None
 
     def set_peek(self, dataset, is_multi_byte=False):
         """Set the peek and blurb text"""
@@ -119,6 +606,13 @@ class ProteomicsXml(GenericXml):
             dataset.blurb = 'file purged from disk'
 
 
+class ParamXml(ProteomicsXml):
+    """store Parameters in XML formal"""
+    file_ext = "paramxml"
+    blurb = "parameters in xmls"
+    root = "parameters|PARAMETERS"
+
+
 class PepXml(ProteomicsXml):
     """pepXML data"""
     edam_format = "format_3655"
@@ -127,6 +621,13 @@ class PepXml(ProteomicsXml):
     root = "msms_pipeline_analysis"
 
 
+class MascotXML(ProteomicsXml):
+    """mzXML data"""
+    file_ext = "mascotxml"
+    blurb = "mascot Mass Spectrometry data"
+    root = "mascot_search_results"
+
+
 class MzML(ProteomicsXml):
     """mzML data"""
     edam_format = "format_3244"
@@ -180,6 +681,12 @@ class TraML(ProteomicsXml):
     root = "TraML"
 
 
+class TrafoXML(ProteomicsXml):
+    file_ext = "trafoxml"
+    blurb = "RT alignment tranformation"
+    root = "TrafoXML"
+
+
 class MzQuantML(ProteomicsXml):
     edam_format = "format_3248"
     file_ext = "mzq"
@@ -218,6 +725,29 @@ class UniProtXML(ProteomicsXml):
     root = "uniprot"
 
 
+class XquestXML(ProteomicsXml):
+    file_ext = "xquest.xml"
+    blurb = "XQuest XML file"
+    root = "xquest_results"
+
+
+class XquestSpecXML(ProteomicsXml):
+    """spec.xml"""
+    file_ext = "spec.xml"
+    blurb = 'xquest_spectra'
+    root = "xquest_spectra"
+
+
+class QCML(ProteomicsXml):
+    """qcml
+    https://github.com/OpenMS/OpenMS/blob/113c49d01677f7f03343ce7cd542d83c99b351ee/share/OpenMS/SCHEMAS/mzQCML_0_0_5.xsd
+    https://github.com/OpenMS/OpenMS/blob/3cfc57ad1788e7ab2bd6dd9862818b2855234c3f/share/OpenMS/SCHEMAS/qcML_0.0.7.xsd
+    """
+    file_ext = "qcml"
+    blurb = 'QualityAssessments to runs'
+    root = "qcML|MzQualityML)"
+
+
 class Mgf(Text):
     """Mascot Generic Format data"""
     edam_data = "data_2536"
@@ -278,7 +808,7 @@ class ThermoRAW(Binary):
     """Class describing a Thermo Finnigan binary RAW file"""
     edam_data = "data_2536"
     edam_format = "format_3712"
-    file_ext = "raw"
+    file_ext = "thermo.raw"
 
     def sniff(self, filename):
         # Thermo Finnigan RAW format is proprietary and hence not well documented.

lib/galaxy/datatypes/registry.py

@@ -765,23 +765,19 @@ class Registry(object):
                 'coverage'      : coverage.LastzCoverage(),
                 'customtrack'   : interval.CustomTrack(),
                 'csfasta'       : sequence.csFasta(),
-                'db3'           : binary.SQlite(),
                 'fasta'         : sequence.Fasta(),
                 'eland'         : tabular.Eland(),
                 'fastq'         : sequence.Fastq(),
                 'fastqsanger'   : sequence.FastqSanger(),
-                'gemini.sqlite' : binary.GeminiSQLite(),
                 'gtf'           : interval.Gtf(),
                 'gff'           : interval.Gff(),
                 'gff3'          : interval.Gff3(),
                 'genetrack'     : tracks.GeneTrack(),
                 'h5'            : binary.H5(),
-                'idpdb'         : binary.IdpDB(),
                 'interval'      : interval.Interval(),
                 'laj'           : images.Laj(),
                 'lav'           : sequence.Lav(),
                 'maf'           : sequence.Maf(),
-                'mz.sqlite'     : binary.MzSQlite(),
                 'pileup'        : tabular.Pileup(),
                 'qualsolid'     : qualityscore.QualityScoreSOLiD(),
                 'qualsolexa'    : qualityscore.QualityScoreSolexa(),
@@ -801,26 +797,21 @@ class Registry(object):
                 'axt'           : 'text/plain',
                 'bam'           : 'application/octet-stream',
                 'bed'           : 'text/plain',
-                'blib'          : 'application/octet-stream',
                 'customtrack'   : 'text/plain',
                 'csfasta'       : 'text/plain',
-                'db3'           : 'application/octet-stream',
                 'eland'         : 'application/octet-stream',
                 'fasta'         : 'text/plain',
                 'fastq'         : 'text/plain',
                 'fastqsanger'   : 'text/plain',
-                'gemini.sqlite' : 'application/octet-stream',
                 'gtf'           : 'text/plain',
                 'gff'           : 'text/plain',
                 'gff3'          : 'text/plain',
                 'h5'            : 'application/octet-stream',
-                'idpdb'         : 'application/octet-stream',
                 'interval'      : 'text/plain',
                 'laj'           : 'text/plain',
                 'lav'           : 'text/plain',
                 'maf'           : 'text/plain',
                 'memexml'       : 'application/xml',
-                'mz.sqlite'     : 'application/octet-stream',
                 'pileup'        : 'text/plain',
                 'qualsolid'     : 'text/plain',
                 'qualsolexa'    : 'text/plain',
@@ -846,10 +837,6 @@ class Registry(object):
                 binary.Bam(),
                 binary.Sff(),
                 binary.H5(),
-                binary.GeminiSQLite(),
-                binary.MzSQlite(),
-                binary.IdpDB(),
-                binary.SQlite(),
                 xml.GenericXml(),
                 sequence.Maf(),
                 sequence.Lav(),

lib/galaxy/datatypes/test/A-3105.paf

@@ -0,0 +1,245 @@
+gi|568815454:1200216-1203631	3416	0	3416	+	gi|568815529:1421891-1425306	3416	0	3416	3416	3416	0	NM:i:0	ms:i:6832	AS:i:6832	nn:i:0	tp:A:S	cm:i:637	s1:i:3404	de:f:0	rl:i:0	cg:Z:3416M
+gi|568815454:1200216-1203631	3416	0	3416	+	gi|568815592:29942469-29945883	3415	0	3415	3371	3416	0	NM:i:45	ms:i:6560	AS:i:6560	nn:i:0	tp:A:S	cm:i:540	s1:i:3085	de:f:0.0132	rl:i:0	cg:Z:1212M1I2203M
+gi|568815454:1200216-1203631	3416	0	3411	+	gi|568815567:1196244-1200852	4609	1184	4609	3297	3432	0	NM:i:135	ms:i:6090	AS:i:6090	nn:i:0	tp:A:S	cm:i:381	s1:i:2452	de:f:0.0329	rl:i:0	cg:Z:1339M4D149M17D495M3I183M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	0	3411	+	gi|568815551:1197321-1201446	4126	701	4126	3289	3432	0	NM:i:143	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:385	s1:i:2485	de:f:0.0355	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	0	3411	+	gi|568815561:1196951-1200436	3486	60	3486	3290	3434	0	NM:i:144	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:371	s1:i:2447	de:f:0.0352	rl:i:0	cg:Z:175M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	5	3411	+	gi|568815569:1240288-1243708	3421	0	3421	3284	3429	0	NM:i:145	ms:i:6022	AS:i:6022	nn:i:0	tp:A:S	cm:i:383	s1:i:2483	de:f:0.0355	rl:i:0	cg:Z:170M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815454:1200216-1203631	3416	92	3411	+	gi|568815564:1286641-1289973	3333	0	3333	3198	3340	0	NM:i:142	ms:i:5860	AS:i:5860	nn:i:0	tp:A:S	cm:i:372	s1:i:2412	de:f:0.0362	rl:i:0	cg:Z:1251M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	0	3416	+	gi|568815592:29942469-29945883	3415	0	3415	3371	3416	0	NM:i:45	ms:i:6560	AS:i:6560	nn:i:0	tp:A:S	cm:i:540	s1:i:3085	de:f:0.0132	rl:i:0	cg:Z:1212M1I2203M
+gi|568815529:1421891-1425306	3416	0	3411	+	gi|568815567:1196244-1200852	4609	1184	4609	3297	3432	0	NM:i:135	ms:i:6090	AS:i:6090	nn:i:0	tp:A:S	cm:i:381	s1:i:2452	de:f:0.0329	rl:i:0	cg:Z:1339M4D149M17D495M3I183M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	0	3411	+	gi|568815561:1196951-1200436	3486	60	3486	3290	3434	0	NM:i:144	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:371	s1:i:2447	de:f:0.0352	rl:i:0	cg:Z:175M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	0	3411	+	gi|568815551:1197321-1201446	4126	701	4126	3289	3432	0	NM:i:143	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:385	s1:i:2485	de:f:0.0355	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	5	3411	+	gi|568815569:1240288-1243708	3421	0	3421	3284	3429	0	NM:i:145	ms:i:6022	AS:i:6022	nn:i:0	tp:A:S	cm:i:383	s1:i:2483	de:f:0.0355	rl:i:0	cg:Z:170M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|568815529:1421891-1425306	3416	92	3411	+	gi|568815564:1286641-1289973	3333	0	3333	3198	3340	0	NM:i:142	ms:i:5860	AS:i:5860	nn:i:0	tp:A:S	cm:i:372	s1:i:2412	de:f:0.0362	rl:i:0	cg:Z:1251M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|568815551:1197321-1201446	4126	0	4126	+	gi|568815567:1196244-1200852	4609	483	4609	4061	4126	0	NM:i:65	ms:i:7862	AS:i:7862	nn:i:0	tp:A:S	cm:i:604	s1:i:3595	de:f:0.0158	rl:i:0	cg:Z:4126M
+gi|568815551:1197321-1201446	4126	793	4126	+	gi|568815564:1286641-1289973	3333	0	3333	3333	3333	0	NM:i:0	ms:i:6666	AS:i:6666	nn:i:0	tp:A:S	cm:i:615	s1:i:3324	de:f:0	rl:i:0	cg:Z:3333M
+gi|568815551:1197321-1201446	4126	641	4126	+	gi|568815561:1196951-1200436	3486	0	3486	3409	3487	0	NM:i:78	ms:i:6504	AS:i:6504	nn:i:0	tp:A:S	cm:i:456	s1:i:2855	de:f:0.0221	rl:i:0	cg:Z:235M1I1996M2D1253M
+gi|568815551:1197321-1201446	4126	706	4126	+	gi|568815569:1240288-1243708	3421	0	3421	3343	3422	0	NM:i:79	ms:i:6368	AS:i:6368	nn:i:0	tp:A:S	cm:i:455	s1:i:2819	de:f:0.0228	rl:i:0	cg:Z:170M1I1996M2D1253M
+gi|568815551:1197321-1201446	4126	701	4126	+	gi|568815592:29942469-29945883	3415	0	3410	3296	3432	0	NM:i:136	ms:i:6078	AS:i:6078	nn:i:0	tp:A:S	cm:i:381	s1:i:2471	de:f:0.0334	rl:i:0	cg:Z:1212M1I130M3I1M1I144M17I495M3D183M1D238M3D1000M
+gi|568815561:1196951-1200436	3486	65	3486	+	gi|568815569:1240288-1243708	3421	0	3421	3398	3421	0	NM:i:23	ms:i:6704	AS:i:6704	nn:i:0	tp:A:S	cm:i:574	s1:i:3257	de:f:0.0067	rl:i:0	cg:Z:3421M
+gi|568815561:1196951-1200436	3486	0	3486	+	gi|568815567:1196244-1200852	4609	1124	4609	3435	3487	0	NM:i:52	ms:i:6660	AS:i:6660	nn:i:0	tp:A:S	cm:i:518	s1:i:3068	de:f:0.0146	rl:i:0	cg:Z:235M1D1996M2I1253M
+gi|568815561:1196951-1200436	3486	152	3486	+	gi|568815564:1286641-1289973	3333	0	3333	3257	3335	0	NM:i:78	ms:i:6200	AS:i:6200	nn:i:0	tp:A:S	cm:i:426	s1:i:2708	de:f:0.0231	rl:i:0	cg:Z:83M1D1996M2I1253M
+gi|568815561:1196951-1200436	3486	60	3486	+	gi|568815592:29942469-29945883	3415	0	3410	3298	3434	0	NM:i:136	ms:i:6084	AS:i:6084	nn:i:0	tp:A:S	cm:i:380	s1:i:2501	de:f:0.0328	rl:i:0	cg:Z:175M1D1036M1I126M4I149M17I495M3D165M2I18M1D238M3D1000M
+gi|568815564:1286641-1289973	3333	0	3333	+	gi|568815567:1196244-1200852	4609	1276	4609	3271	3333	0	NM:i:62	ms:i:6294	AS:i:6294	nn:i:0	tp:A:S	cm:i:459	s1:i:2836	de:f:0.0186	rl:i:0	cg:Z:3333M
+gi|568815564:1286641-1289973	3333	0	3333	+	gi|568815569:1240288-1243708	3421	87	3421	3256	3335	0	NM:i:79	ms:i:6194	AS:i:6194	nn:i:0	tp:A:S	cm:i:439	s1:i:2735	de:f:0.0234	rl:i:0	cg:Z:83M1I1996M2D1253M
+gi|568815564:1286641-1289973	3333	0	3333	+	gi|568815592:29942469-29945883	3415	92	3410	3206	3340	0	NM:i:134	ms:i:5906	AS:i:5906	nn:i:0	tp:A:S	cm:i:370	s1:i:2404	de:f:0.0338	rl:i:0	cg:Z:1120M1I130M3I1M1I144M17I495M3D183M1D238M3D1000M
+gi|568815567:1196244-1200852	4609	1189	4609	+	gi|568815569:1240288-1243708	3421	0	3421	3368	3422	0	NM:i:54	ms:i:6518	AS:i:6518	nn:i:0	tp:A:S	cm:i:514	s1:i:3034	de:f:0.0155	rl:i:0	cg:Z:170M1I1996M2D1253M
+gi|568815567:1196244-1200852	4609	1184	4609	+	gi|568815592:29942469-29945883	3415	0	3410	3293	3432	0	NM:i:139	ms:i:6064	AS:i:6064	nn:i:0	tp:A:S	cm:i:374	s1:i:2444	de:f:0.0340	rl:i:0	cg:Z:1212M1I126M4I149M17I495M3D183M1D238M3D1000M
+gi|568815569:1240288-1243708	3421	0	3421	+	gi|568815592:29942469-29945883	3415	5	3410	3289	3429	0	NM:i:140	ms:i:6050	AS:i:6050	nn:i:0	tp:A:S	cm:i:388	s1:i:2487	de:f:0.0341	rl:i:0	cg:Z:170M1D1036M1I126M4I149M17I495M3D165M2I18M1D238M3D1000M
+gi|342187237:5004-8419	3416	0	3416	+	gi|568815529:1421891-1425306	3416	0	3416	3416	3416	0	NM:i:0	ms:i:6832	AS:i:6832	nn:i:0	tp:A:S	cm:i:637	s1:i:3404	de:f:0	rl:i:0	cg:Z:3416M
+gi|342187237:5004-8419	3416	0	3416	+	gi|568815454:1200216-1203631	3416	0	3416	3416	3416	0	NM:i:0	ms:i:6832	AS:i:6832	nn:i:0	tp:A:S	cm:i:637	s1:i:3404	de:f:0	rl:i:0	cg:Z:3416M
+gi|342187237:5004-8419	3416	0	3416	+	gi|568815592:29942469-29945883	3415	0	3415	3371	3416	0	NM:i:45	ms:i:6560	AS:i:6560	nn:i:0	tp:A:S	cm:i:540	s1:i:3085	de:f:0.0132	rl:i:0	cg:Z:1212M1I2203M
+gi|342187237:5004-8419	3416	0	3411	+	gi|568815567:1196244-1200852	4609	1184	4609	3297	3432	0	NM:i:135	ms:i:6090	AS:i:6090	nn:i:0	tp:A:S	cm:i:381	s1:i:2452	de:f:0.0329	rl:i:0	cg:Z:1339M4D149M17D495M3I183M1I238M3I1000M
+gi|342187237:5004-8419	3416	0	3416	+	gi|528476637:29857558-29915771	58214	54784	58214	3296	3437	0	NM:i:141	ms:i:6060	AS:i:6060	nn:i:0	tp:A:S	cm:i:389	s1:i:2505	de:f:0.0348	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1005M
+gi|342187237:5004-8419	3416	0	3411	+	gi|568815551:1197321-1201446	4126	701	4126	3289	3432	0	NM:i:143	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:385	s1:i:2485	de:f:0.0355	rl:i:0	cg:Z:1343M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|342187237:5004-8419	3416	0	3411	+	gi|568815561:1196951-1200436	3486	60	3486	3290	3434	0	NM:i:144	ms:i:6038	AS:i:6038	nn:i:0	tp:A:S	cm:i:371	s1:i:2447	de:f:0.0352	rl:i:0	cg:Z:175M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|342187237:5004-8419	3416	5	3411	+	gi|568815569:1240288-1243708	3421	0	3421	3284	3429	0	NM:i:145	ms:i:6022	AS:i:6022	nn:i:0	tp:A:S	cm:i:383	s1:i:2483	de:f:0.0355	rl:i:0	cg:Z:170M1I1163M4D149M17D495M3I165M2D18M1I238M3I1000M
+gi|342187237:5004-8419	3416	92	3411	+	gi|568815564:1286641-1289973	3333	0	3333	3198	3340	0	NM:i:142	ms:i:5860	AS:i:5860	nn:i:0	tp:A:S	cm:i:372	s1:i:2412	de:f:0.0362	rl:i:0	cg:Z:1251M3D1M1D144M17D495M3I183M1I238M3I1000M
+gi|342187237:5004-8419	3416	0	3416	+	gi|528476637:29857558-29915771	58214	0	3428	3142	3464	0	NM:i:322	ms:i:5064	AS:i:5064	nn:i:0	tp:A:S	cm:i:215	s1:i:1596	de:f:0.0772	rl:i:0	cg:Z:185M2I2M4I224M1D3M1I61M1I5M1D108M3D13M1I118M1I486M12I112M4D22M19D127M17D296M1I433M2I589M1I40M1D33M1I37M1I48M1I57M1D1M2I31M4I96M1D88M1I165M
+gi|342187237:5004-8419	3416	3	3416	+	gi|528476637:29857558-29915771	58214	38484	41952	3039	3493	0	NM:i:454	ms:i:4320	AS:i:4320	nn:i:0	tp:A:S	cm:i:107	s1:i:1001	de:f:0.1130	rl:i:0	cg:Z:34M1D52M1I123M2I1M1D255M1I4M1D11M1I21M1D12M4I3M1D2M1D4M2D59M3D33M3D38M1I3M2D60M1I25M1D277M1I327M1D132M16D164M5D6M2D207M2I74M7D52M20D363M1D41M3D90M1I103M6I96M1D6M1I117M1D2M1I208M1I132M2D26M4D60M1I165M
+gi|342187237:5004-8419	3416	1488	3158	+	gi|528476637:29857558-29915771	58214	8636	10269	1295	1729	0	NM:i:434	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2026	rl:i:0	cg:Z:35M1I414M1D3M1I7M1I12M3D44M20D84M3I2M2I2M10I42M1D3M1I9M3I2M4I21M1D24M2I2M4I11M9D11M1D1M1D11M4I8M1D4M1D8M4I60M3I11M1D6M1D17M2I8M1D5M2D38M2D4M1D3M1I39M2I15M26I105M2D1M5D59M1I108M1I2M1D47M2I71M2I47M1D6M7I3M3I40M2I3M1D19M1D7M1D37M3I12M1I41M
+gi|342187237:5004-8419	3416	891	1307	+	gi|528476637:29857558-29915771	58214	44457	44873	392	416	0	NM:i:24	ms:i:688	AS:i:688	nn:i:0	tp:A:S	cm:i:36	s1:i:238	de:f:0.0577	rl:i:0	cg:Z:416M
+gi|528476637:29857558-29915771	58214	53600	58209	+	gi|568815567:1196244-1200852	4609	0	4609	4559	4609	0	NM:i:50	ms:i:8918	AS:i:8918	nn:i:0	tp:A:S	cm:i:729	s1:i:4180	de:f:0.0108	rl:i:25	cg:Z:4609M
+gi|528476637:29857558-29915771	58214	33375	41952	+	gi|528476637:29857558-29915771	58214	49822	58214	7180	8967	0	NM:i:1787	ms:i:8814	AS:i:9504	nn:i:0	tp:A:S	cm:i:225	s1:i:2063	de:f:0.1118	rl:i:25	cg:Z:24M4D11M3I103M2I43M2I32M3D51M1D139M5D1M1D573M3I3M2I49M1D3M1D13M2D5M1I189M1D36M17D448M1I3M1D215M3I35M4I263M8I23M1D91M1D279M1I137M310D48M4I225M6I3M1D3M350I6M2I46M1D379M1I54M1I85M2I21M1I6M90I167M1I74M1D1M2D236M1D10M4D48M19I109M4D346M1I52M1D125M1D271M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D311M3D2M1D14M1I148M1D170M7I207M2D66M2I5M6I2M1D39M3I10M20I173M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D165M
+gi|528476637:29857558-29915771	58214	49822	58214	+	gi|528476637:29857558-29915771	58214	33375	41952	7180	8967	0	NM:i:1787	ms:i:8814	AS:i:9504	nn:i:0	tp:A:S	cm:i:225	s1:i:2063	de:f:0.1118	rl:i:25	cg:Z:24M4I11M3D103M2D43M2D32M3I51M1I139M5I1M1I573M3D3M2D49M1I3M1I13M2I5M1D189M1I36M17I448M1D3M1I215M3D35M4D263M8D23M1I91M1I279M1D137M310I48M4D225M6D3M1I3M350D6M2D46M1I379M1D54M1D85M2D21M1D6M90D167M1D74M1I1M2I236M1I10M4I48M19D109M4I346M1D52M1I125M1I271M1I21M1D12M4I3M1D2M1D4M2D57M2D3M1D32M3D40M1D62M1I25M1D277M1I311M3I2M1I14M1D148M1I170M7D207M2I66M2D5M6D2M1I39M3D10M20D173M1D189M1D41M3D8M3D79M1I103M6I96M1D6M1I328M1I132M2D26M4D60M1I165M
+gi|528476637:29857558-29915771	58214	54083	58209	+	gi|568815551:1197321-1201446	4126	0	4126	4107	4126	0	NM:i:19	ms:i:8138	AS:i:8138	nn:i:0	tp:A:S	cm:i:726	s1:i:3964	de:f:0.0046	rl:i:25	cg:Z:4126M
+gi|528476637:29857558-29915771	58214	54876	58209	+	gi|568815564:1286641-1289973	3333	0	3333	3317	3333	0	NM:i:16	ms:i:6570	AS:i:6570	nn:i:0	tp:A:S	cm:i:578	s1:i:3203	de:f:0.0048	rl:i:25	cg:Z:3333M
+gi|528476637:29857558-29915771	58214	54724	58209	+	gi|568815561:1196951-1200436	3486	0	3486	3417	3487	0	NM:i:70	ms:i:6552	AS:i:6552	nn:i:0	tp:A:S	cm:i:469	s1:i:2920	de:f:0.0198	rl:i:25	cg:Z:235M1I1996M2D1253M
+gi|528476637:29857558-29915771	58214	54789	58209	+	gi|568815569:1240288-1243708	3421	0	3421	3347	3422	0	NM:i:75	ms:i:6392	AS:i:6392	nn:i:0	tp:A:S	cm:i:462	s1:i:2853	de:f:0.0216	rl:i:25	cg:Z:170M1I1996M2D1253M
+gi|528476637:29857558-29915771	58214	54784	58214	+	gi|568815592:29942469-29945883	3415	0	3415	3305	3437	0	NM:i:132	ms:i:6112	AS:i:6112	nn:i:0	tp:A:S	cm:i:393	s1:i:2554	de:f:0.0322	rl:i:25	cg:Z:1212M1I130M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|528476637:29857558-29915771	58214	54784	58214	+	gi|568815454:1200216-1203631	3416	0	3416	3296	3437	0	NM:i:141	ms:i:6060	AS:i:6060	nn:i:0	tp:A:S	cm:i:389	s1:i:2505	de:f:0.0348	rl:i:25	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|528476637:29857558-29915771	58214	54784	58214	+	gi|568815529:1421891-1425306	3416	0	3416	3296	3437	0	NM:i:141	ms:i:6060	AS:i:6060	nn:i:0	tp:A:S	cm:i:389	s1:i:2505	de:f:0.0348	rl:i:25	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
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+gi|528476637:29857558-29915771	58214	38421	41947	+	gi|568815561:1196951-1200436	3486	0	3486	3090	3555	0	NM:i:465	ms:i:4352	AS:i:4352	nn:i:0	tp:A:S	cm:i:95	s1:i:919	de:f:0.1166	rl:i:25	cg:Z:97M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D311M1D2M3D14M1I148M1D170M7I207M2D74M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|528476637:29857558-29915771	58214	38484	41952	+	gi|568815592:29942469-29945883	3415	3	3415	3041	3495	0	NM:i:454	ms:i:4326	AS:i:4326	nn:i:0	tp:A:S	cm:i:110	s1:i:990	de:f:0.1121	rl:i:25	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I40M1I62M1D25M1I222M3D4M3I48M1D180M1I146M1I132M16I164M5I6M2I207M2D74M7I52M20I363M1I41M3I90M1D103M6D96M1I6M1D117M1I2M1D208M1D132M2I26M4I60M1D165M
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+gi|528476637:29857558-29915771	58214	38484	41952	+	gi|568815529:1421891-1425306	3416	3	3416	3039	3493	0	NM:i:454	ms:i:4320	AS:i:4320	nn:i:0	tp:A:S	cm:i:107	s1:i:1001	de:f:0.1130	rl:i:25	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I164M5I6M2I207M2D74M7I52M20I363M1I41M3I90M1D103M6D96M1I6M1D117M1I2M1D208M1D132M2I26M4I60M1D165M
+gi|528476637:29857558-29915771	58214	38486	41947	+	gi|568815569:1240288-1243708	3421	0	3421	3037	3486	0	NM:i:449	ms:i:4310	AS:i:4310	nn:i:0	tp:A:S	cm:i:97	s1:i:949	de:f:0.1154	rl:i:25	cg:Z:32M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I82M2I3M1I32M3I40M1I62M1D25M1I277M1D311M1D2M3D14M1I148M1D170M7I207M2D74M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D103M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
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+gi|528476637:29857558-29915771	58214	3555	4654	+	gi|528476637:29857558-29915771	58214	43020	44118	982	1103	0	NM:i:121	ms:i:1478	AS:i:1478	nn:i:0	tp:A:S	cm:i:30	s1:i:230	de:f:0.1065	rl:i:25	cg:Z:156M1I416M3D62M3I27M1I156M1D277M
+gi|528476637:29857558-29915771	58214	43020	44118	+	gi|528476637:29857558-29915771	58214	3555	4654	982	1103	0	NM:i:121	ms:i:1478	AS:i:1478	nn:i:0	tp:A:S	cm:i:30	s1:i:230	de:f:0.1065	rl:i:25	cg:Z:156M1D416M3I62M3D27M1D156M1I277M
+gi|528476637:29857558-29915771	58214	48998	49823	+	gi|528476637:29857558-29915771	58214	31581	32408	735	834	0	NM:i:99	ms:i:1062	AS:i:1062	nn:i:0	tp:A:S	cm:i:17	s1:i:194	de:f:0.1134	rl:i:25	cg:Z:9M2D100M1I166M1I2M1D93M1D142M1D28M2D3M2D113M1I3M3I4M1I155M
+gi|528476637:29857558-29915771	58214	31581	32408	+	gi|528476637:29857558-29915771	58214	48998	49823	735	834	0	NM:i:99	ms:i:1062	AS:i:1062	nn:i:0	tp:A:S	cm:i:17	s1:i:194	de:f:0.1134	rl:i:25	cg:Z:9M2I100M1D166M1D2M1I93M1I142M1I28M2I3M2I113M1D3M3D4M1D155M
+gi|528476637:29857558-29915771	58214	1488	3170	+	gi|528476637:29857558-29915771	58214	8615	10269	1320	1753	0	NM:i:433	ms:i:1012	AS:i:1018	nn:i:0	tp:A:S	cm:i:12	s1:i:120	de:f:0.1961	rl:i:25	cg:Z:11M2I45M1I260M1D153M1D3M1I7M1I12M3D41M14D4M6D78M3I6M5I3M7I55M5I2M2I21M1D26M2D2M6D11M1I6M2I5M2D11M4I8M1D4M1D8M4I59M3I12M1D6M1D17M2I8M1D5M2D38M2D47M2I15M26I22M1I7M1D75M2D1M5D22M1I5M1I6M1I3M3D20M1I115M1D44M5I3M1D1M1D17M1D41M1D2M2I7M1I3M1D36M2D6M7I3M3I63M1D3M5D37M3I2M2I9M1D41M
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+gi|528476637:29857558-29915771	58214	8636	10269	+	gi|568815454:1200216-1203631	3416	1488	3158	1295	1726	0	NM:i:431	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2041	rl:i:25	cg:Z:35M1D414M1I3M1D7M1D12M3I44M20I84M3D2M2D2M10D42M1I3M1D9M3D2M4D21M1I30M6I7M1D3M2D11M1I1M1I11M4D8M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I38M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
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+gi|528476637:29857558-29915771	58214	8629	10269	+	gi|568815564:1286641-1289973	3333	1410	3080	1286	1731	0	NM:i:445	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2115	rl:i:25	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M6D1M2D58M3D2M3D21M1I30M6I11M1D6M1I4M3I13M3D10M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|528476637:29857558-29915771	58214	8629	10269	+	gi|568815551:1197321-1201446	4126	2203	3873	1286	1731	0	NM:i:445	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2115	rl:i:25	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M6D1M2D58M3D2M3D21M1I30M6I11M1D6M1I4M3I13M3D10M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
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+gi|528476637:29857558-29915771	58214	56286	57956	+	gi|528476637:29857558-29915771	58214	8629	10269	1286	1732	0	NM:i:446	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2110	rl:i:25	cg:Z:42M1I414M1D3M1I7M1I12M3D21M1D2M2D18M20D78M12I3M2I1M2I2M1D58M3I2M3I21M1D30M6D11M1I6M1D4M3D13M3I10M1I2M2I7M4I60M3I11M1D6M1D17M2I8M1D5M2D8M2D2M1D25M2D4M1D3M1I39M2I15M26I105M2D1M5D59M1I108M1I2M1D47M2I69M2I49M1D6M7I3M3I40M2I3M1D19M1D7M1D37M3I12M1I41M
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+gi|528476637:29857558-29915771	58214	8629	10269	+	gi|568815569:1240288-1243708	3421	1496	3168	1284	1736	0	NM:i:452	ms:i:868	AS:i:874	nn:i:0	tp:A:S	cm:i:10	s1:i:116	de:f:0.2118	rl:i:25	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D3M8D48M2D10M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M7D7M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
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+gi|528476637:29857558-29915771	58214	4739	5908	+	gi|528476637:29857558-29915771	58214	27052	28249	925	1207	0	NM:i:282	ms:i:726	AS:i:726	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2174	rl:i:25	cg:Z:100M1I5M1D139M7D13M1D133M7D80M1I58M1D6M1I70M1D31M2I5M1D15M1D3M1D17M1I2M1D168M9D2M1D48M2D113M2I73M2I4M2D15M1D23M1D36M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815569:1240288-1243708	3421	885	1301	398	416	0	NM:i:18	ms:i:724	AS:i:724	nn:i:0	tp:A:S	cm:i:39	s1:i:284	de:f:0.0433	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815567:1196244-1200852	4609	2075	2491	398	416	0	NM:i:18	ms:i:724	AS:i:724	nn:i:0	tp:A:S	cm:i:39	s1:i:295	de:f:0.0433	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815592:29942469-29945883	3415	891	1306	398	416	0	NM:i:18	ms:i:722	AS:i:722	nn:i:0	tp:A:S	cm:i:42	s1:i:282	de:f:0.0433	rl:i:25	cg:Z:321M1I94M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815561:1196951-1200436	3486	950	1366	397	416	0	NM:i:19	ms:i:718	AS:i:718	nn:i:0	tp:A:S	cm:i:36	s1:i:274	de:f:0.0457	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	55675	56091	+	gi|528476637:29857558-29915771	58214	44457	44873	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815551:1197321-1201446	4126	1592	2008	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815564:1286641-1289973	3333	799	1215	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|528476637:29857558-29915771	58214	55675	56091	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815454:1200216-1203631	3416	891	1307	392	416	0	NM:i:24	ms:i:688	AS:i:688	nn:i:0	tp:A:S	cm:i:36	s1:i:238	de:f:0.0577	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	44457	44873	+	gi|568815529:1421891-1425306	3416	891	1307	392	416	0	NM:i:24	ms:i:688	AS:i:688	nn:i:0	tp:A:S	cm:i:36	s1:i:238	de:f:0.0577	rl:i:25	cg:Z:416M
+gi|528476637:29857558-29915771	58214	886	1289	+	gi|528476637:29857558-29915771	58214	44457	44872	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:17	s1:i:133	de:f:0.0891	rl:i:25	cg:Z:324M12D79M
+gi|528476637:29857558-29915771	58214	44457	44872	+	gi|528476637:29857558-29915771	58214	886	1289	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:17	s1:i:133	de:f:0.0891	rl:i:25	cg:Z:324M12I79M
+gi|528476637:29857558-29915771	58214	44457	44872	+	gi|528476637:29857558-29915771	58214	39378	39792	361	418	0	NM:i:57	ms:i:496	AS:i:496	nn:i:0	tp:A:S	cm:i:7	s1:i:93	de:f:0.1280	rl:i:25	cg:Z:85M3I4M3D48M1I274M
+gi|528476637:29857558-29915771	58214	39378	39792	+	gi|528476637:29857558-29915771	58214	44457	44872	361	418	0	NM:i:57	ms:i:496	AS:i:496	nn:i:0	tp:A:S	cm:i:7	s1:i:93	de:f:0.1280	rl:i:25	cg:Z:85M3D4M3I48M1D274M
+gi|528476637:29857558-29915771	58214	49208	49824	+	gi|528476637:29857558-29915771	58214	7043	7661	489	643	0	NM:i:154	ms:i:370	AS:i:370	nn:i:0	tp:A:S	cm:i:5	s1:i:47	de:f:0.2049	rl:i:25	cg:Z:26M4I20M1D64M2I7M1D1M1D39M9D5M2D5M4D75M2I8M1D4M2I25M1I11M1D5M1D2M2I4M1D4M1D7M5I7M1I133M1I49M1I29M4I5M3D3M1D53M
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+gi|528476637:29857558-29915771	58214	45137	45465	-	gi|528476637:29857558-29915771	58214	14421	14731	269	329	0	NM:i:60	ms:i:318	AS:i:318	nn:i:0	tp:A:S	cm:i:3	s1:i:42	de:f:0.1433	rl:i:25	cg:Z:35M1D115M1I2M14I113M1I28M3I16M
+gi|528476637:29857558-29915771	58214	14421	14731	-	gi|528476637:29857558-29915771	58214	45137	45465	269	329	0	NM:i:60	ms:i:318	AS:i:318	nn:i:0	tp:A:S	cm:i:3	s1:i:42	de:f:0.1433	rl:i:25	cg:Z:14M3D30M1D113M14D2M1D114M1I36M
+gi|528476637:29857558-29915771	58214	6307	7004	-	gi|528476637:29857558-29915771	58214	6307	7004	528	727	0	NM:i:199	ms:i:272	AS:i:272	nn:i:0	tp:A:S	cm:i:4	s1:i:44	de:f:0.2392	rl:i:25	cg:Z:11M1D155M1I43M2D64M2I1M1I6M3I5M2I1M2I6M1D9M2I3M3D6M8I5M1I8M1I5M1I10M1D5M1D5M1D8M8D5M3I4M2D3M2D13M2D7M5D70M2I43M1D154M1I12M
+gi|528476637:29857558-29915771	58214	8056	8300	+	gi|528476637:29857558-29915771	58214	8056	8376	225	321	0	NM:i:96	ms:i:258	AS:i:271	nn:i:0	tp:A:S	cm:i:7	s1:i:51	de:f:0.0816	rl:i:25	cg:Z:129M77D89M1I25M
+gi|528476637:29857558-29915771	58214	8056	8376	+	gi|528476637:29857558-29915771	58214	8056	8300	225	321	0	NM:i:96	ms:i:258	AS:i:271	nn:i:0	tp:A:S	cm:i:7	s1:i:51	de:f:0.0816	rl:i:25	cg:Z:129M77I89M1D25M
+gi|528476637:29857558-29915771	58214	17754	17858	+	gi|528476637:29857558-29915771	58214	17845	17947	98	104	0	NM:i:6	ms:i:172	AS:i:172	nn:i:0	tp:A:S	cm:i:8	s1:i:52	de:f:0.0485	rl:i:25	cg:Z:13M2I89M
+gi|528476637:29857558-29915771	58214	17845	17947	+	gi|528476637:29857558-29915771	58214	17754	17858	98	104	0	NM:i:6	ms:i:172	AS:i:172	nn:i:0	tp:A:S	cm:i:8	s1:i:52	de:f:0.0485	rl:i:25	cg:Z:13M2D89M
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+gi|157734152:29655295-29712160	56866	12900	22956	+	gi|528476637:29857558-29915771	58214	12858	22836	9939	10067	0	NM:i:128	ms:i:19554	AS:i:19623	nn:i:0	tp:A:S	cm:i:5	s1:i:51	de:f:0.0031	rl:i:96	cg:Z:1820M9D806M2D2415M89I4926M
+gi|157734152:29655295-29712160	56866	47082	56866	+	gi|528476637:29857558-29915771	58214	48429	58214	9630	9801	0	NM:i:171	ms:i:18606	AS:i:18606	nn:i:0	tp:A:S	cm:i:1505	s1:i:8643	de:f:0.0150	rl:i:96	cg:Z:179M2D335M1D587M2D3229M2I161M13I113M1I180M8D563M1D518M3D3903M
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+gi|157734152:29655295-29712160	56866	52256	56861	+	gi|568815567:1196244-1200852	4609	0	4609	4503	4609	0	NM:i:106	ms:i:8582	AS:i:8582	nn:i:0	tp:A:S	cm:i:628	s1:i:3840	de:f:0.0226	rl:i:96	cg:Z:189M1D518M3D3898M
+gi|157734152:29655295-29712160	56866	52738	56861	+	gi|568815551:1197321-1201446	4126	0	4126	4100	4126	0	NM:i:26	ms:i:8098	AS:i:8098	nn:i:0	tp:A:S	cm:i:722	s1:i:3930	de:f:0.0058	rl:i:96	cg:Z:225M3D3898M
+gi|157734152:29655295-29712160	56866	53528	56861	+	gi|568815564:1286641-1289973	3333	0	3333	3317	3333	0	NM:i:16	ms:i:6570	AS:i:6570	nn:i:0	tp:A:S	cm:i:585	s1:i:3212	de:f:0.0048	rl:i:96	cg:Z:3333M
+gi|157734152:29655295-29712160	56866	53376	56861	+	gi|568815561:1196951-1200436	3486	0	3486	3397	3487	0	NM:i:90	ms:i:6432	AS:i:6432	nn:i:0	tp:A:S	cm:i:442	s1:i:2777	de:f:0.0255	rl:i:96	cg:Z:235M1I1996M2D1253M
+gi|157734152:29655295-29712160	56866	53441	56861	+	gi|568815569:1240288-1243708	3421	0	3421	3331	3422	0	NM:i:91	ms:i:6296	AS:i:6296	nn:i:0	tp:A:S	cm:i:441	s1:i:2741	de:f:0.0263	rl:i:96	cg:Z:170M1I1996M2D1253M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|342187237:5004-8419	3416	0	3416	3310	3437	0	NM:i:127	ms:i:6144	AS:i:6144	nn:i:0	tp:A:S	cm:i:427	s1:i:2612	de:f:0.0307	rl:i:96	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|568815454:1200216-1203631	3416	0	3416	3310	3437	0	NM:i:127	ms:i:6144	AS:i:6144	nn:i:0	tp:A:S	cm:i:427	s1:i:2612	de:f:0.0307	rl:i:96	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|568815529:1421891-1425306	3416	0	3416	3310	3437	0	NM:i:127	ms:i:6144	AS:i:6144	nn:i:0	tp:A:S	cm:i:427	s1:i:2612	de:f:0.0307	rl:i:96	cg:Z:1343M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	53436	56866	+	gi|568815592:29942469-29945883	3415	0	3415	3305	3437	0	NM:i:132	ms:i:6112	AS:i:6112	nn:i:0	tp:A:S	cm:i:396	s1:i:2527	de:f:0.0322	rl:i:96	cg:Z:1212M1I130M3I1M1I144M17I495M3D183M1D238M3D1005M
+gi|157734152:29655295-29712160	56866	37319	42069	+	gi|568815567:1196244-1200852	4609	4	4609	4082	4789	0	NM:i:707	ms:i:5566	AS:i:5636	nn:i:0	tp:A:S	cm:i:119	s1:i:1112	de:f:0.1165	rl:i:96	cg:Z:48M1I54M1I85M2I21M1I6M90I167M1I74M1D1M2D247M4D48M19I109M4D346M1I52M1D125M1D271M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I40M1I62M1D25M1I217M3D9M3I48M1D307M4D20M1I148M1D169M3I276M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	43615	46576	+	gi|157734152:29655295-29712160	56866	43615	46614	2915	3042	0	NM:i:127	ms:i:5546	AS:i:5600	nn:i:0	tp:A:S	cm:i:16	s1:i:120	de:f:0.0031	rl:i:96	cg:Z:1340M41D41I1438M32D17M6D6M2D100M2I17M
+gi|157734152:29655295-29712160	56866	43615	46614	+	gi|157734152:29655295-29712160	56866	43615	46576	2915	3042	0	NM:i:127	ms:i:5546	AS:i:5600	nn:i:0	tp:A:S	cm:i:16	s1:i:120	de:f:0.0031	rl:i:96	cg:Z:1340M41I41D1438M32I17M6I6M2I100M2D17M
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+gi|157734152:29655295-29712160	56866	5	3401	+	gi|568815569:1240288-1243708	3421	0	3421	3152	3439	0	NM:i:287	ms:i:5158	AS:i:5158	nn:i:0	tp:A:S	cm:i:196	s1:i:1628	de:f:0.0751	rl:i:96	cg:Z:167M1D2M2I9M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I168M2D16M1I47M2D188M3I398M1D40M1I33M1D37M1D11M1D3M1I33M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|568815529:1421891-1425306	3416	0	3416	3143	3441	0	NM:i:298	ms:i:5126	AS:i:5126	nn:i:0	tp:A:S	cm:i:206	s1:i:1579	de:f:0.0764	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|342187237:5004-8419	3416	0	3416	3143	3441	0	NM:i:298	ms:i:5126	AS:i:5126	nn:i:0	tp:A:S	cm:i:206	s1:i:1579	de:f:0.0764	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|568815454:1200216-1203631	3416	0	3416	3143	3441	0	NM:i:298	ms:i:5126	AS:i:5126	nn:i:0	tp:A:S	cm:i:206	s1:i:1579	de:f:0.0764	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	37891	42069	+	gi|568815551:1197321-1201446	4126	0	4126	3654	4213	0	NM:i:559	ms:i:5120	AS:i:5120	nn:i:0	tp:A:S	cm:i:117	s1:i:1076	de:f:0.1174	rl:i:96	cg:Z:227M4D48M19I109M4D346M1I52M1D123M1I1M2D254M1D5M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D172M2I2M1I271M1I3M1I2M1I2M4I40M3I10M20I173M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	0	3401	+	gi|568815561:1196951-1200436	3486	60	3486	3149	3444	0	NM:i:295	ms:i:5120	AS:i:5120	nn:i:0	tp:A:S	cm:i:189	s1:i:1603	de:f:0.0774	rl:i:96	cg:Z:172M1D2M2I9M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I168M2D16M1I47M2D188M3I398M1D40M1I33M1D37M1D11M1D3M1I33M1D57M1I1M2D31M4D96M1I88M1D160M
+gi|157734152:29655295-29712160	56866	0	3406	+	gi|568815592:29942469-29945883	3415	0	3415	3142	3440	0	NM:i:298	ms:i:5118	AS:i:5118	nn:i:0	tp:A:S	cm:i:207	s1:i:1610	de:f:0.0770	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D485M10D1M1D132M1I129M17I296M1D433M2D589M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
+gi|157734152:29655295-29712160	56866	0	3401	+	gi|568815551:1197321-1201446	4126	701	4126	3142	3440	0	NM:i:298	ms:i:5100	AS:i:5100	nn:i:0	tp:A:S	cm:i:198	s1:i:1597	de:f:0.0789	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D160M
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+gi|157734152:29655295-29712160	56866	0	3406	+	gi|157734152:29655295-29712160	56866	53436	56866	3142	3445	0	NM:i:303	ms:i:5080	AS:i:5080	nn:i:0	tp:A:S	cm:i:193	s1:i:1577	de:f:0.0802	rl:i:96	cg:Z:185M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D165M
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+gi|157734152:29655295-29712160	56866	92	3401	+	gi|568815564:1286641-1289973	3333	0	3333	3058	3348	0	NM:i:290	ms:i:4964	AS:i:4964	nn:i:0	tp:A:S	cm:i:193	s1:i:1559	de:f:0.0786	rl:i:96	cg:Z:93M2D2M4D289M1D5M1I108M3I13M1D118M1D486M12D112M4D20M1I442M1D198M3I184M1I47M2D188M3I398M1D40M1I33M1D37M1D48M1D57M1I1M2D31M4D96M1I88M1D160M
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+gi|157734152:29655295-29712160	56866	38606	42207	+	gi|157734152:29655295-29712160	56866	3	3539	3166	3622	0	NM:i:456	ms:i:4550	AS:i:4550	nn:i:0	tp:A:S	cm:i:135	s1:i:1116	de:f:0.1102	rl:i:96	cg:Z:34M1I52M1D95M2I2M4I22M1D272M1D19M1I104M1I9M3I47M1I87M1I222M5D3M5I47M1D106M1D7M2I2M1D68M12I279M1D169M3I121M1I162M7I58M14I6M5I1M1I209M2I139M1I42M2I1M1I88M1D30M1I1M1I72M6D96M1I6M1D106M1I40M1D33M1I37M1I52M1I85M4I100M1I26M4I358M
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+gi|157734152:29655295-29712160	56866	38606	42207	+	gi|528476637:29857558-29915771	58214	3	3561	3162	3640	0	NM:i:478	ms:i:4470	AS:i:4470	nn:i:0	tp:A:S	cm:i:132	s1:i:1092	de:f:0.1130	rl:i:96	cg:Z:34M1I52M1D95M2I2M4I22M1D202M1D2M1I67M1D19M1I104M1I9M3I47M1I87M1I277M1D106M1D7M2I2M1D68M12I110M4D26M17D1M1D142M1D169M3I121M1I162M7I58M14I6M5I1M1I209M2I139M1I42M2I1M1I88M1D30M1I1M1I72M6D96M1I6M1D106M1I40M1D33M1I37M1I52M1I85M4I100M1I26M4I358M
+gi|157734152:29655295-29712160	56866	38543	42069	+	gi|568815561:1196951-1200436	3486	0	3486	3089	3554	0	NM:i:465	ms:i:4338	AS:i:4338	nn:i:0	tp:A:S	cm:i:95	s1:i:925	de:f:0.1177	rl:i:96	cg:Z:97M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I57M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D169M3I284M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|568815592:29942469-29945883	3415	3	3415	3036	3493	0	NM:i:457	ms:i:4300	AS:i:4300	nn:i:0	tp:A:S	cm:i:112	s1:i:1008	de:f:0.1138	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I40M1I62M1D25M1I222M3D4M3I48M1D180M1I146M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|342187237:5004-8419	3416	3	3416	3034	3491	0	NM:i:457	ms:i:4294	AS:i:4294	nn:i:0	tp:A:S	cm:i:108	s1:i:1013	de:f:0.1147	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|568815454:1200216-1203631	3416	3	3416	3034	3491	0	NM:i:457	ms:i:4294	AS:i:4294	nn:i:0	tp:A:S	cm:i:108	s1:i:1013	de:f:0.1147	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38606	42074	+	gi|568815529:1421891-1425306	3416	3	3416	3034	3491	0	NM:i:457	ms:i:4294	AS:i:4294	nn:i:0	tp:A:S	cm:i:108	s1:i:1013	de:f:0.1147	rl:i:96	cg:Z:34M1I52M1D123M1I1M2D255M1D4M1I11M1D21M1I12M4D3M1I2M1I4M2I59M3I33M3I38M1D3M2I60M1D25M1I277M1D327M1I132M16I169M3I284M7I52M20I363M1I41M3I90M1D29M2I74M6D96M1I6M1D116M1I3M1D208M1D132M2I26M4I60M1D165M
+gi|157734152:29655295-29712160	56866	38608	42069	+	gi|568815569:1240288-1243708	3421	0	3421	3034	3485	0	NM:i:451	ms:i:4284	AS:i:4284	nn:i:0	tp:A:S	cm:i:97	s1:i:955	de:f:0.1170	rl:i:96	cg:Z:32M1I52M1D81M1I43M1D255M1D4M1I11M1D21M1I82M2I3M1I32M3I40M1I62M1D25M1I277M1D307M4D20M1I148M1D169M3I284M7I39M3I10M20I158M2D15M1I189M1I41M3I8M3I79M1D17M1D3M1I9M1I1M1I72M6D96M1I6M1D328M1D132M2I26M4I60M1D160M
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+gi|157734152:29655295-29712160	56866	43143	44241	+	gi|528476637:29857558-29915771	58214	3555	4654	977	1103	0	NM:i:126	ms:i:1448	AS:i:1448	nn:i:0	tp:A:S	cm:i:31	s1:i:245	de:f:0.1110	rl:i:96	cg:Z:156M1D416M3I62M3D27M1D156M1I277M
+gi|157734152:29655295-29712160	56866	43143	44241	+	gi|157734152:29655295-29712160	56866	3533	4632	975	1103	0	NM:i:128	ms:i:1436	AS:i:1436	nn:i:0	tp:A:S	cm:i:28	s1:i:232	de:f:0.1128	rl:i:96	cg:Z:156M1D416M3I62M3D27M1D156M1I277M
+gi|157734152:29655295-29712160	56866	3533	4632	+	gi|157734152:29655295-29712160	56866	43143	44241	975	1103	0	NM:i:128	ms:i:1436	AS:i:1436	nn:i:0	tp:A:S	cm:i:28	s1:i:232	de:f:0.1128	rl:i:96	cg:Z:156M1I416M3D62M3I27M1I156M1D277M
+gi|157734152:29655295-29712160	56866	47648	48471	+	gi|528476637:29857558-29915771	58214	31581	32408	734	834	0	NM:i:100	ms:i:1064	AS:i:1064	nn:i:0	tp:A:S	cm:i:19	s1:i:213	de:f:0.1114	rl:i:96	cg:Z:9M2D100M1I166M1I2M1D93M1D142M1D29M6D113M2I3M2I4M1I155M
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+gi|157734152:29655295-29712160	56866	47648	48471	+	gi|157734152:29655295-29712160	56866	31699	32530	732	838	0	NM:i:106	ms:i:1044	AS:i:1044	nn:i:0	tp:A:S	cm:i:19	s1:i:213	de:f:0.1138	rl:i:96	cg:Z:9M2D100M1I166M1I2M1D93M1D142M1D29M10D113M2I3M2I4M1I155M
+gi|157734152:29655295-29712160	56866	31699	32530	+	gi|157734152:29655295-29712160	56866	47648	48471	732	838	0	NM:i:106	ms:i:1044	AS:i:1044	nn:i:0	tp:A:S	cm:i:19	s1:i:213	de:f:0.1138	rl:i:96	cg:Z:9M2I100M1D166M1D2M1I93M1I142M1I29M10I113M2D3M2D4M1D155M
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+gi|157734152:29655295-29712160	56866	8715	10348	+	gi|342187237:5004-8419	3416	1488	3158	1295	1726	0	NM:i:431	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2041	rl:i:96	cg:Z:35M1D414M1I3M1D7M1D12M3I44M20I84M3D2M2D2M10D42M1I3M1D9M3D2M4D21M1I30M6I7M1D3M2D11M1I1M1I11M4D8M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I38M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8715	10348	+	gi|568815529:1421891-1425306	3416	1488	3158	1295	1726	0	NM:i:431	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2041	rl:i:96	cg:Z:35M1D414M1I3M1D7M1D12M3I44M20I84M3D2M2D2M10D42M1I3M1D9M3D2M4D21M1I30M6I7M1D3M2D11M1I1M1I11M4D8M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I38M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8715	10348	+	gi|568815454:1200216-1203631	3416	1488	3158	1295	1726	0	NM:i:431	ms:i:964	AS:i:970	nn:i:0	tp:A:S	cm:i:10	s1:i:118	de:f:0.2041	rl:i:96	cg:Z:35M1D414M1I3M1D7M1D12M3I44M20I84M3D2M2D2M10D42M1I3M1D9M3D2M4D21M1I30M6I7M1D3M2D11M1I1M1I11M4D8M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I38M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	45590	46424	+	gi|528476637:29857558-29915771	58214	30702	31514	718	856	0	NM:i:138	ms:i:944	AS:i:956	nn:i:0	tp:A:S	cm:i:50	s1:i:439	de:f:0.1114	zd:i:1	rl:i:96	cg:Z:36M2I6M1D4M3D8M3I14M2D4M1D10M2D15M1D27M1D80M1D63M1D128M32I197M7D1M2D3M1I15M2I1M1I138M3I40M
+gi|157734152:29655295-29712160	56866	8715	10348	+	gi|568815592:29942469-29945883	3415	1487	3157	1291	1726	0	NM:i:435	ms:i:944	AS:i:950	nn:i:0	tp:A:S	cm:i:9	s1:i:103	de:f:0.2060	rl:i:96	cg:Z:35M1D414M1I3M1D7M1D12M3I44M20I84M3D2M2D2M10D42M1I3M1D9M3D2M4D21M1I30M6I7M1D3M2D11M2I12M4D8M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I38M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	30823	31632	+	gi|157734152:29655295-29712160	56866	45590	46426	716	858	0	NM:i:142	ms:i:934	AS:i:946	nn:i:0	tp:A:S	cm:i:47	s1:i:408	de:f:0.1106	zd:i:1	rl:i:96	cg:Z:36M2D5M7D20M4I3M2I4M1I10M2I15M1I27M1I80M1I63M1I128M32D48M1D148M7I1M2I3M1D15M2D1M1D138M3D42M
+gi|157734152:29655295-29712160	56866	45590	46426	+	gi|157734152:29655295-29712160	56866	30823	31632	716	858	0	NM:i:142	ms:i:934	AS:i:946	nn:i:0	tp:A:S	cm:i:47	s1:i:408	de:f:0.1106	zd:i:1	rl:i:96	cg:Z:36M2I5M7I20M4D3M2D4M1D10M2D15M1D27M1D80M1D63M1D128M32I48M1I148M7D1M2D3M1I15M2I1M1I138M3I42M
+gi|157734152:29655295-29712160	56866	30823	31630	+	gi|528476637:29857558-29915771	58214	45466	46300	713	856	0	NM:i:143	ms:i:924	AS:i:936	nn:i:0	tp:A:S	cm:i:47	s1:i:312	de:f:0.1121	rl:i:96	cg:Z:36M2D5M7D20M4I3M2I4M1I10M2I15M1I27M1I80M1I63M1I128M32D48M1D148M7I1M2I3M1D15M2D1M1D138M3D40M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815551:1197321-1201446	4126	2203	3873	1286	1731	0	NM:i:445	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2115	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M6D1M2D58M3D2M3D21M1I30M6I11M1D6M1I4M3I13M3D10M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|157734152:29655295-29712160	56866	54938	56608	1286	1731	0	NM:i:445	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2115	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M6D1M2D58M3D2M3D21M1I30M6I11M1D6M1I4M3I13M3D10M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D71M2D47M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815564:1286641-1289973	3333	1410	3080	1286	1731	0	NM:i:445	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2115	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M6D1M2D58M3D2M3D21M1I30M6I11M1D6M1I4M3I13M3D10M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	54938	56608	+	gi|157734152:29655295-29712160	56866	8708	10348	1286	1732	0	NM:i:446	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2110	rl:i:96	cg:Z:42M1I414M1D3M1I7M1I12M3D21M1D2M2D18M20D78M12I3M2I1M2I2M1D58M3I2M3I21M1D30M6D11M1I6M1D4M3D13M3I10M1I2M2I7M4I60M3I11M1D6M1D17M2I8M1D5M2D8M2D2M1D25M2D4M1D3M1I39M2I15M26I105M2D1M5D59M1I108M1I2M1D47M2I71M2I47M1D6M7I3M3I40M2I3M1D19M1D7M1D37M3I12M1I41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|528476637:29857558-29915771	58214	56286	57956	1286	1731	0	NM:i:445	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2115	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M6D1M2D58M3D2M3D21M1I30M6I11M1D6M1I4M3I13M3D10M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	54938	56608	+	gi|528476637:29857558-29915771	58214	8629	10269	1286	1732	0	NM:i:446	ms:i:888	AS:i:894	nn:i:0	tp:A:S	cm:i:12	s1:i:132	de:f:0.2110	rl:i:96	cg:Z:42M1I414M1D3M1I7M1I12M3D21M1D2M2D18M20D78M12I3M2I1M2I2M1D58M3I2M3I21M1D30M6D11M1I6M1D4M3D13M3I10M1I2M2I7M4I60M3I11M1D6M1D17M2I8M1D5M2D8M2D2M1D25M2D4M1D3M1I39M2I15M26I105M2D1M5D59M1I108M1I2M1D47M2I71M2I47M1D6M7I3M3I40M2I3M1D19M1D7M1D37M3I12M1I41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815561:1196951-1200436	3486	1561	3233	1285	1737	0	NM:i:452	ms:i:874	AS:i:880	nn:i:0	tp:A:S	cm:i:10	s1:i:116	de:f:0.2107	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I78M14D4M2D2M1I48M2D10M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M7D7M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815567:1196244-1200852	4609	2686	4356	1284	1732	0	NM:i:448	ms:i:868	AS:i:874	nn:i:0	tp:A:S	cm:i:9	s1:i:100	de:f:0.2132	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D2M3D1M5D58M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M1D1M1D11M1D2M2D7M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	8708	10348	+	gi|568815569:1240288-1243708	3421	1496	3168	1284	1736	0	NM:i:452	ms:i:868	AS:i:874	nn:i:0	tp:A:S	cm:i:10	s1:i:116	de:f:0.2118	rl:i:96	cg:Z:42M1D414M1I3M1D7M1D12M3I21M1I2M2I18M20I79M3D3M4D3M8D48M2D10M3D2M3D21M1I30M6I11M1D6M2D7M4I4M1I3M7D7M1I4M1I8M4D60M3D11M1I6M1I17M2D8M1I5M2I8M2I2M1I25M2I4M1I3M1D39M2D15M26D105M2I1M5I59M1D108M1D2M1I47M2D69M2D49M1I6M7D3M3D40M2D3M1I19M1I7M1I37M3D12M1D41M
+gi|157734152:29655295-29712160	56866	46634	47076	+	gi|157734152:29655295-29712160	56866	46006	46443	427	443	0	NM:i:16	ms:i:796	AS:i:796	nn:i:0	tp:A:S	cm:i:59	s1:i:350	de:f:0.0251	rl:i:96	cg:Z:405M6I20M1D11M
+gi|157734152:29655295-29712160	56866	46006	46443	+	gi|157734152:29655295-29712160	56866	46634	47076	427	442	0	NM:i:15	ms:i:796	AS:i:796	nn:i:0	tp:A:S	cm:i:59	s1:i:350	de:f:0.0273	rl:i:96	cg:Z:405M4D21M1D11M
+gi|157734152:29655295-29712160	56866	46634	47073	+	gi|528476637:29857558-29915771	58214	45882	46332	428	450	0	NM:i:22	ms:i:782	AS:i:782	nn:i:0	tp:A:S	cm:i:56	s1:i:327	de:f:0.0295	rl:i:96	cg:Z:393M10D38M1D8M
+gi|157734152:29655295-29712160	56866	4717	5886	+	gi|528476637:29857558-29915771	58214	27052	28249	926	1207	0	NM:i:281	ms:i:732	AS:i:732	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2166	rl:i:96	cg:Z:100M1I5M1D139M7D13M1D133M7D80M1I58M1D6M1I70M1D31M2I5M1D15M1D3M1D17M1I2M1D168M9D2M1D48M2D113M2I73M2I4M2D15M1D23M1D36M
+gi|157734152:29655295-29712160	56866	27171	28370	+	gi|157734152:29655295-29712160	56866	4717	5886	925	1208	0	NM:i:283	ms:i:722	AS:i:722	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2181	rl:i:96	cg:Z:100M1D5M1I139M9I13M1I133M7I80M1D58M1I6M1D70M1I31M2D5M1I15M1I3M1I16M1I3M1D168M9I2M1I48M2I113M2D73M1I5M1D15M1I23M1I36M
+gi|157734152:29655295-29712160	56866	4717	5886	+	gi|157734152:29655295-29712160	56866	27171	28370	925	1209	0	NM:i:284	ms:i:722	AS:i:722	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2174	rl:i:96	cg:Z:100M1I5M1D139M9D13M1D133M7D80M1I58M1D6M1I70M1D31M2I5M1D15M1D3M1D17M1I2M1D168M9D2M1D48M2D113M2I73M2I4M2D15M1D23M1D36M
+gi|157734152:29655295-29712160	56866	27171	28370	+	gi|528476637:29857558-29915771	58214	4739	5908	924	1208	0	NM:i:284	ms:i:716	AS:i:716	nn:i:0	tp:A:S	cm:i:8	s1:i:95	de:f:0.2189	rl:i:96	cg:Z:100M1D5M1I139M9I13M1I133M7I80M1D58M1I6M1D70M1I31M2D5M1I15M1I3M1I16M1I3M1D168M9I2M1I48M2I113M2D73M1I5M1D15M1I23M1I36M
+gi|157734152:29655295-29712160	56866	54327	54743	+	gi|528476637:29857558-29915771	58214	44457	44873	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:37	s1:i:254	de:f:0.0481	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815569:1240288-1243708	3421	885	1301	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:32	s1:i:246	de:f:0.0481	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815567:1196244-1200852	4609	2075	2491	396	416	0	NM:i:20	ms:i:712	AS:i:712	nn:i:0	tp:A:S	cm:i:32	s1:i:257	de:f:0.0481	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815592:29942469-29945883	3415	891	1306	396	416	0	NM:i:20	ms:i:710	AS:i:710	nn:i:0	tp:A:S	cm:i:35	s1:i:244	de:f:0.0481	rl:i:96	cg:Z:321M1I94M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815561:1196951-1200436	3486	950	1366	395	416	0	NM:i:21	ms:i:706	AS:i:706	nn:i:0	tp:A:S	cm:i:29	s1:i:236	de:f:0.0505	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|528476637:29857558-29915771	58214	55675	56091	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815551:1197321-1201446	4126	1592	2008	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815564:1286641-1289973	3333	799	1215	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|157734152:29655295-29712160	56866	54327	54743	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	54327	54743	+	gi|157734152:29655295-29712160	56866	44580	44996	393	416	0	NM:i:23	ms:i:694	AS:i:694	nn:i:0	tp:A:S	cm:i:30	s1:i:216	de:f:0.0553	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815529:1421891-1425306	3416	891	1307	390	416	0	NM:i:26	ms:i:676	AS:i:676	nn:i:0	tp:A:S	cm:i:29	s1:i:188	de:f:0.0625	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|568815454:1200216-1203631	3416	891	1307	390	416	0	NM:i:26	ms:i:676	AS:i:676	nn:i:0	tp:A:S	cm:i:29	s1:i:188	de:f:0.0625	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	44580	44996	+	gi|342187237:5004-8419	3416	891	1307	390	416	0	NM:i:26	ms:i:676	AS:i:676	nn:i:0	tp:A:S	cm:i:29	s1:i:188	de:f:0.0625	rl:i:96	cg:Z:416M
+gi|157734152:29655295-29712160	56866	886	1289	+	gi|528476637:29857558-29915771	58214	44457	44872	370	415	0	NM:i:45	ms:i:580	AS:i:580	nn:i:0	tp:A:S	cm:i:16	s1:i:142	de:f:0.0842	rl:i:96	cg:Z:324M12D79M
+gi|157734152:29655295-29712160	56866	46651	47139	+	gi|528476637:29857558-29915771	58214	31111	31578	418	497	0	NM:i:79	ms:i:570	AS:i:573	nn:i:0	tp:A:S	cm:i:18	s1:i:159	de:f:0.1011	rl:i:96	cg:Z:196M7D1M2D3M1I15M2I1M1I138M3I30M23I74M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|157734152:29655295-29712160	56866	886	1289	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:11	s1:i:116	de:f:0.0891	rl:i:96	cg:Z:324M12I79M
+gi|157734152:29655295-29712160	56866	886	1289	+	gi|157734152:29655295-29712160	56866	44580	44995	368	415	0	NM:i:47	ms:i:568	AS:i:568	nn:i:0	tp:A:S	cm:i:11	s1:i:116	de:f:0.0891	rl:i:96	cg:Z:324M12D79M
+gi|157734152:29655295-29712160	56866	31228	31696	+	gi|157734152:29655295-29712160	56866	46651	47139	418	497	0	NM:i:79	ms:i:560	AS:i:560	nn:i:0	tp:A:S	cm:i:16	s1:i:161	de:f:0.1068	rl:i:96	cg:Z:47M1D148M7I1M2I3M1D15M2D1M1D138M3D25M8D7M13D74M
+gi|157734152:29655295-29712160	56866	46651	47139	+	gi|157734152:29655295-29712160	56866	31228	31696	418	497	0	NM:i:79	ms:i:560	AS:i:560	nn:i:0	tp:A:S	cm:i:16	s1:i:161	de:f:0.1068	rl:i:96	cg:Z:47M1I148M7D1M2D3M1I15M2I1M1I138M3I25M8I7M13I74M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|528476637:29857558-29915771	58214	886	1289	366	415	0	NM:i:49	ms:i:556	AS:i:556	nn:i:0	tp:A:S	cm:i:12	s1:i:107	de:f:0.0941	rl:i:96	cg:Z:324M12I79M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|528476637:29857558-29915771	58214	39378	39792	363	418	0	NM:i:55	ms:i:508	AS:i:508	nn:i:0	tp:A:S	cm:i:7	s1:i:93	de:f:0.1232	rl:i:96	cg:Z:85M3I4M3D48M1I274M
+gi|157734152:29655295-29712160	56866	44580	44995	+	gi|157734152:29655295-29712160	56866	39500	39914	362	418	0	NM:i:56	ms:i:502	AS:i:502	nn:i:0	tp:A:S	cm:i:6	s1:i:78	de:f:0.1256	rl:i:96	cg:Z:85M3I4M3D48M1I274M
+gi|157734152:29655295-29712160	56866	39500	39914	+	gi|157734152:29655295-29712160	56866	44580	44995	362	418	0	NM:i:56	ms:i:502	AS:i:502	nn:i:0	tp:A:S	cm:i:6	s1:i:78	de:f:0.1256	rl:i:96	cg:Z:85M3D4M3I48M1D274M
+gi|157734152:29655295-29712160	56866	39500	39914	+	gi|528476637:29857558-29915771	58214	44457	44872	360	418	0	NM:i:58	ms:i:490	AS:i:490	nn:i:0	tp:A:S	cm:i:6	s1:i:78	de:f:0.1304	rl:i:96	cg:Z:85M3D4M3I48M1D274M
+gi|157734152:29655295-29712160	56866	7021	7639	+	gi|528476637:29857558-29915771	58214	49208	49824	489	643	0	NM:i:154	ms:i:370	AS:i:370	nn:i:0	tp:A:S	cm:i:5	s1:i:47	de:f:0.2049	rl:i:96	cg:Z:26M4D20M1I64M2D7M1I1M1I39M9I5M2I5M4I75M2D8M1I4M2D25M1D11M1I5M1I2M2D4M1I4M1I7M5D7M1D133M1D49M1D29M4D5M3I3M1I53M
+gi|157734152:29655295-29712160	56866	7021	7639	+	gi|157734152:29655295-29712160	56866	47858	48472	488	641	0	NM:i:153	ms:i:364	AS:i:364	nn:i:0	tp:A:S	cm:i:5	s1:i:48	de:f:0.2078	rl:i:96	cg:Z:26M4D20M1I64M2D7M1I1M1I39M9I5M2I5M4I75M2D9M1I3M2D25M1D11M1I5M1I3M1D8M1I7M3D7M1D90M1I5M1D37M1D49M1D30M4D4M3I3M1I53M
+gi|157734152:29655295-29712160	56866	47858	48472	+	gi|528476637:29857558-29915771	58214	7043	7661	488	641	0	NM:i:153	ms:i:364	AS:i:364	nn:i:0	tp:A:S	cm:i:5	s1:i:48	de:f:0.2078	rl:i:96	cg:Z:26M4I20M1D64M2I7M1D1M1D39M9D5M2D5M4D75M2I9M1D3M2I25M1I11M1D5M1D3M1I8M1D7M3I7M1I90M1D5M1I37M1I49M1I30M4I4M3D3M1D53M
+gi|157734152:29655295-29712160	56866	47858	48472	+	gi|157734152:29655295-29712160	56866	7021	7639	488	641	0	NM:i:153	ms:i:364	AS:i:364	nn:i:0	tp:A:S	cm:i:5	s1:i:48	de:f:0.2078	rl:i:96	cg:Z:26M4I20M1D64M2I7M1D1M1D39M9D5M2D5M4D75M2I9M1D3M2I25M1I11M1D5M1D3M1I8M1D7M3I7M1I90M1D5M1I37M1I49M1I30M4I4M3D3M1D53M
+gi|157734152:29655295-29712160	56866	28499	28764	-	gi|528476637:29857558-29915771	58214	29092	29357	235	265	41	NM:i:30	ms:i:350	AS:i:350	nn:i:0	tp:A:P	cm:i:4	s1:i:46	s2:i:0	de:f:0.1132	zd:i:2	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	14465	14764	-	gi|528476637:29857558-29915771	58214	45149	45463	266	316	0	NM:i:50	ms:i:350	AS:i:350	nn:i:0	tp:A:S	cm:i:3	s1:i:40	de:f:0.1192	rl:i:96	cg:Z:5M1I26M2D116M14D2M1D114M1I34M
+gi|157734152:29655295-29712160	56866	29213	29478	-	gi|528476637:29857558-29915771	58214	28378	28643	234	265	0	NM:i:31	ms:i:344	AS:i:344	nn:i:0	tp:A:S	cm:i:4	s1:i:46	de:f:0.1170	zd:i:1	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	28499	28764	-	gi|157734152:29655295-29712160	56866	29213	29478	233	265	40	NM:i:32	ms:i:338	AS:i:338	nn:i:0	tp:A:P	cm:i:4	s1:i:46	s2:i:0	de:f:0.1208	zd:i:2	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	29213	29478	-	gi|157734152:29655295-29712160	56866	28499	28764	233	265	0	NM:i:32	ms:i:338	AS:i:338	nn:i:0	tp:A:S	cm:i:4	s1:i:46	de:f:0.1208	zd:i:1	rl:i:96	cg:Z:265M
+gi|157734152:29655295-29712160	56866	17792	17978	+	gi|157734152:29655295-29712160	56866	17883	18067	176	186	0	NM:i:10	ms:i:312	AS:i:312	nn:i:0	tp:A:S	cm:i:11	s1:i:86	de:f:0.0486	rl:i:96	cg:Z:6M2I178M
+gi|157734152:29655295-29712160	56866	17883	18067	+	gi|157734152:29655295-29712160	56866	17792	17978	176	186	0	NM:i:10	ms:i:312	AS:i:312	nn:i:0	tp:A:S	cm:i:11	s1:i:86	de:f:0.0486	rl:i:96	cg:Z:6M2D178M
+gi|157734152:29655295-29712160	56866	6285	6982	-	gi|528476637:29857558-29915771	58214	6307	7004	528	727	0	NM:i:199	ms:i:272	AS:i:272	nn:i:0	tp:A:S	cm:i:4	s1:i:44	de:f:0.2392	rl:i:96	cg:Z:11M1D155M1I43M2D64M2I1M1I6M3I5M2I1M2I6M1D9M2I3M3D6M8I5M1I8M1I5M1I9M1D6M1D5M1D8M8D5M3I4M2D3M2D13M2D7M5D70M2I43M1D154M1I12M
+gi|157734152:29655295-29712160	56866	6285	6982	-	gi|157734152:29655295-29712160	56866	6285	6982	528	723	0	NM:i:195	ms:i:272	AS:i:272	nn:i:0	tp:A:S	cm:i:4	s1:i:44	de:f:0.2436	rl:i:96	cg:Z:11M1D155M1I43M2D64M2I1M1I6M3I5M2I1M2I6M1D9M2I3M3D6M1I7M2D2M2I3M2D26M2I3M2D2M2I7M1D5M3I4M2D3M2D13M2D7M5D70M2I43M1D154M1I12M
+gi|157734152:29655295-29712160	56866	8039	8361	+	gi|157734152:29655295-29712160	56866	8039	8285	228	323	0	NM:i:95	ms:i:262	AS:i:281	nn:i:0	tp:A:S	cm:i:8	s1:i:53	de:f:0.0769	rl:i:96	cg:Z:131M77I89M1D25M
+gi|157734152:29655295-29712160	56866	8039	8285	+	gi|157734152:29655295-29712160	56866	8039	8361	228	323	0	NM:i:95	ms:i:262	AS:i:281	nn:i:0	tp:A:S	cm:i:8	s1:i:53	de:f:0.0769	rl:i:96	cg:Z:131M77D89M1I25M
+gi|157734152:29655295-29712160	56866	46497	46603	-	gi|157734152:29655295-29712160	56866	46497	46603	92	106	0	NM:i:14	ms:i:128	AS:i:128	nn:i:0	tp:A:S	cm:i:4	s1:i:54	de:f:0.1321	rl:i:96	cg:Z:106M
+gi|157734152:29655295-29712160	56866	8206	8392	+	gi|157734152:29655295-29712160	56866	8003	8199	154	201	0	NM:i:47	ms:i:116	AS:i:116	nn:i:0	tp:A:S	cm:i:5	s1:i:41	de:f:0.1979	rl:i:96	cg:Z:14M3D43M2I1M1I28M1D2M2D3M1D14M1D11M2D3M2D5M2I5M3D52M
+gi|157734152:29655295-29712160	56866	8003	8199	+	gi|157734152:29655295-29712160	56866	8206	8392	154	201	0	NM:i:47	ms:i:116	AS:i:116	nn:i:0	tp:A:S	cm:i:5	s1:i:41	de:f:0.1979	rl:i:96	cg:Z:14M3I43M2D1M1D28M1I2M2I3M1I14M1I11M2I3M2I5M2D5M3I52M
+gi|157734152:29655295-29712160	56866	46537	46603	-	gi|157734152:29655295-29712160	56866	46537	46603	60	66	0	NM:i:6	ms:i:96	AS:i:96	nn:i:0	tp:A:S	cm:i:4	s1:i:48	de:f:0.0909	rl:i:96	cg:Z:66M

lib/galaxy/datatypes/test/big.gfa1

@@ -0,0 +1,137 @@
+# Downloaded from https://github.com/sjackman/gfalint/blob/master/examples/big1.gfa
+H	VN:Z:1.0
+S	3	*	LN:i:5376	KC:i:485841
+S	5	*	LN:i:124	KC:i:6306
+S	7	*	LN:i:3602	KC:i:327981
+S	8	*	LN:i:52	KC:i:2218
+S	9	*	LN:i:48	KC:i:154
+S	10	*	LN:i:144	KC:i:4604
+S	11	*	LN:i:6491	KC:i:611916
+S	13	*	LN:i:10648	KC:i:1023627
+S	14	*	LN:i:48	KC:i:16
+S	15	*	LN:i:5930	KC:i:599587
+S	17	*	LN:i:9404	KC:i:991226
+S	18	*	LN:i:2206	KC:i:240150
+S	19	*	LN:i:893	KC:i:82277
+S	20	*	LN:i:12201	KC:i:1351219
+S	21	*	LN:i:49	KC:i:300
+S	22	*	LN:i:11669	KC:i:1131776
+S	23	*	LN:i:7665	KC:i:766424
+S	27	*	LN:i:48	KC:i:35
+S	28	*	LN:i:1597	KC:i:142681
+S	30	*	LN:i:48	KC:i:7874
+S	31	*	LN:i:94	KC:i:805
+S	32	*	LN:i:3065	KC:i:275287
+S	33	*	LN:i:70	KC:i:5123
+S	34	*	LN:i:49	KC:i:23
+S	36	*	LN:i:12335	KC:i:1315304
+S	37	*	LN:i:130	KC:i:5258
+S	38	*	LN:i:4516	KC:i:440430
+S	39	*	LN:i:59	KC:i:4094
+S	41	*	LN:i:215	KC:i:11423
+S	42	*	LN:i:146	KC:i:3161
+S	43	*	LN:i:50	KC:i:563
+S	44	*	LN:i:3913	KC:i:434585
+S	46	*	LN:i:2710	KC:i:268203
+S	47	*	LN:i:49	KC:i:200
+S	49	*	LN:i:61	KC:i:3442
+S	50	*	LN:i:5010	KC:i:532820
+S	51	*	LN:i:9644	KC:i:950549
+S	52	*	LN:i:417	KC:i:16750
+S	54	*	LN:i:50	KC:i:600
+S	55	*	LN:i:69	KC:i:11532
+S	56	*	LN:i:1550	KC:i:141042
+S	57	*	LN:i:346	KC:i:12512
+S	58	*	LN:i:3825	KC:i:349334
+S	59	*	LN:i:11508	KC:i:1237494
+S	60	*	LN:i:720	KC:i:72448
+S	61	*	LN:i:1086	KC:i:83405
+S	62	*	LN:i:4818	KC:i:464490
+S	63	*	LN:i:8207	KC:i:822244
+S	65	*	LN:i:67	KC:i:2088
+S	66	*	LN:i:4375	KC:i:421128
+S	67	*	LN:i:5063	KC:i:530425
+S	68	*	LN:i:78	KC:i:10057
+S	69	*	LN:i:10204	KC:i:1039066
+S	71	*	LN:i:789	KC:i:65350
+S	72	*	LN:i:95	KC:i:6170
+S	73	*	LN:i:48	KC:i:14
+S	76	*	LN:i:54	KC:i:1373
+S	77	*	LN:i:4167	KC:i:460259
+S	78	*	LN:i:49	KC:i:925
+S	79	*	LN:i:95	KC:i:5402
+S	83	*	LN:i:15015	KC:i:1487985
+S	84	*	LN:i:9811	KC:i:1021233
+S	85	*	LN:i:3483	KC:i:365113
+S	86	*	LN:i:7953	KC:i:722908
+L	3	+	65	-	47M
+L	3	-	76	-	47M
+L	5	+	47	-	47M
+L	5	-	22	-	47M
+L	5	-	32	+	47M
+L	7	+	49	-	47M
+L	8	+	33	-	47M
+L	8	+	55	-	36M
+L	8	-	78	+	47M
+L	8	-	79	+	47M
+L	9	+	37	-	47M
+L	9	+	47	+	46M
+L	9	-	67	-	47M
+L	9	-	69	-	47M
+L	10	+	47	+	47M
+L	11	-	43	-	47M
+L	14	+	30	+	47M
+L	14	+	31	+	47M
+L	14	+	73	-	47M
+L	17	+	21	-	47M
+L	18	+	78	-	47M
+L	19	+	76	+	47M
+L	19	-	76	-	47M
+L	20	-	76	+	47M
+L	21	+	51	-	47M
+L	21	-	32	-	47M
+L	21	-	66	+	47M
+L	22	+	63	+	47M
+L	23	+	68	-	47M
+L	27	+	30	+	47M
+L	27	+	31	+	47M
+L	27	+	73	-	47M
+L	27	-	31	-	47M
+L	27	-	83	+	47M
+L	28	+	43	+	47M
+L	30	+	30	+	47M
+L	30	+	31	+	47M
+L	30	+	73	-	47M
+L	30	-	34	-	47M
+L	31	-	34	-	47M
+L	32	-	63	+	47M
+L	33	+	72	-	47M
+L	33	-	44	-	47M
+L	33	-	55	-	16M
+L	34	+	73	-	47M
+L	36	-	63	-	47M
+L	36	-	85	+	47M
+L	37	-	49	+	47M
+L	39	+	56	+	47M
+L	39	+	67	+	47M
+L	39	-	71	-	47M
+L	39	-	65	+	14M
+L	41	+	43	+	47M
+L	42	+	65	-	47M
+L	43	+	60	+	47M
+L	47	+	59	+	47M
+L	49	+	71	+	47M
+L	49	-	84	+	47M
+L	52	-	65	+	47M
+L	54	+	77	-	47M
+L	54	+	54	+	46M
+L	54	-	58	-	47M
+L	55	+	72	-	36M
+L	55	-	79	-	47M
+L	55	-	78	-	44M
+L	57	+	63	-	47M
+L	57	+	85	+	47M
+L	61	+	68	+	47M
+L	68	+	68	+	26M
+L	72	-	78	+	47M
+L	72	-	79	+	47M

lib/galaxy/datatypes/test/test.dta2d

@@ -0,0 +1,9 @@
+#MZ	SEC	INT
+500.0	0	50
+600.0	1	100
+700.0	2	200
+800.0	3	400
+900.0	4	200
+1000.0	5	100
+1100.0	6	50
+900.0	2	200

lib/galaxy/datatypes/test/test.edta

@@ -0,0 +1,7 @@
+RT	mz	Int	charge	Meta2
+10	114	2342	1
+10	115	232	2
+10	116	523	2
+14	220	343	1	value
+14	431.1	343	2
+15	543.2393	343	3	b

lib/galaxy/datatypes/test/test.kroenik

@@ -0,0 +1,23 @@
+File	First Scan	Last Scan	Num of Scans	Charge	Monoisotopic Mass	Base Isotope Peak	Best Intensity	Summed Intensity	First RTime	Last RTime	Best RTime	Best Correlation	Modifications
+20060502data08_exc_RTf.mzXML	1480	1578	15	3	1345.607960	449.543300	60834.925781	506348.656250	521.106018	553.833008	533.018982	0.991700	_
+20060502data08_exc_RTf.mzXML	1487	1557	11	2	1345.608400	673.811500	26904.589844	199969.046875	523.559998	546.731018	533.018982	0.995300	_
+20060502data08_exc_RTf.mzXML	1557	1620	10	3	2002.810800	668.945100	38904.792969	217929.312500	546.731018	567.784973	553.833008	0.986300	_
+20060502data08_exc_RTf.mzXML	1571	1592	4	2	2002.811525	1002.913800	4603.663086	14353.689453	551.427979	558.577026	556.184998	0.978400	_
+20060502data08_exc_RTf.mzXML	1592	1690	15	3	1772.892100	591.971200	91715.507813	502103.500000	558.577026	590.963013	567.784973	0.986900	_
+20060502data08_exc_RTf.mzXML	1599	1683	13	4	1772.891285	444.230100	72974.398438	417335.125000	560.914001	588.521973	570.002014	0.974700	_
+20060502data08_exc_RTf.mzXML	1599	1676	11	2	1772.889336	887.452600	22342.041016	122096.265625	560.914001	586.155029	567.784973	0.994600	_
+20060502data08_exc_RTf.mzXML	1690	1774	13	2	1401.655615	701.834900	37010.062500	262936.343750	590.963013	619.705017	605.291992	0.995500	_
+20060502data08_exc_RTf.mzXML	1746	1816	11	2	1065.545100	533.779800	48403.296875	347601.562500	610.046997	634.202026	622.135986	0.979800	_
+20060502data08_exc_RTf.mzXML	1816	1851	6	4	2095.873767	525.226300	17985.734375	73192.179688	634.202026	646.385986	641.471008	0.986700	_
+20060502data08_exc_RTf.mzXML	1858	1879	4	4	1904.987400	477.504500	7037.772461	16893.957031	648.786011	656.114014	656.114014	0.962100	_
+20060502data08_exc_RTf.mzXML	1879	1907	4	2	994.581075	498.297700	28557.644531	92082.468750	656.114014	665.525024	660.861023	0.996100	_
+20060502data08_exc_RTf.mzXML	1886	1994	15	3	1506.688193	503.236500	223091.640625	1329185.625000	658.479980	693.369995	670.021973	0.989100	_
+20060502data08_exc_RTf.mzXML	1893	1955	10	2	1506.689740	754.352500	49197.664063	307397.281250	660.861023	680.966003	672.174988	0.990500	_
+20060502data08_exc_RTf.mzXML	1907	2056	23	4	2239.081209	561.027900	189284.390625	1359320.875000	665.525024	713.080994	685.143005	0.973600	_
+20060502data08_exc_RTf.mzXML	1914	1994	13	2	1336.644692	669.329400	174888.703125	994234.375000	667.744019	693.369995	676.612000	0.990700	_
+20060502data08_exc_RTf.mzXML	1921	1988	10	2	1478.675160	740.344800	119720.226563	577115.250000	670.021973	691.309998	678.859985	0.985600	_
+20060502data08_exc_RTf.mzXML	1928	1948	3	2	1697.803500	849.907800	3211.451660	7545.761719	672.174988	678.859985	672.174988	0.927400	_
+20060502data08_exc_RTf.mzXML	1935	1955	4	2	1127.618850	564.816500	67462.703125	183348.593750	674.471985	680.966003	680.966003	0.950400	_
+20060502data08_exc_RTf.mzXML	1941	2021	12	3	2239.081067	747.701800	67137.210938	463090.031250	676.612000	701.872009	683.143982	0.991200	_
+20060502data08_exc_RTf.mzXML	1948	2028	13	2	1583.758454	792.886000	36854.781250	262471.843750	678.859985	704.109009	691.309998	0.993400	_
+20060502data08_exc_RTf.mzXML	1955	2021	11	3	1583.757945	528.926500	128648.492188	829892.062500	680.966003	701.872009	691.309998	0.990400	_

lib/galaxy/datatypes/test/test.mztab

@@ -0,0 +1,28 @@
+MTD	mzTab-version	1.0 rc5
+MTD	mzTab-mode	Summary
+MTD	mzTab-type	Identification
+MTD	mzTab-ID	Cytidine
+MTD	description	LC-MS/MS Reference Standard
+MTD	sample_processing[1]	[MS, MS:1000544, Conversion to mzML, ]|[MS, MS:1000035, Peak picking, ]|[MS, MS:1001994, Top Hat baseline reduction, ]|[MS, MS:1000782, Savitzky-Golay smoothing, ]|[MS, MS:1000594, Low intensity data point removal, ]
+MTD	instrument[1]-name	[MS, MS:1000483, Thermo Fisher Scientific instrument model, LTQ Orbitrap Velos]
+MTD	instrument[1]-source	[MS, MS:1000008, Ionization Type, ESI]
+MTD	instrument[1]-analyzer[1]	[MS, MS:1000443, Mass Analyzer Type, Orbitrap]
+MTD	instrument[1]-detector	[MS, MS:1000453, Detector, Dynode Detector]
+MTD	software[1]	[MS, MS:1002205, ProteoWizard msconvert, ]
+MTD	software[1]-setting[1]	Peak Picking MS1
+MTD	software[1]	[MS, MS:1001457, data processing software, MassCascade-KNIME]
+MTD	smallmolecule_search_engine_score[1]	[MS, MS:1001153, search engine specific score,]
+MTD	contact[1]-name	Stephan Beisken
+MTD	contact[1]-affiliation	European Bioinformatics Institute (EMBL-EBI)
+MTD	contact[1]-email	beiken@ebi.ac.uk
+MTD	uri[1]	http://www.ebi.ac.uk/metabolights/MTBLS38
+MTD	fixed_mod[1]	[MS, MS:1002453, No fixed modifications searched, ]
+MTD	variable_mod[1]	[ , , CHEMMOD:2M+H, ]
+MTD	variable_mod[2]	[ , , CHEMMOD:M-C5H8O4, ]
+MTD	ms_run[1]-format	[MS, MS:1000584, Proteomics Standards Inititative mzML file format, mzML file]
+MTD	ms_run[1]-location	ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS38/cytidine.mzML
+MTD	ms_run[1]-id_format	[MS, MS:1000767, Native spectrum identifier format, ]
+MTD	ms_run[1]-fragmentation_method	[MS, MS:1000133, Collision-induced dissociation, ]
+
+SMH	identifier	chemical_formula	smiles	inchi_key	description	exp_mass_to_charge	calc_mass_to_charge	charge	retention_time	taxid	species	database	database_version	spectra_ref	search_engine	best_search_engine_score[1]	modifications
+SML	CHEBI:17562	C9H13N3O5	Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1	UHDGCWIWMRVCDJ-XVFCMESISA-N	Cytidine	244.0928	null	1	193.25	null	null	ChEBI	109	null	[MS, MS:1001083, ms-ms search, MassBank]	977	CHEMMOD:2M+H,CHEMMOD:M-C5H8O4

lib/galaxy/datatypes/test/test.mztab2

@@ -0,0 +1,92 @@
+COM	Meta data section																		
+MTD	mzTab-version	2.0.0-M																	
+MTD	mzTab-ID	mzTab-GCxGC-MS																	
+MTD	description	Minimal sample file for GCxGC-MS quantification of small molecules between two experiments																	
+MTD	instrument[1]-name	[MS, MS:1001945, Pegasus 4D, ]																	
+MTD	instrument[1]-source	[MS, MS:1000389, electron Ionization, ]																	
+MTD	instrument[1]-analyzer[1]	[MS, MS:1000084, time-of-flight, ]																	
+MTD	instrument[1]-detector	[MS, MS:1000114, microchannel plate detector, ]																	
+MTD	software[1]	[MS, MS:1001799, ChromaTOF software, 3.21]
+MTD	software[1]-setting[1]	baseline=0.2
+MTD	software[1]-setting[2]	dbMatchTreshold=900
+MTD	sample[1]-species[1]	[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]																	
+MTD	sample[1]-cell_type[1]	[CL, CL:0000233, platelet, ]																	
+MTD	sample[1]-description	Unstimulated human blood platelets																	
+MTD	sample[2]-species[1]	[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]																	
+MTD	sample[2]-cell_type[1]	[CL, CL:0000233, platelet, ]																	
+MTD	sample[2]-description	Unstimulated human blood platelets																	
+MTD	ms_run[1]-location	file://c:/data/control.mzML																	
+MTD	ms_run[1]-format	[MS, MS:1000584, mzML file, ]																	
+MTD	ms_run[1]-id_format	[MS, MS:1000776, scan number only nativeID format, ]
+MTD	ms_run[1]-scan_polarity[1]	[MS, MS:1000130, positive scan, ]																	
+MTD	ms_run[2]-location	file://c:/data/treatment.mzML																	
+MTD	ms_run[2]-format	[MS, MS:1000584, mzML file, ]																	
+MTD	ms_run[2]-id_format	[MS, MS:1000776, scan number only nativeID format, ]
+MTD	ms_run[2]-scan_polarity[1]	[MS, MS:1000130, positive scan, ]																	
+MTD	assay[1]-sample_ref	sample[1]																	
+MTD	assay[1]-ms_run_ref	ms_run[1]																	
+MTD	assay[2]-sample_ref	sample[2]																	
+MTD	assay[2]-ms_run_ref	ms_run[2]																	
+MTD	study_variable[1]	Untreated																	
+MTD	study_variable[1]-assay_refs	assay[1]																	
+MTD	study_variable[1]-description	drug response control																	
+MTD	study_variable[1]-average_function	[MS, MS:1002962, mean, ]																	
+MTD	study_variable[1]-variation_function	[MS, MS:1002885, standard error, ]																	
+MTD	study_variable[2]	Treated																	
+MTD	study_variable[2]-assay_refs	assay[2]																	
+MTD	study_variable[2]-description	drug response treatment																	
+MTD	study_variable[2]-average_function	[MS, MS:1002962, mean, ]																	
+MTD	study_variable[2]-variation_function	[MS, MS:1002885, standard error, ]																	
+MTD	cv[1]-label	MS																	
+MTD	cv[1]-full_name	PSI-MS controlled vocabulary																	
+MTD	cv[1]-version	20-06-2018																	
+MTD	cv[1]-uri	https://www.ebi.ac.uk/ols/ontologies/ms																	
+MTD	cv[2]-label	NCBITaxon																	
+MTD	cv[2]-full_name	An ontology representation of the NCBI organismal taxonomy Ontology																	
+MTD	cv[2]-version	2018-03-02																	
+MTD	cv[2]-uri	https://www.ebi.ac.uk/ols/ontologies/ncbitaxon																	
+MTD	cv[3]-label	CL																	
+MTD	cv[3]-full_name	The Cell Ontology is a structured controlled vocabulary for cell types in animals.																	
+MTD	cv[3]-version	2017-12-11																	
+MTD	cv[3]-uri	https://www.ebi.ac.uk/ols/ontologies/cl																	
+MTD	cv[4]-label	PRIDE																	
+MTD	cv[4]-full_name	PRIDE PRoteomics IDEntifications (PRIDE) database controlled vocabulary																	
+MTD	cv[4]-version	14-06-2018																	
+MTD	cv[4]-uri	https://www.ebi.ac.uk/ols/ontologies/pride																	
+MTD	cv[5]-label	CHEBI																	
+MTD	cv[5]-full_name	Chemical Entities of Biological Interest
+MTD	cv[5]-version	08-02-2019																	
+MTD	cv[5]-uri	https://www.ebi.ac.uk/ols/ontologies/chebi
+MTD	database[1]	[, ,Golm Metabolite Database, ]																	
+MTD	database[1]-prefix	GMD																	
+MTD	database[1]-version	2.3																	
+MTD	database[1]-uri	http://gmd.mpimp-golm.mpg.de/																	
+MTD	database[2]	[, , no database, null]																	
+MTD	database[2]-prefix	null																	
+MTD	database[2]-uri	null																	
+MTD	database[2]-version	Unknown																	
+MTD	derivatization_agent[1]	[,,Methoxylamine hydrochloride,]																	
+MTD	derivatization_agent[2]	[CHEBI, CHEBI:85064, N-methyl-N-(trimethylsilyl)trifluoroacetamide,]																	
+MTD	small_molecule-identification_reliability	[MS, MS:1002896, compound identification confidence level, ]																	
+MTD	id_confidence_measure[1]	[MS, MS:1002890, fragmentation score, ]																	
+MTD	small_molecule-quantification_unit	[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]																	
+MTD	small_molecule_feature-quantification_unit	[PRIDE, PRIDE:0000330, Arbitrary quantification unit, ]																	
+MTD	quantification_method	[,,baseline-corrected intensity quantification,]																	
+MTD	custom[1]	[MS, MS:1000901, retention time normalization standard, n-alkanes C10–C36]																	
+																			
+COM	Small molecule summary rows (similar to Protein section). 																		
+COM	Evidences (e.g. multiple modifications, adducts incl. charge variants are summarized). 																		
+COM	For most use cases this summary lines might be sufficient.																		
+SMH	SML_ID	SMF_ID_REFS	database_identifier	chemical_formula	smiles	inchi	chemical_name	uri	theoretical_neutral_mass	adduct_ions	reliability	best_id_confidence_measure	best_id_confidence_value	abundance_assay[1]	abundance_study_variable[1]	abundance_variation_study_variable[1]	abundance_assay[2]	abundance_study_variable[2]	abundance_variation_study_variable[2]
+SML	1	1 | 2	GMD:cd7993ea-ad14-452a-a907-33376cc98790	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid	http://identifiers.org/gmd/cd7993ea-ad14-452a-a907-33376cc98790	284.478	[M+H]1+	2	[MS, MS:1002890, fragmentation score, ]	978	805.16	805.16	0	589.9	589.9	0
+																			
+COM	Small molecule feature rows (only reported in Complete Quantification files and if feature information like e.g. mass traces are important)																		
+SFH	SMF_ID	SME_ID_REFS	SME_ID_REF_ambiguity_code	adduct_ion	isotopomer	exp_mass_to_charge	charge	retention_time_in_seconds	retention_time_in_seconds_start	retention_time_in_seconds_end	abundance_assay[1]	abundance_assay[2]	opt_global_retention_time_nd	opt_global_retention_time_nd_window_start	opt_global_retention_time_nd_window_end				
+SMF	1	1	null	[M+H]1+	null	285.484	1	1564.47	1559.45	1564.48	805.16	805.16	1562 | 2.47 	1557 | 2.45 	1562 | 2.48				
+SMF	2	2	null	[M+H]1+	null	285.484	1	1564.48	1554.45	1569.47	589.9	589.9	1562 | 2.48	1552 | 2.45	1567| 2.47				
+																			
+COM	Small molecule evidence rows for parent ions. Analog to PSM. 																		
+COM	Primary use case: report single hits from spectral library or accurate mass searches without quantification.																		
+SEH	SME_ID	evidence_input_id	database_identifier	chemical_formula	smiles	inchi	chemical_name	uri	derivatized_form	adduct_ion	exp_mass_to_charge	charge	theoretical_mass_to_charge	spectra_ref	identification_method	ms_level	id_confidence_measure[1]	rank	
+SME	1	ms_run[1]:scan=8	GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid (1TMS)	http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3	[CHEBI, CHEBI:51088, trimethylsilyl group, 1]	[M+H]+	356.6588	1	356.659	ms_run[1]:scan=8	[,, ChromaTOF database search,]	[MS, MS:1000511, ms level, 1]	957	1	
+SME	2	ms_run[2]:scan=23	GMD:f634c736-39e8-4323-8155-fa3cc26ac9e3	C18H36O2	CCCCCCCCCCCCCCCCCC(O)=O	InChI=1S/C18H36O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18(19)20/h2-17H2,1H3,(H,19,20)	Octadecanoic acid (1TMS)	http://identifiers.org/gmd.analyte/f634c736-39e8-4323-8155-fa3cc26ac9e3	[CHEBI, CHEBI:51088, trimethylsilyl group, 1]	[M+H]+	356.6589	1	356.659	ms_run[2]:scan=23	[,, ChromaTOF database search,]	[MS, MS:1000511, ms level, 1]	972	1	

lib/galaxy/datatypes/test/test.peff

@@ -0,0 +1,11 @@
+# PEFF 1.0
+# //
+# DbName=Minimal Test example PEFF_Minimal_Valid.peff
+# Prefix=sp
+# DbSource=http://www.peptideatlas.org/formats/PEFF/PEFF_Minimal_Valid.peff
+# DbVersion=1
+# SequenceType=AA
+# NumberOfEntries=1
+# //
+>sp:Q9Y2X3 \Length=1
+M

lib/galaxy/datatypes/test/test.peplist

@@ -0,0 +1,36 @@
+       m/z	     rt(min)	       snr	      charge	   intensity
+  706.0656	     47.997	     70.443	          3	   3709.630
+  740.4292	     60.127	     28.895	          4	   2153.832
+  708.7055	     63.321	     28.970	          3	   2377.576
+  728.7255	     56.390	     28.530	          3	   1820.929
+  721.3855	     57.410	     25.965	          3	   1332.942
+  740.4400	     64.272	     16.639	          2	   1024.329
+  707.3855	     63.423	     20.248	          3	   1495.899
+  735.7055	     50.275	     29.838	          3	    804.873
+  726.7255	     63.966	     13.282	          3	   1364.349
+  723.4000	     57.647	     13.069	          2	    713.563
+  700.4400	     61.588	     11.435	          2	    579.007
+  736.3400	     61.113	      9.765	          2	    464.364
+  705.4000	     54.454	     12.855	          2	    457.507
+  709.0056	     57.104	     12.614	          3	    454.622
+  710.3000	     49.459	     18.364	          2	    534.519
+  719.4000	     64.714	      7.860	          3	    447.372
+  742.4400	     64.170	      6.799	          2	    357.583
+  752.4000	     55.983	      7.138	          2	    290.348
+  714.1492	     47.114	     22.442	          4	    576.568
+  753.4256	     61.486	      7.788	          3	    318.019
+  730.3800	     53.536	      8.914	          2	    284.038
+  708.8400	     58.836	      6.272	          2	    246.319
+  737.0400	     50.207	     12.257	          3	    309.824
+  716.9200	     58.123	      6.188	          2	    283.297
+  729.7456	     50.308	      9.760	          3	    428.650
+  712.3200	     49.391	      8.749	          2	    235.981
+  748.9400	     51.294	      9.114	          2	    250.202
+  712.8800	     53.672	      6.466	          2	    160.206
+  714.9000	     53.604	      6.417	          2	    202.450
+  716.8800	     54.080	      6.920	          2	    225.521
+  715.7055	     49.017	     10.866	          3	    198.560
+  728.3600	     53.299	      6.913	          3	    156.242
+  753.8800	     49.527	      6.406	          2	    113.352
+  724.0400	     47.997	      6.559	          3	    281.194
+  745.9200	     47.521	      6.732	          2	     87.974

lib/galaxy/datatypes/test/test.psms

@@ -0,0 +1,122 @@
+PSMId	score	q-value	posterior_error_prob	peptide	proteinIds
+query:161610;rank:1;spectrum:1093.0258_2187.96_spectrum=40633_uteruspremenopause;rt:2187.96;mz:1093.0258;charge:2	11.0472	0	1.48741e-12	X.SLAGSSGPGASSGTSGDHGELVVR.X	UniProt_E9PI39	UniProt_E9PIZ1	UniProt_E9PK01	UniProt_E9PL12	UniProt_E9PMW7	UniProt_E9PPR1	UniProt_E9PQ49	UniProt_E9PRY8	UniProt_H0YCK7	UniProt_P29692	UniProt_P29692-2	genCDS_ENST00000317198_8_143579792-143586845_-1	genCDS_ENST00000395119_8_143579792-143586845_-1	genCDS_ENST00000419152_8_143579792-143586845_-1	genCDS_ENST00000423316_8_143579792-143590081_-1	genCDS_ENST00000442189_8_143579792-143590081_-1	genCDS_ENST00000524397_8_143580630-143586845_-1	genCDS_ENST00000529007_8_143580630-143586845_-1	genCDS_ENST00000529272_8_143579792-143586845_-1	genCDS_ENST00000530191_8_143580506-143586845_-1	genCDS_ENST00000530445_8_143580620-143586845_-1	genCDS_ENST00000530616_8_143580630-143589222_-1	genCDS_ENST00000531218_8_143580522-143586845_-1	genCDS_ENST00000532741_8_143579792-143590231_-1	genCDS_ENST00000533204_8_143580506-143586845_-1	genCDS_ENST00000533494_8_143580613-143586845_-1	genCDS_ENST00000533749_8_143581079-143599321_-1	genCDS_ENST00000534380_8_143580034-143586845_-1	genCDS_ENST00000618139_8_143580019-143590081_-1
+query:132093;rank:1;spectrum:832.40479_2605.29_spectrum=72602_uteruspremenopause;rt:2605.29;mz:832.40479;charge:2	9.36298	0	7.2763e-11	X.AAAFEEQENETVVVK.X	UniProt_Q5TCU6	UniProt_Q9Y490	genCDS_ENST00000314888_9_35697791-35725694_-1
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+query:35867;rank:1;spectrum:503.7821_2660.72_spectrum=19332_uteruspremenopause;rt:2660.72;mz:503.7821;charge:2	2.36667	6.99035e-05	0.000613454	X.LVLEYVDR.X	UniProt_E7ETH0	UniProt_G3XAM2	UniProt_P05156	genCDS_ENST00000394634_4_109740893-109801971_-1	genCDS_ENST00000394635_4_109740893-109801971_-1	genCDS_ENST00000512148_4_109740893-109801971_-1
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+query:58423;rank:1;spectrum:571.82373_3329.4_spectrum=28523_uteruspremenopause;rt:3329.4;mz:571.82373;charge:2	-0.0664699	0.0118764	0.276689	X.VKGDVDVSVPK.X	UniProt_Q09666	genCDS_ENST00000378024_11_62516744-62536098_-1
+query:4273;rank:1;spectrum:388.21448_1441.57_spectrum=147307_uteruspremenopause;rt:1441.57;mz:388.21448;charge:2	-0.0871283	0.0123296	0.291726	X.LASLDEK.X	UniProt_E9PNR6	UniProt_H0YE29	UniProt_Q07960	genCDS_ENST00000311956_11_46679037-46696107_-1	genCDS_ENST00000525488_11_46681069-46696107_-1	genCDS_ENST00000528837_11_46679217-46696099_-1
+query:981;rank:1;spectrum:366.20657_1827.57_spectrum=78717_uteruspremenopause;rt:1827.57;mz:366.20657;charge:2	-0.266624	0.0180136	0.438278	X.DNTLLR.X	UniProt_A6NN80	UniProt_H0YG46	UniProt_J3KNE4	UniProt_P08133	UniProt_P08133-2	UniProt_Q8WZ42	UniProt_Q8WZ42-11	UniProt_Q8WZ42-12	UniProt_Q8WZ42-13	UniProt_Q8WZ42-2	UniProt_Q8WZ42-4	UniProt_Q8WZ42-5	UniProt_Q8WZ42-7	UniProt_Q8WZ42-8	UniProt_Q99550	UniProt_Q99550-2	UniProt_U3KQ28	XXX_3776517	XXX_3780596	XXX_3818260	XXX_3846030	XXX_3896565	XXX_4087153	XXX_4095718	XXX_4139454	XXX_4158810	XXX_4177746	genCDS_ENST00000302373_12_123161368-123221847_-1	genCDS_ENST00000342992_2_178527012-178804642_-1	genCDS_ENST00000354546_5_151101448-151147901_-1	genCDS_ENST00000523714_5_151101448-151140165_-1	genCDS_ENST00000539024_12_123161368-123218478_-1	genCDS_ENST00000541076_12_123156807-123230364_-1	genCDS_ENST00000589042_2_178527012-178804642_-1	genCDS_ENST00000591111_2_178527012-178804642_-1	genCDS_ENST00000606320_12_123156807-123230364_-1	genCDS_ENST00000615779_2_178527012-178804642_-1
+query:33052;rank:1;spectrum:494.77515_1390.27_spectrum=155237_uteruspremenopause;rt:1390.27;mz:494.77515;charge:2	-0.390915	0.0229485	0.545281	X.KQVENKN(Deamidated)K.X	UniProt_Q15431	UniProt_Q5VXJ5	genCDS_ENST00000369518_1_114855465-114995019_1	genCDS_ENST00000369522_1_114855465-114995019_1	genCDS_ENST00000455987_1_114855465-114977610_1	genCDS_ENST00000613524_1_114855465-114995019_1	genCDS_ENST00000618516_1_114855465-114995019_1
+query:15821;rank:1;spectrum:438.23367_2620.9_spectrum=88556_uteruspremenopause;rt:2620.9;mz:438.23367;charge:2	-0.554281	0.0308507	0.671862	X.QGGPEFLK.X	calCuffs_CUFF.56789.1_16_67551854-67597900_-1_1_ORF3	calCuffs_CUFF.56789.2_16_67551854-67562677_-1_1_ORF3	calCuffs_CUFF.56789.3_16_67551854-67562643_-1_3_ORF2	calCuffs_CUFF.56789.4_16_67551854-67564404_-1_2_ORF5	calCuffs_CUFF.56789.5_16_67551854-67556024_-1_1_ORF2	ensBodymap_RNASEQT00000108700_16_67551703-67597612_-1	genlncRNA_ENST00000613438_16_67517862-67528632_-1_3_ORF2	genlncRNA_ENST00000621378_16_67517950-67528675_-1_2_ORF4	mitSBM_kidney_16_67551858-67562264_-1_3_ORF1	mitSBM_lymphNode_16_67551861-67562262_-1_1_ORF1
+query:149496;rank:1;spectrum:951.48413_3058.62_spectrum=89727_uteruspremenopause;rt:3058.62;mz:951.48413;charge:2	-0.634256	0.0352042	0.722362	X.(Acetyl)KPGAAGQHPAPFDPQSVR.X	genlncRNA_ENST00000449990_9_90463659-90582744_-1_3_ORF1
+query:106872;rank:1;spectrum:720.35449_2699.4_spectrum=150809_uteruspremenopause;rt:2699.4;mz:720.35449;charge:2	-0.816145	0.0457039	0.814517	X.STDNVFLACWVK.X	calCuffs_CUFF.6079.5_1_107514034-107541205_-1_3_ORF3
+query:44599;rank:1;spectrum:531.28_2604.3_spectrum=19171_uteruspremenopause;rt:2604.3;mz:531.28;charge:2	-0.98233	0.0555745	0.881893	X.KQ(Deamidated)WERTGR.X	calCuffs_CUFF.84105.1_2_227648862-227677259_1_3_ORF138	calCuffs_CUFF.84105.2_2_227653754-227677259_1_1_ORF74
+query:2044;rank:1;spectrum:374.22897_2891.89_spectrum=135978_uteruspremenopause;rt:2891.89;mz:374.22897;charge:2	-1.04589	0.0593188	0.912796	X.FLLQAR.X	UniProt_P07360	UniProt_Q5SQ08	XXX_2911659	XXX_2911660	XXX_3992543	XXX_4073578	calCuffs_CUFF.65457.2_18_60989274-60994029_1_2_ORF3	genCDS_ENST00000224181_9_136945321-136946781_1	genCDS_ENST00000371634_9_136945321-136946361_1
+query:154157;rank:1;spectrum:664.31238_3596.01_spectrum=176082_uteruspremenopause;rt:3596.01;mz:664.31238;charge:3	-1.09757	0.0622534	0.94086	X.(Acetyl)SKCFASN(Deamidated)SQ(Deamidated)LLYSQGEK.X	genlncRNA_ENST00000428520_10_10934524-10952095_-1_1_ORF2
+query:109576;rank:1;spectrum:730.34552_2652.62_spectrum=142764_uteruspremenopause;rt:2652.62;mz:730.34552;charge:2	-1.13897	0.0647164	0.964364	X.(Carbamidomethyl)NN(Deamidated)PVMSLQDQ(Deamidated)VR.X	UniProt_A6ND99	UniProt_K7EP71	UniProt_Q7LGA3	UniProt_Q7LGA3-2	UniProt_Q7LGA3-3	genCDS_ENST00000370548_1_86993082-87168176_1	genCDS_ENST00000370550_1_86915037-87104696_1	genCDS_ENST00000370551_1_86915037-87097939_1	genCDS_ENST00000591456_1_87072984-87092588_1
+query:10757;rank:1;spectrum:419.25119_2212.53_spectrum=126558_uteruspremenopause;rt:2212.53;mz:419.25119;charge:2	-1.35549	0.0765402	1	X.KSRFTAK.X	calCuffs_CUFF.117687.1_5_43436710-43444350_-1_3_ORF32
+query:81984;rank:1;spectrum:634.33673_1983.63_spectrum=10106_uteruspremenopause;rt:1983.63;mz:634.33673;charge:2	-1.63897	0.0885601	1	X.(Acetyl)KGLDVAEPGPSR.X	UniProt_Q01433	genCDS_ENST00000256578_1_109621014-109631152_1	genCDS_ENST00000528667_1_109621014-109631152_1
+query:58730;rank:1;spectrum:572.7724_1350.11_spectrum=155143_uteruspremenopause;rt:1350.11;mz:572.7724;charge:2	-1.85044	0.0949322	1	X.LGGQ(Deamidated)M(Oxidation)Q(Deamidated)VHQ(Deamidated)K.X	genpseudogene_ENST00000442645_7_14985378-14986074_-1_3_ORF2
+query:175487;rank:1;spectrum:943.40503_1694.59_spectrum=101873_uteruspremenopause;rt:1694.59;mz:943.40503;charge:3	-2.1027	0.100208	1	X.(Acetyl)YEDSQQ(Deamidated)EEAQ(Deamidated)YGAMFQ(Deamidated)EQLM(Oxidation)TLK.X	UniProt_F5H4J1	UniProt_Q14980	UniProt_Q14980-2	UniProt_Q14980-3	UniProt_Q14980-4	genCDS_ENST00000358965_11_72003527-72035943_-1	genCDS_ENST00000393695_11_72003527-72035943_-1	genCDS_ENST00000542977_11_72014948-72035943_-1	genCDS_ENST00000616538_11_72003527-72035943_-1	genCDS_ENST00000620566_11_72003527-72035943_-1
+query:90871;rank:1;spectrum:660.8255_2297.68_spectrum=111599_uteruspremenopause;rt:2297.68;mz:660.8255;charge:2	-2.46345	0.104155	1	X.(Carbamidomethyl)AHN(Deamidated)FDERVFK.X	UniProt_Q96M60	UniProt_Q96M60-2	genCDS_ENST00000299338_15_49328568-49615171_-1	genCDS_ENST00000561064_15_49422710-49615171_-1

lib/galaxy/datatypes/text.py

@@ -730,3 +730,84 @@ class IQTree(Text):
         False
         """
         return file_prefix.startswith("IQ-TREE")
+
+
+@build_sniff_from_prefix
+class Paf(Text):
+    """
+    PAF: a Pairwise mApping Format
+
+    https://github.com/lh3/miniasm/blob/master/PAF.md
+    """
+    file_ext = "paf"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('A-3105.paf')
+        >>> Paf().sniff(fname)
+        True
+        """
+        found_valid_lines = False
+        for line in iter_headers(file_prefix, "\t"):
+            if len(line) < 12:
+                return False
+            for i in (1, 2, 3, 6, 7, 8, 9, 10, 11):
+                int(line[i])
+            if line[4] not in ('+', '-'):
+                return False
+            if not (0 <= int(line[11]) <= 255):
+                return False
+            # Check that the optional columns after the 12th contain SAM-like typed key-value pairs
+            for i in range(12, len(line)):
+                if len(line[i].split(':')) != 3:
+                    return False
+            found_valid_lines = True
+        return found_valid_lines
+
+
+@build_sniff_from_prefix
+class Gfa1(Text):
+    """
+    Graphical Fragment Assembly (GFA) 1.0
+
+    http://gfa-spec.github.io/GFA-spec/GFA1.html
+    """
+    file_ext = "gfa1"
+
+    def sniff_prefix(self, file_prefix):
+        """
+        >>> from galaxy.datatypes.sniff import get_test_fname
+        >>> fname = get_test_fname('big.gfa1')
+        >>> Gfa1().sniff(fname)
+        True
+        """
+        found_valid_lines = False
+        for line in iter_headers(file_prefix, "\t"):
+            if line[0].startswith('#'):
+                continue
+            if line[0] == 'H':
+                return len(line) == 2 and line[1] == 'VN:Z:1.0'
+            elif line[0] == 'S':
+                if len(line) < 3:
+                    return False
+            elif line[0] == 'L':
+                if len(line) < 6:
+                    return False
+                for i in (2, 4):
+                    if line[i] not in ('+', '-'):
+                        return False
+            elif line[0] == 'C':
+                if len(line) < 7:
+                    return False
+                for i in (2, 4):
+                    if line[i] not in ('+', '-'):
+                        return False
+                int(line[5])
+            elif line[0] == 'P':
+                if len(line) < 4:
+                    return False
+            else:
+                return False
+            found_valid_lines = True
+        return found_valid_lines

lib/galaxy/dependencies/__init__.py

@@ -175,6 +175,9 @@ class ConditionalDependencies(object):
     def check_kamaki(self):
         return 'pithos' in self.object_stores
 
+    def check_python_irodsclient(self):
+        return 'irods' in self.object_stores
+
     def check_watchdog(self):
         install_set = {'auto', 'True', 'true', 'polling'}
         return (self.config['watch_tools'] in install_set or

lib/galaxy/dependencies/conditional-requirements.txt

@@ -8,7 +8,7 @@ drmaa
 statsd
 docker
 azure-storage==0.32.0
-# PyRods not in PyPI
+python-irodsclient==0.8.2
 python-ldap==3.2.0
 python-pam
 galaxycloudrunner
@@ -31,4 +31,4 @@ influxdb
 
 # Deep learning packages for tool recommendation
 keras==2.2.4
-tensorflow==1.12.2
+tensorflow==1.15.2

lib/galaxy/dependencies/pipfiles/default/Pipfile

@@ -25,8 +25,9 @@ Sphinx = "*"
 sphinx_markdown_tables = "*"
 sphinx_rtd_theme = "*"
 testfixtures = "*"
-twill = {version = "==0.9.1", markers = "python_version < '3'"}
+twill = "*"
 watchdog = "*"
+python-irodsclient = "*"
 
 [packages]
 numpy = "*"

lib/galaxy/dependencies/pipfiles/default/pinned-dev-requirements.txt

@@ -4,20 +4,20 @@ alabaster==0.7.12
 atomicwrites==1.3.0
 attrs==19.3.0
 babel==2.8.0
-certifi==2019.11.28
+certifi==2020.4.5.1
 chardet==3.0.4
 commonmark==0.9.1
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-coverage==5.0.3
-deprecated==1.2.7
+coverage==5.0.4
+deprecated==1.2.9
 docutils==0.15.2
 funcsigs==1.0.2 ; python_version < '3.3'
 future==0.18.2
 gunicorn==19.10.0
 idna==2.9
 imagesize==1.2.0
-importlib-metadata==1.5.0 ; python_version < '3.8'
+importlib-metadata==1.6.0 ; python_version < '3.8'
 jinja2==2.11.1
 lxml==4.5.0
 markdown==3.1.1
@@ -27,23 +27,25 @@ mock==3.0.5
 more-itertools==5.0.0
 nose==1.3.7
 nosehtml==0.4.5
-packaging==20.1
+packaging==20.3
 pathlib2==2.3.5 ; python_version < '3.6'
 pathtools==0.1.2
 pluggy==0.13.1
 port-for==0.4
+prettytable==0.7.2
 psutil==5.7.0
 py==1.8.1
 pygithub==1.45
 pygments==2.5.2
 pyjwt==1.7.1
-pyparsing==2.4.6
+pyparsing==2.4.7
 pytest-cov==2.8.1
 pytest-html==1.22.1
 pytest-metadata==1.8.0
 pytest-postgresql==1.4.1
 pytest-pythonpath==0.7.3
 pytest==4.6.9
+python-irodsclient==0.8.2
 pytz==2019.3
 recommonmark==0.6.0
 requests==2.23.0
@@ -56,10 +58,11 @@ sphinx-rtd-theme==0.4.3
 sphinx==1.8.5
 sphinxcontrib-websupport==1.1.2
 testfixtures==6.14.0
-twill==0.9.1 ; python_version < '3'
+twill==2.0
 typing==3.7.4.1 ; python_version < '3.5'
 urllib3==1.25.8
 watchdog==0.10.2
-wcwidth==0.1.8
-wrapt==1.12.0
+wcwidth==0.1.9
+wrapt==1.12.1
+xmlrunner==1.7.7
 zipp==1.2.0

lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt

@@ -23,8 +23,8 @@ bcrypt==3.1.7
 bdbag==1.5.6
 beaker==1.11.0
 bioblend==0.13.0
-bleach==3.1.1
-boltons==20.0.0
+bleach==3.1.4
+boltons==20.1.0
 boto3==1.9.114
 boto==2.49.0
 botocore==1.12.253
@@ -32,7 +32,7 @@ bx-python==0.8.8
 bz2file==0.98 ; python_version < '3.3'
 cachecontrol==0.11.7
 cachetools==3.1.1
-certifi==2019.11.28
+certifi==2020.4.5.1
 cffi==1.14.0
 chardet==3.0.4
 cheetah3==3.2.4
@@ -43,18 +43,18 @@ cmd2==0.8.9
 coloredlogs==14.0
 configparser==4.0.2 ; python_version < '3.2'
 contextlib2==0.6.0.post1 ; python_version < '3.5'
-cryptography==2.8
+cryptography==2.9
 cwltool==1.0.20191225192155
 debtcollector==1.22.0
 decorator==4.4.2
-deprecated==1.2.7
+deprecated==1.2.9
 deprecation==2.0.7
 dictobj==0.4
 docopt==0.6.2
 docutils==0.15.2
 dogpile.cache==0.9.0
 ecdsa==0.15
-enum34==1.1.9 ; python_version < '3.4'
+enum34==1.1.10 ; python_version < '3.4'
 fabric3==1.14.post1
 funcsigs==1.0.2 ; python_version < '3.3'
 functools32==3.2.3.post2 ; python_version < '3.2'
@@ -63,13 +63,13 @@ futures==3.3.0 ; python_version == '2.6' or python_version == '2.7'
 galaxy-sequence-utils==1.1.5
 google-api-python-client==1.7.8
 google-auth-httplib2==0.0.3
-google-auth==1.11.2
-gxformat2==0.10.1
+google-auth==1.13.1
+gxformat2==0.11.1
 h5py==2.10.0
-httplib2==0.17.0
-humanfriendly==7.1.1
+httplib2==0.17.2
+humanfriendly==8.1
 idna==2.9
-importlib-metadata==1.5.0 ; python_version < '3.8'
+importlib-metadata==1.6.0 ; python_version < '3.8'
 ipaddress==1.0.23 ; python_version < '3.3'
 isa-rwval==0.10.7
 iso8601==0.1.12
@@ -78,14 +78,14 @@ jmespath==0.9.5
 jsonpatch==1.25
 jsonpointer==2.0
 jsonschema==3.2.0
-keystoneauth1==3.18.0
-kombu==4.6.7
+keystoneauth1==4.0.0
+kombu==4.6.8
 lockfile==0.12.2
 lxml==4.5.0
-mako==1.1.1
+mako==1.1.2
 markdown==3.1.1
 markupsafe==1.1.1
-mercurial==5.3
+mercurial==5.3.2
 mistune==0.8.4
 monotonic==1.5
 msgpack==1.0.0
@@ -102,7 +102,7 @@ numpy==1.16.6
 oauth2client==4.1.3
 oauthlib==3.1.0
 openstacksdk==0.17.0
-os-client-config==2.0.0
+os-client-config==2.1.0
 os-service-types==1.7.0
 osc-lib==2.0.0
 oslo.config==7.0.0
@@ -111,21 +111,21 @@ oslo.i18n==3.25.1
 oslo.log==3.45.2
 oslo.serialization==2.29.2
 oslo.utils==3.42.1
-packaging==20.1
+packaging==20.3
 paramiko==2.7.1
 parsley==1.3
 paste==3.4.0
 pastedeploy==2.1.0
 pastescript==3.2.0
 pathlib2==2.3.5 ; python_version < '3.6'
-pbr==5.4.4
+pbr==5.4.5
 prettytable==0.7.2
 prov==1.5.1
 psutil==5.7.0
 pulsar-galaxy-lib==0.14.0.dev1
 pyasn1-modules==0.2.8
 pyasn1==0.4.8
-pycparser==2.19
+pycparser==2.20
 pycryptodome==3.9.7
 pyeventsystem==0.1.0
 pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
@@ -133,9 +133,9 @@ pyjwt==1.7.1
 pykwalify==1.7.0
 pynacl==1.3.0
 pyopenssl==19.1.0
-pyparsing==2.4.6
-pyperclip==1.7.0
-pyrsistent==0.15.7
+pyparsing==2.4.7
+pyperclip==1.8.0
+pyrsistent==0.16.0
 pysam==0.15.2
 pysftp==0.2.9
 python-cinderclient==4.0.0
@@ -149,7 +149,7 @@ python-openid==2.2.5 ; python_version < '3.0'
 python-swiftclient==3.6.0
 pytz==2019.3
 pyuwsgi==2.0.18.post0
-pyyaml==5.3
+pyyaml==5.3.1
 rdflib-jsonld==0.4.0
 rdflib==4.2.2
 repoze.lru==0.7
@@ -157,7 +157,7 @@ requests-oauthlib==1.3.0
 requests-toolbelt==0.9.1
 requests==2.23.0
 requestsexceptions==1.4.0
-rfc3986==1.3.2
+rfc3986==1.4.0
 routes==2.4.1
 rsa==4.0
 ruamel.ordereddict==0.4.14 ; platform_python_implementation == 'CPython' and python_version <= '2.7'
@@ -172,15 +172,15 @@ simplejson==3.17.0
 six==1.11.0
 social-auth-core[openidconnect]==3.3.0
 sqlalchemy-migrate==0.13.0
-sqlalchemy-utils==0.36.1
-sqlalchemy==1.3.13
+sqlalchemy-utils==0.36.3
+sqlalchemy==1.3.16
 sqlparse==0.3.1
 stevedore==1.32.0
 subprocess32==3.5.4 ; python_version < '3.0'
 svgwrite==1.3.1
 tempita==0.5.2
 tenacity==4.12.0
-typing-extensions==3.7.4.1
+typing-extensions==3.7.4.2
 typing==3.7.4.1 ; python_version < '3.5'
 tzlocal==2.0.0
 unicodecsv==0.14.1 ; python_version < '3.0'
@@ -188,9 +188,9 @@ uritemplate==3.0.1
 urllib3==1.25.8
 vine==1.3.0
 warlock==1.3.3
-wcwidth==0.1.8
+wcwidth==0.1.9
 webencodings==0.5.1
 webob==1.8.6
 whoosh==2.7.4
-wrapt==1.12.0
+wrapt==1.12.1
 zipp==1.2.0

lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt

@@ -1,7 +1,7 @@
 -i https://pypi.python.org/simple
 configparser==4.0.2 ; python_version < '3.2'
 entrypoints==0.3
-enum34==1.1.9 ; python_version < '3.4'
+enum34==1.1.10 ; python_version < '3.4'
 flake8-import-order==0.18.1
 flake8==3.7.9
 functools32==3.2.3.post2 ; python_version < '3.2'

lib/galaxy/managers/interactivetool.py

@@ -139,7 +139,7 @@ class InteractiveToolManager(object):
         self.security = app.security
         self.sa_session = app.model.context
         self.job_manager = app.job_manager
-        self.propagator = InteractiveToolSqlite(app.config.interactivetool_map, app.security.encode_id)
+        self.propagator = InteractiveToolSqlite(app.config.interactivetools_map, app.security.encode_id)
 
     def create_entry_points(self, job, tool, entry_points=None, flush=True):
         entry_points = entry_points or tool.ports
@@ -260,8 +260,13 @@ class InteractiveToolManager(object):
     def target_if_active(self, trans, entry_point):
         if entry_point.active and not entry_point.deleted:
             request_host = trans.request.host
-            rval = '%s//%s-%s.%s.%s.%s/' % (trans.request.host_url.split('//', 1)[0], trans.security.encode_id(entry_point.id),
-                    entry_point.token, entry_point.__class__.__name__.lower(), self.app.config.interactivetool_prefix, request_host)
+            protocol = trans.request.host_url.split('//', 1)[0]
+            entry_point_encoded_id = trans.security.encode_id(entry_point.id)
+            entry_point_class = entry_point.__class__.__name__.lower()
+            entry_point_prefix = self.app.config.interactivetool_prefix
+            interactivetool_proxy_host = self.app.config.interactivetool_proxy_host or request_host
+            rval = '%s//%s-%s.%s.%s.%s/' % (protocol, entry_point_encoded_id,
+                    entry_point.token, entry_point_class, entry_point_prefix, interactivetool_proxy_host)
             if entry_point.entry_url:
                 rval = '%s/%s' % (rval.rstrip('/'), entry_point.entry_url.lstrip('/'))
             return rval

lib/galaxy/managers/jobs.py

@@ -498,6 +498,20 @@ def summarize_job_metrics(trans, job):
     return list(map(metric_to_dict, metrics))
 
 
+def summarize_destination_params(trans, job):
+    """Produce a dict-ified version of job destination parameters ready for tabular rendering.
+
+    Precondition: the caller has verified the job is accessible to the user
+    represented by the trans parameter.
+    """
+
+    destination_params = {'Runner': job.job_runner_name,
+                          'Runner Job ID': job.job_runner_external_id,
+                          'Handler': job.handler}
+    destination_params.update(job.destination_params)
+    return destination_params
+
+
 def summarize_job_parameters(trans, job):
     """Produce a dict-ified version of job parameters ready for tabular rendering.
 

lib/galaxy/managers/workflows.py

@@ -617,8 +617,8 @@ class WorkflowContentsManager(UsesAnnotations):
                 else:
                     data['upgrade_messages'][step.order_index] = {module.tool.name: "\n".join(module.version_changes)}
             # Get user annotation.
-            annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
             config_form = module.get_config_form(step=step)
+            annotation_str = self.get_item_annotation_str(trans.sa_session, trans.user, step) or ''
             # Pack attributes into plain dictionary
             step_dict = {
                 'id': step.order_index,

lib/galaxy/model/tool_shed_install/migrate/check.py

@@ -12,6 +12,10 @@ from sqlalchemy import (
     Table
 )
 from sqlalchemy.exc import NoSuchTableError
+from sqlalchemy_utils import (
+    create_database,
+    database_exists,
+)
 
 from galaxy.model.tool_shed_install import mapping
 
@@ -27,6 +31,11 @@ def create_or_verify_database(url, engine_options={}, app=None):
     """
     """
     # Create engine and metadata
+    if not database_exists(url):
+        message = "Creating database for URI [%s]" % url
+        log.info(message)
+        create_database(url)
+
     engine = create_engine(url, **engine_options)
 
     def migrate():

lib/galaxy/objectstore/__init__.py

@@ -5,6 +5,7 @@ all providers ensure that data can be accessed on the filesystem for running
 tools
 """
 
+import abc
 import logging
 import os
 import random
@@ -39,8 +40,9 @@ log = logging.getLogger(__name__)
 
 
 class ObjectStore(object):
+    __metaclass__ = abc.ABCMeta
 
-    """ObjectStore abstract interface.
+    """ObjectStore interface.
 
     FIELD DESCRIPTIONS (these apply to all the methods in this class):
 
@@ -82,6 +84,120 @@ class ObjectStore(object):
         000/obj.id)
     """
 
+    @abc.abstractmethod
+    def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+        """Return True if the object identified by `obj` exists, False otherwise."""
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Mark the object (`obj`) as existing in the store, but with no content.
+
+        This method will create a proper directory structure for
+        the file if the directory does not already exist.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Test if the object identified by `obj` has content.
+
+        If the object does not exist raises `ObjectNotFound`.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Return size of the object identified by `obj`.
+
+        If the object does not exist, return 0.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Delete the object identified by `obj`.
+
+        :type entire_dir: boolean
+        :param entire_dir: If True, delete the entire directory pointed to by
+                           extra_dir. For safety reasons, this option applies
+                           only for and in conjunction with the extra_dir or
+                           obj_dir options.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
+
+        If the object does not exist raises `ObjectNotFound`.
+
+        :type start: int
+        :param start: Set the position to start reading the dataset file
+
+        :type count: int
+        :param count: Read at most `count` bytes from the dataset
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Get the expected filename with absolute path for object with id `obj.id`.
+
+        This can be used to access the contents of the object.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False):
+        """
+        Inform the store that the file associated with `obj.id` has been updated.
+
+        If `file_name` is provided, update from that file instead of the
+        default.
+        If the object does not exist raises `ObjectNotFound`.
+
+        :type file_name: string
+        :param file_name: Use file pointed to by `file_name` as the source for
+                          updating the dataset identified by `obj`
+
+        :type create: boolean
+        :param create: If True and the default dataset does not exist, create
+            it first.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+        """
+        Return the URL for direct acces if supported, otherwise return None.
+
+        Note: need to be careful to not bypass dataset security with this.
+        """
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_store_usage_percent(self):
+        """Return the percentage indicating how full the store is."""
+        raise NotImplementedError()
+
+    @abc.abstractmethod
+    def get_store_by(self, obj):
+        """Return how object is stored (by 'uuid', 'id', or None if not yet saved).
+
+        Certain Galaxy remote data features aren't available if objects are stored by 'id'.
+        """
+        raise NotImplementedError()
+
+
+class BaseObjectStore(ObjectStore):
+
     def __init__(self, config, config_dict=None, **kwargs):
         """
         :type config: object
@@ -111,10 +227,6 @@ class ObjectStore(object):
         """Close any connections for this ObjectStore."""
         self.running = False
 
-    def exists(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None):
-        """Return True if the object identified by `obj` exists, False otherwise."""
-        raise NotImplementedError()
-
     def file_ready(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Check if a file corresponding to a dataset is ready to be used.
@@ -123,102 +235,6 @@ class ObjectStore(object):
         """
         return True
 
-    def create(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Mark the object (`obj`) as existing in the store, but with no content.
-
-        This method will create a proper directory structure for
-        the file if the directory does not already exist.
-        """
-        raise NotImplementedError()
-
-    def empty(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Test if the object identified by `obj` has content.
-
-        If the object does not exist raises `ObjectNotFound`.
-        """
-        raise NotImplementedError()
-
-    def size(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Return size of the object identified by `obj`.
-
-        If the object does not exist, return 0.
-        """
-        raise NotImplementedError()
-
-    def delete(self, obj, entire_dir=False, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Delete the object identified by `obj`.
-
-        :type entire_dir: boolean
-        :param entire_dir: If True, delete the entire directory pointed to by
-                           extra_dir. For safety reasons, this option applies
-                           only for and in conjunction with the extra_dir or
-                           obj_dir options.
-        """
-        raise NotImplementedError()
-
-    def get_data(self, obj, start=0, count=-1, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Fetch `count` bytes of data offset by `start` bytes using `obj.id`.
-
-        If the object does not exist raises `ObjectNotFound`.
-
-        :type start: int
-        :param start: Set the position to start reading the dataset file
-
-        :type count: int
-        :param count: Read at most `count` bytes from the dataset
-        """
-        raise NotImplementedError()
-
-    def get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Get the expected filename with absolute path for object with id `obj.id`.
-
-        This can be used to access the contents of the object.
-        """
-        raise NotImplementedError()
-
-    def update_from_file(self, obj, base_dir=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, file_name=None, create=False):
-        """
-        Inform the store that the file associated with `obj.id` has been updated.
-
-        If `file_name` is provided, update from that file instead of the
-        default.
-        If the object does not exist raises `ObjectNotFound`.
-
-        :type file_name: string
-        :param file_name: Use file pointed to by `file_name` as the source for
-                          updating the dataset identified by `obj`
-
-        :type create: boolean
-        :param create: If True and the default dataset does not exist, create
-            it first.
-        """
-        raise NotImplementedError()
-
-    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
-        """
-        Return the URL for direct acces if supported, otherwise return None.
-
-        Note: need to be careful to not bypass dataset security with this.
-        """
-        raise NotImplementedError()
-
-    def get_store_usage_percent(self):
-        """Return the percentage indicating how full the store is."""
-        raise NotImplementedError()
-
-    def get_store_by(self, obj):
-        """Return how object is stored (by 'uuid', 'id', or None if not yet saved).
-
-        Certain Galaxy remote data features aren't available if objects are stored by 'id'.
-        """
-        raise NotImplementedError()
-
     @classmethod
     def parse_xml(clazz, config_xml):
         """Parse an XML description of a configuration for this object store.
@@ -251,8 +267,44 @@ class ObjectStore(object):
             # job working directories.
             return obj.id
 
+    def _invoke(self, delegate, obj=None, **kwargs):
+        return self.__getattribute__("_" + delegate)(obj=obj, **kwargs)
 
-class ConcreteObjectStore(ObjectStore):
+    def exists(self, obj, **kwargs):
+        return self._invoke('exists', obj, **kwargs)
+
+    def create(self, obj, **kwargs):
+        return self._invoke('create', obj, **kwargs)
+
+    def empty(self, obj, **kwargs):
+        return self._invoke('empty', obj, **kwargs)
+
+    def size(self, obj, **kwargs):
+        return self._invoke('size', obj, **kwargs)
+
+    def delete(self, obj, **kwargs):
+        return self._invoke('delete', obj, **kwargs)
+
+    def get_data(self, obj, **kwargs):
+        return self._invoke('get_data', obj, **kwargs)
+
+    def get_filename(self, obj, **kwargs):
+        return self._invoke('get_filename', obj, **kwargs)
+
+    def update_from_file(self, obj, **kwargs):
+        return self._invoke('update_from_file', obj, **kwargs)
+
+    def get_object_url(self, obj, **kwargs):
+        return self._invoke('get_object_url', obj, **kwargs)
+
+    def get_store_usage_percent(self):
+        return self._invoke('get_store_usage_percent')
+
+    def get_store_by(self, obj, **kwargs):
+        return self._invoke('get_store_by', obj, **kwargs)
+
+
+class ConcreteObjectStore(BaseObjectStore):
     """Subclass of ObjectStore for stores that don't delegate (non-nested).
 
     Currently only adds store_by functionality. Which doesn't make
@@ -280,7 +332,7 @@ class ConcreteObjectStore(ObjectStore):
         rval["store_by"] = self.store_by
         return rval
 
-    def get_store_by(self, obj):
+    def _get_store_by(self, obj):
         return self.store_by
 
 
@@ -343,7 +395,7 @@ class DiskObjectStore(ConcreteObjectStore):
         as_dict["files_dir"] = self.file_path
         return as_dict
 
-    def _get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
+    def __get_filename(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False):
         """
         Return the absolute path for the file corresponding to the `obj.id`.
 
@@ -425,7 +477,7 @@ class DiskObjectStore(ConcreteObjectStore):
             path = os.path.join(path, alt_name if alt_name else "dataset_%s.dat" % obj_id)
         return os.path.abspath(path)
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Override `ObjectStore`'s stub and check on disk."""
         if self.check_old_style:
             path = self._construct_path(obj, old_style=True, **kwargs)
@@ -435,9 +487,9 @@ class DiskObjectStore(ConcreteObjectStore):
                 return True
         return os.path.exists(self._construct_path(obj, **kwargs))
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by creating any files and folders on disk."""
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
             dir_only = kwargs.get('dir_only', False)
             # Create directory if it does not exist
@@ -448,18 +500,18 @@ class DiskObjectStore(ConcreteObjectStore):
                 open(path, 'w').close()  # Should be rb?
                 umask_fix_perms(path, self.config.umask, 0o666)
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by checking file size on disk."""
         return self.size(obj, **kwargs) == 0
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """Override `ObjectStore`'s stub by return file size on disk.
 
         Returns 0 if the object doesn't exist yet or other error.
         """
-        if self.exists(obj, **kwargs):
+        if self._exists(obj, **kwargs):
             try:
-                filepath = self.get_filename(obj, **kwargs)
+                filepath = self._get_filename(obj, **kwargs)
                 for _ in range(0, 2):
                     size = os.path.getsize(filepath)
                     if size != 0:
@@ -472,31 +524,31 @@ class DiskObjectStore(ConcreteObjectStore):
         else:
             return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         """Override `ObjectStore`'s stub; delete the file or folder on disk."""
-        path = self.get_filename(obj, **kwargs)
+        path = self._get_filename(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         obj_dir = kwargs.get('obj_dir', False)
         try:
             if entire_dir and (extra_dir or obj_dir):
                 shutil.rmtree(path)
                 return True
-            if self.exists(obj, **kwargs):
+            if self._exists(obj, **kwargs):
                 os.remove(path)
                 return True
         except OSError as ex:
-            log.critical('%s delete error %s' % (self._get_filename(obj, **kwargs), ex))
+            log.critical('%s delete error %s' % (self.__get_filename(obj, **kwargs), ex))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         """Override `ObjectStore`'s stub; retrieve data directly from disk."""
-        data_file = open(self.get_filename(obj, **kwargs), 'r')  # Should be rb?
+        data_file = open(self._get_filename(obj, **kwargs), 'r')  # Should be rb?
         data_file.seek(start)
         content = data_file.read(count)
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """
         Override `ObjectStore`'s stub.
 
@@ -514,27 +566,27 @@ class DiskObjectStore(ConcreteObjectStore):
             raise ObjectNotFound
         return path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         """`create` parameter is not used in this implementation."""
         preserve_symlinks = kwargs.pop('preserve_symlinks', False)
         # FIXME: symlinks and the object store model may not play well together
         # these should be handled better, e.g. registering the symlink'd file
         # as an object
         if create:
-            self.create(obj, **kwargs)
-        if file_name and self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if file_name and self._exists(obj, **kwargs):
             try:
                 if preserve_symlinks and os.path.islink(file_name):
-                    force_symlink(os.readlink(file_name), self.get_filename(obj, **kwargs))
+                    force_symlink(os.readlink(file_name), self._get_filename(obj, **kwargs))
                 else:
-                    path = self.get_filename(obj, **kwargs)
+                    path = self._get_filename(obj, **kwargs)
                     shutil.copy(file_name, path)
                     umask_fix_perms(path, self.config.umask, 0o666)
             except IOError as ex:
-                log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex))
+                log.critical('Error copying %s to %s: %s' % (file_name, self.__get_filename(obj, **kwargs), ex))
                 raise ex
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """
         Override `ObjectStore`'s stub.
 
@@ -542,13 +594,13 @@ class DiskObjectStore(ConcreteObjectStore):
         """
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self, **kwargs):
         """Override `ObjectStore`'s stub by return percent storage used."""
         st = os.statvfs(self.file_path)
         return (float(st.f_blocks - st.f_bavail) / st.f_blocks) * 100
 
 
-class NestedObjectStore(ObjectStore):
+class NestedObjectStore(BaseObjectStore):
 
     """
     Base for ObjectStores that use other ObjectStores.
@@ -567,51 +619,51 @@ class NestedObjectStore(ObjectStore):
             store.shutdown()
         super(NestedObjectStore, self).shutdown()
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Determine if the `obj` exists in any of the backends."""
-        return self._call_method('exists', obj, False, False, **kwargs)
+        return self._call_method('_exists', obj, False, False, **kwargs)
 
     def file_ready(self, obj, **kwargs):
         """Determine if the file for `obj` is ready to be used by any of the backends."""
         return self._call_method('file_ready', obj, False, False, **kwargs)
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Create a backing file in a random backend."""
         random.choice(list(self.backends.values())).create(obj, **kwargs)
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """For the first backend that has this `obj`, determine if it is empty."""
-        return self._call_method('empty', obj, True, False, **kwargs)
+        return self._call_method('_empty', obj, True, False, **kwargs)
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """For the first backend that has this `obj`, return its size."""
-        return self._call_method('size', obj, 0, False, **kwargs)
+        return self._call_method('_size', obj, 0, False, **kwargs)
 
-    def delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs):
         """For the first backend that has this `obj`, delete it."""
-        return self._call_method('delete', obj, False, False, **kwargs)
+        return self._call_method('_delete', obj, False, False, **kwargs)
 
-    def get_data(self, obj, **kwargs):
+    def _get_data(self, obj, **kwargs):
         """For the first backend that has this `obj`, get data from it."""
-        return self._call_method('get_data', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_get_data', obj, ObjectNotFound, True, **kwargs)
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its filename."""
-        return self._call_method('get_filename', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_get_filename', obj, ObjectNotFound, True, **kwargs)
 
-    def update_from_file(self, obj, **kwargs):
+    def _update_from_file(self, obj, **kwargs):
         """For the first backend that has this `obj`, update it from the given file."""
         if kwargs.get('create', False):
-            self.create(obj, **kwargs)
+            self._create(obj, **kwargs)
             kwargs['create'] = False
-        return self._call_method('update_from_file', obj, ObjectNotFound, True, **kwargs)
+        return self._call_method('_update_from_file', obj, ObjectNotFound, True, **kwargs)
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """For the first backend that has this `obj`, get its URL."""
-        return self._call_method('get_object_url', obj, None, False, **kwargs)
+        return self._call_method('_get_object_url', obj, None, False, **kwargs)
 
-    def get_store_by(self, obj):
-        return self._call_method('get_store_by', obj, None, False)
+    def _get_store_by(self, obj):
+        return self._call_method('_get_store_by', obj, None, False)
 
     def _repr_object_for_exception(self, obj):
         try:
@@ -791,9 +843,9 @@ class DistributedObjectStore(NestedObjectStore):
             self.weighted_backend_ids = new_weighted_backend_ids
             self.sleeper.sleep(120)  # Test free space every 2 minutes
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """The only method in which obj.object_store_id may be None."""
-        if obj.object_store_id is None or not self.exists(obj, **kwargs):
+        if obj.object_store_id is None or not self._exists(obj, **kwargs):
             if obj.object_store_id is None or obj.object_store_id not in self.backends:
                 try:
                     obj.object_store_id = random.choice(self.weighted_backend_ids)
@@ -880,14 +932,14 @@ class HierarchicalObjectStore(NestedObjectStore):
         as_dict["backends"] = backends
         return as_dict
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Check all child object stores."""
         for store in self.backends.values():
             if store.exists(obj, **kwargs):
                 return True
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Call the primary object store."""
         self.backends[0].create(obj, **kwargs)
 
@@ -913,7 +965,7 @@ def type_to_object_store_class(store, fsmon=False):
         objectstore_class = HierarchicalObjectStore
         objectstore_constructor_kwds["fsmon"] = fsmon
     elif store == 'irods':
-        from .rods import IRODSObjectStore
+        from .irods import IRODSObjectStore
         objectstore_class = IRODSObjectStore
     elif store == 'azure_blob':
         from .azure_blob import AzureBlobObjectStore

lib/galaxy/objectstore/azure_blob.py

@@ -310,7 +310,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
     # Public Methods #
     ##################
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_azure = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -357,9 +357,9 @@ class AzureBlobObjectStore(ConcreteObjectStore):
 
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
 
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -393,25 +393,25 @@ class AzureBlobObjectStore(ConcreteObjectStore):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try Azure. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_azure(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -445,10 +445,10 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         except AzureHttpError:
             log.exception("Could not delete blob '%s' from Azure", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -460,7 +460,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
@@ -483,7 +483,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -495,10 +495,10 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         #     return cache_path
         raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create is True:
-            self.create(obj, **kwargs)
-        elif self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        elif self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -520,8 +520,8 @@ class AzureBlobObjectStore(ConcreteObjectStore):
         else:
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s' % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 url = self.service.make_blob_url(container_name=self.container_name, blob_name=rel_path)
@@ -530,7 +530,7 @@ class AzureBlobObjectStore(ConcreteObjectStore):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
     ##################

lib/galaxy/objectstore/cloud.py

@@ -510,7 +510,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_cloud(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -543,8 +543,8 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -572,26 +572,26 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try cloud. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_cloud(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -626,10 +626,10 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         except Exception:
             log.exception("Could not delete key '%s' from cloud", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -641,7 +641,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -664,7 +664,7 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -678,10 +678,10 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -703,8 +703,8 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 key = self.bucket.objects.get(rel_path)
@@ -713,5 +713,5 @@ class Cloud(ConcreteObjectStore, CloudConfigMixin):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0

lib/galaxy/objectstore/irods.py

@@ -0,0 +1,653 @@
+"""
+Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
+"""
+import logging
+import os
+import shutil
+from datetime import datetime
+from functools import partial
+try:
+    from pathlib import Path
+except ImportError:
+    # Use backport on python 2
+    from pathlib2 import Path
+
+try:
+    import irods
+    import irods.keywords as kw
+    from irods.exception import CollectionDoesNotExist
+    from irods.exception import DataObjectDoesNotExist
+    from irods.exception import NetworkException
+    from irods.session import iRODSSession
+except ImportError:
+    irods = None
+
+from galaxy.exceptions import ObjectInvalid, ObjectNotFound
+from galaxy.util import directory_hash_id, umask_fix_perms
+from galaxy.util.path import safe_relpath
+from ..objectstore import DiskObjectStore
+
+IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this feature, please install it')
+# 1 MB
+CHUNK_SIZE = 2**20
+log = logging.getLogger(__name__)
+
+
+def _config_xml_error(tag):
+    msg = 'No {tag} element in config XML tree'.format(tag=tag)
+    raise Exception(msg)
+
+
+def _config_dict_error(key):
+    msg = 'No {key} key in config dictionary'.forma(key=key)
+    raise Exception(msg)
+
+
+def parse_config_xml(config_xml):
+    try:
+        a_xml = config_xml.findall('auth')
+        if not a_xml:
+            _config_xml_error('auth')
+        username = a_xml[0].get('username')
+        password = a_xml[0].get('password')
+
+        r_xml = config_xml.findall('resource')
+        if not r_xml:
+            _config_xml_error('resource')
+        resource_name = r_xml[0].get('name')
+
+        z_xml = config_xml.findall('zone')
+        if not z_xml:
+            _config_xml_error('zone')
+        zone_name = z_xml[0].get('name')
+
+        c_xml = config_xml.findall('connection')
+        if not c_xml:
+            _config_xml_error('connection')
+        host = c_xml[0].get('host', None)
+        port = int(c_xml[0].get('port', 0))
+        timeout = int(c_xml[0].get('timeout', 30))
+
+        c_xml = config_xml.findall('cache')
+        if not c_xml:
+            _config_xml_error('cache')
+        cache_size = float(c_xml[0].get('size', -1))
+        staging_path = c_xml[0].get('path', None)
+
+        attrs = ('type', 'path')
+        e_xml = config_xml.findall('extra_dir')
+        if not e_xml:
+            _config_xml_error('extra_dir')
+        extra_dirs = [dict(((k, e.get(k)) for k in attrs)) for e in e_xml]
+
+        return {
+            'auth': {
+                'username': username,
+                'password': password,
+            },
+            'resource': {
+                'name': resource_name,
+            },
+            'zone': {
+                'name': zone_name,
+            },
+            'connection': {
+                'host': host,
+                'port': port,
+                'timeout': timeout
+            },
+            'cache': {
+                'size': cache_size,
+                'path': staging_path,
+            },
+            'extra_dirs': extra_dirs,
+        }
+    except Exception:
+        # Toss it back up after logging, we can't continue loading at this point.
+        log.exception("Malformed iRODS ObjectStore Configuration XML -- unable to continue.")
+        raise
+
+
+class CloudConfigMixin(object):
+
+    def _config_to_dict(self):
+        return {
+            'auth': {
+                'username': self.username,
+                'password': self.password,
+            },
+            'resource': {
+                'name': self.resource,
+            },
+            'zone': {
+                'name': self.zone,
+            },
+            'connection': {
+                'host': self.host,
+                'port': self.port,
+                'timeout': self.timeout,
+            },
+            'cache': {
+                'size': self.cache_size,
+                'path': self.staging_path,
+            }
+        }
+
+
+class IRODSObjectStore(DiskObjectStore, CloudConfigMixin):
+    """
+    Object store that stores objects as data objects in an iRODS collections. A local cache
+    exists that is used as an intermediate location for files between Galaxy and iRODS.
+    """
+
+    store_type = 'irods'
+
+    def __init__(self, config, config_dict):
+        super(IRODSObjectStore, self).__init__(config, config_dict)
+
+        auth_dict = config_dict.get('auth')
+        if auth_dict is None:
+            _config_dict_error('auth')
+
+        self.username = auth_dict.get('username')
+        if self.username is None:
+            _config_dict_error('auth->username')
+        self.password = auth_dict.get('password')
+        if self.password is None:
+            _config_dict_error('auth->password')
+
+        resource_dict = config_dict['resource']
+        if resource_dict is None:
+            _config_dict_error('resource')
+        self.resource = resource_dict.get('name')
+        if self.resource is None:
+            _config_dict_error('resource->name')
+
+        zone_dict = config_dict['zone']
+        if zone_dict is None:
+            _config_dict_error('zone')
+        self.zone = zone_dict.get('name')
+        if self.zone is None:
+            _config_dict_error('zone->name')
+
+        connection_dict = config_dict['connection']
+        if connection_dict is None:
+            _config_dict_error('connection')
+        self.host = connection_dict.get('host')
+        if self.host is None:
+            _config_dict_error('connection->host')
+        self.port = connection_dict.get('port')
+        if self.port is None:
+            _config_dict_error('connection->port')
+        self.timeout = connection_dict.get('timeout')
+        if self.timeout is None:
+            _config_dict_error('connection->timeout')
+
+        cache_dict = config_dict['cache']
+        if cache_dict is None:
+            _config_dict_error('cache')
+        self.cache_size = cache_dict.get('size', -1)
+        if self.cache_size is None:
+            _config_dict_error('cache->size')
+        self.staging_path = cache_dict.get('path') or self.config.object_store_cache_path
+        if self.staging_path is None:
+            _config_dict_error('cache->path')
+
+        extra_dirs = dict((e['type'], e['path']) for e in config_dict.get('extra_dirs', []))
+        if not extra_dirs:
+            _config_dict_error('extra_dirs')
+        self.extra_dirs.update(extra_dirs)
+
+        self._initialize()
+
+    def __del__(self):
+        self.session.cleanup()
+
+    def _initialize(self):
+        if irods is None:
+            raise Exception(IRODS_IMPORT_MESSAGE)
+
+        self.home = "/" + self.zone + "/home/" + self.username
+
+        self.session = self._configure_connection(host=self.host, port=self.port, user=self.username, password=self.password, zone=self.zone)
+
+    def _configure_connection(self, host='localhost', port='1247', user='rods', password='rods', zone='tempZone'):
+        with iRODSSession(host=host, port=port, user=user, password=password, zone=zone) as session:
+            # Set connection timeout
+            session.connection_timeout = self.timeout
+            # Throws NetworkException if connection fails
+            try:
+                session.pool.get_connection()
+            except NetworkException as e:
+                log.error('Could not create iRODS session: ' + str(e))
+                raise
+            return session
+
+    @classmethod
+    def parse_xml(cls, config_xml):
+        return parse_config_xml(config_xml)
+
+    def to_dict(self):
+        as_dict = super(IRODSObjectStore, self).to_dict()
+        as_dict.update(self._config_to_dict())
+        return as_dict
+
+    def _fix_permissions(self, rel_path):
+        """ Set permissions on rel_path"""
+        for basedir, _, files in os.walk(rel_path):
+            umask_fix_perms(basedir, self.config.umask, 0o777, self.config.gid)
+            for filename in files:
+                path = os.path.join(basedir, filename)
+                # Ignore symlinks
+                if os.path.islink(path):
+                    continue
+                umask_fix_perms(path, self.config.umask, 0o666, self.config.gid)
+
+    def _construct_path(self, obj, base_dir=None, dir_only=None, extra_dir=None, extra_dir_at_root=False, alt_name=None, obj_dir=False, **kwargs):
+        # extra_dir should never be constructed from provided data but just
+        # make sure there are no shenannigans afoot
+        if extra_dir and extra_dir != os.path.normpath(extra_dir):
+            log.warning('extra_dir is not normalized: %s', extra_dir)
+            raise ObjectInvalid("The requested object is invalid")
+        # ensure that any parent directory references in alt_name would not
+        # result in a path not contained in the directory path constructed here
+        if alt_name:
+            if not safe_relpath(alt_name):
+                log.warning('alt_name would locate path outside dir: %s', alt_name)
+                raise ObjectInvalid("The requested object is invalid")
+            # alt_name can contain parent directory references, but S3 will not
+            # follow them, so if they are valid we normalize them out
+            alt_name = os.path.normpath(alt_name)
+        rel_path = os.path.join(*directory_hash_id(obj.id))
+        if extra_dir is not None:
+            if extra_dir_at_root:
+                rel_path = os.path.join(extra_dir, rel_path)
+            else:
+                rel_path = os.path.join(rel_path, extra_dir)
+
+        # for JOB_WORK directory
+        if obj_dir:
+            rel_path = os.path.join(rel_path, str(obj.id))
+        if base_dir:
+            base = self.extra_dirs.get(base_dir)
+            return os.path.join(base, rel_path)
+
+        if not dir_only:
+            rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+        return rel_path
+
+    def _get_cache_path(self, rel_path):
+        return os.path.abspath(os.path.join(self.staging_path, rel_path))
+
+    # rel_path is file or folder?
+    def _get_size_in_irods(self, rel_path):
+        p = Path(rel_path)
+        data_object_name = p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name)
+
+        try:
+            data_obj = self.session.data_objects.get(data_object_path)
+            return data_obj.__sizeof__()
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return -1
+
+    # rel_path is file or folder?
+    def _data_object_exists(self, rel_path):
+        p = Path(rel_path)
+        data_object_name = p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name)
+
+        try:
+            self.session.data_objects.get(data_object_path)
+            return True
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return False
+
+    def _in_cache(self, rel_path):
+        """ Check if the given dataset is in the local cache and return True if so. """
+        cache_path = self._get_cache_path(rel_path)
+        return os.path.exists(cache_path)
+
+    def _pull_into_cache(self, rel_path):
+        # Ensure the cache directory structure exists (e.g., dataset_#_files/)
+        rel_path_dir = os.path.dirname(rel_path)
+        if not os.path.exists(self._get_cache_path(rel_path_dir)):
+            os.makedirs(self._get_cache_path(rel_path_dir))
+        # Now pull in the file
+        file_ok = self._download(rel_path)
+        self._fix_permissions(self._get_cache_path(rel_path_dir))
+        return file_ok
+
+    def _download(self, rel_path):
+        log.debug("Pulling data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+
+        p = Path(rel_path)
+        data_object_name = p.stem + p.suffix
+        subcollection_name = p.parent
+
+        collection_path = self.home + "/" + str(subcollection_name)
+        data_object_path = collection_path + "/" + str(data_object_name)
+        data_obj = None
+
+        try:
+            data_obj = self.session.data_objects.get(data_object_path)
+        except (DataObjectDoesNotExist, CollectionDoesNotExist):
+            log.warn("Collection or data object (%s) does not exist", data_object_path)
+            return False
+
+        if self.cache_size > 0 and data_obj.__sizeof__() > self.cache_size:
+            log.critical("File %s is larger (%s) than the cache size (%s). Cannot download.",
+                         rel_path, data_obj.__sizeof__(), self.cache_size)
+            return False
+
+        log.debug("Pulled data object '%s' into cache to %s", rel_path, self._get_cache_path(rel_path))
+
+        with data_obj.open('r') as data_obj_fp, open(self._get_cache_path(rel_path), "wb") as cache_fp:
+            for chunk in iter(partial(data_obj_fp.read, CHUNK_SIZE), b''):
+                cache_fp.write(chunk)
+        return True
+
+    def _push_to_irods(self, rel_path, source_file=None, from_string=None):
+        """
+        Push the file pointed to by ``rel_path`` to the iRODS. Extract folder name
+        from rel_path as iRODS collection name, and extract file name from rel_path
+        as iRODS data object name.
+        If ``source_file`` is provided, push that file instead while
+        still using ``rel_path`` for collection and object store names.
+        If ``from_string`` is provided, set contents of the file to the value of the string.
+        """
+        p = Path(rel_path)
+        data_object_name = p.stem + p.suffix
+        subcollection_name = p.parent
+
+        source_file = source_file if source_file else self._get_cache_path(rel_path)
+        options = {kw.FORCE_FLAG_KW: ''}
+
+        if os.path.exists(source_file):
+            # Check if the data object exists in iRODS
+            collection_path = self.home + "/" + str(subcollection_name)
+            data_object_path = collection_path + "/" + str(data_object_name)
+            exists = self.session.data_objects.exists(data_object_path)
+            if os.path.getsize(source_file) == 0 and exists:
+                log.debug("Wanted to push file '%s' to iRODS collection '%s' but its size is 0; skipping.", source_file, rel_path)
+                return True
+            if from_string:
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
+                with data_obj.open('w') as data_obj_fp:
+                    data_obj_fp.write(from_string)
+                log.debug("Pushed data from string '%s' to collection '%s'", from_string, data_object_path)
+            else:
+                start_time = datetime.now()
+                log.debug("Pushing cache file '%s' of size %s bytes to collection '%s'", source_file, os.path.getsize(source_file), rel_path)
+
+                # Create sub-collection first
+                self.session.collections.create(collection_path, recurse=True)
+                data_obj = self.session.data_objects.create(data_object_path, self.resource, **options)
+
+                # Write to file in subcollection created above
+                with open(source_file, 'rb') as content_file, data_obj.open('w') as data_obj_fp:
+                    for chunk in iter(partial(content_file.read, CHUNK_SIZE), b''):
+                        data_obj_fp.write(chunk)
+
+                end_time = datetime.now()
+                log.debug("Pushed cache file '%s' to collection '%s' (%s bytes transfered in %s sec)",
+                          source_file, rel_path, os.path.getsize(source_file), end_time - start_time)
+            return True
+        else:
+            log.error("Tried updating key '%s' from source file '%s', but source file does not exist.",
+                      rel_path, source_file)
+        return False
+
+    def file_ready(self, obj, **kwargs):
+        """
+        A helper method that checks if a file corresponding to a dataset is
+        ready and available to be used. Return ``True`` if so, ``False`` otherwise.
+        """
+        rel_path = self._construct_path(obj, **kwargs)
+        # Make sure the size in cache is available in its entirety
+        if self._in_cache(rel_path):
+            if os.path.getsize(self._get_cache_path(rel_path)) == self._get_size_in_irods(rel_path):
+                return True
+            log.debug("Waiting for dataset %s to transfer from OS: %s/%s", rel_path,
+                      os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_irods(rel_path))
+        return False
+
+    def _exists(self, obj, **kwargs):
+        in_cache = in_irods = False
+        rel_path = self._construct_path(obj, **kwargs)
+
+        # Check cache
+        if self._in_cache(rel_path):
+            in_cache = True
+        # Check iRODS
+        in_irods = self._data_object_exists(rel_path)
+
+        # dir_only does not get synced so shortcut the decision
+        dir_only = kwargs.get('dir_only', False)
+        base_dir = kwargs.get('base_dir', None)
+        if dir_only:
+            if in_cache or in_irods:
+                return True
+            # for JOB_WORK directory
+            elif base_dir:
+                if not os.path.exists(rel_path):
+                    os.makedirs(rel_path)
+                return True
+            else:
+                return False
+
+        if in_cache and not in_irods:
+            return True
+        elif in_irods:
+            return True
+        else:
+            return False
+
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
+            # Pull out locally used fields
+            extra_dir = kwargs.get('extra_dir', None)
+            extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
+            dir_only = kwargs.get('dir_only', False)
+            alt_name = kwargs.get('alt_name', None)
+
+            # Construct hashed path
+            rel_path = os.path.join(*directory_hash_id(obj.id))
+
+            # Optionally append extra_dir
+            if extra_dir is not None:
+                if extra_dir_at_root:
+                    rel_path = os.path.join(extra_dir, rel_path)
+                else:
+                    rel_path = os.path.join(rel_path, extra_dir)
+
+            # Create given directory in cache
+            cache_dir = os.path.join(self.staging_path, rel_path)
+            if not os.path.exists(cache_dir):
+                os.makedirs(cache_dir)
+
+            if not dir_only:
+                rel_path = os.path.join(rel_path, alt_name if alt_name else "dataset_%s.dat" % obj.id)
+                open(os.path.join(self.staging_path, rel_path), 'w').close()
+                self._push_to_irods(rel_path, from_string='')
+
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
+        else:
+            raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
+                                 % (str(obj), str(kwargs)))
+
+    def _size(self, obj, **kwargs):
+        rel_path = self._construct_path(obj, **kwargs)
+        if self._in_cache(rel_path):
+            try:
+                return os.path.getsize(self._get_cache_path(rel_path))
+            except OSError as ex:
+                log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
+        elif self._exists(obj, **kwargs):
+            return self._get_size_in_irods(rel_path)
+        log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
+        return 0
+
+    def _delete(self, obj, entire_dir=False, **kwargs):
+        rel_path = self._construct_path(obj, **kwargs)
+        extra_dir = kwargs.get('extra_dir', None)
+        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get('dir_only', False)
+        obj_dir = kwargs.get('obj_dir', False)
+        try:
+            # Remove temparory data in JOB_WORK directory
+            if base_dir and dir_only and obj_dir:
+                shutil.rmtree(os.path.abspath(rel_path))
+                return True
+
+            # For the case of extra_files, because we don't have a reference to
+            # individual files we need to remove the entire directory structure
+            # with all the files in it. This is easy for the local file system,
+            # but requires iterating through each individual key in irods and deleing it.
+            if entire_dir and extra_dir:
+                shutil.rmtree(self._get_cache_path(rel_path))
+
+                col_path = self.home + "/" + str(rel_path)
+                col = None
+                try:
+                    col = self.session.collections.get(col_path)
+                except CollectionDoesNotExist:
+                    log.warn("Collection (%s) does not exist!", col_path)
+                    return False
+
+                cols = col.walk()
+                # Traverse the tree only one level deep
+                for _ in range(2):
+                    # get next result
+                    _, _, data_objects = next(cols)
+
+                    # Delete data objects
+                    for data_object in data_objects:
+                        data_object.unlink(force=True)
+
+                return True
+
+            else:
+                # Delete from cache first
+                os.unlink(self._get_cache_path(rel_path))
+                # Delete from irods as well
+                p = Path(rel_path)
+                data_object_name = p.stem + p.suffix
+                subcollection_name = p.parent
+
+                collection_path = self.home + "/" + str(subcollection_name)
+                data_object_path = collection_path + "/" + str(data_object_name)
+
+                try:
+                    data_obj = self.session.data_objects.get(data_object_path)
+                    # remove object
+                    data_obj.unlink(force=True)
+                    return True
+                except (DataObjectDoesNotExist, CollectionDoesNotExist):
+                    log.info("Collection or data object (%s) does not exist", data_object_path)
+                    return True
+
+        except OSError:
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
+        return False
+
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
+        rel_path = self._construct_path(obj, **kwargs)
+        # Check cache first and get file if not there
+        if not self._in_cache(rel_path):
+            self._pull_into_cache(rel_path)
+        # Read the file content from cache
+        data_file = open(self._get_cache_path(rel_path), 'r')
+        data_file.seek(start)
+        content = data_file.read(count)
+        data_file.close()
+        return content
+
+    def _get_filename(self, obj, **kwargs):
+        base_dir = kwargs.get('base_dir', None)
+        dir_only = kwargs.get('dir_only', False)
+        obj_dir = kwargs.get('obj_dir', False)
+        rel_path = self._construct_path(obj, **kwargs)
+
+        # for JOB_WORK directory
+        if base_dir and dir_only and obj_dir:
+            return os.path.abspath(rel_path)
+
+        cache_path = self._get_cache_path(rel_path)
+        # iRODS does not recognize directories as files so cannot check if those exist.
+        # So, if checking dir only, ensure given dir exists in cache and return
+        # the expected cache path.
+        # dir_only = kwargs.get('dir_only', False)
+        # if dir_only:
+        #     if not os.path.exists(cache_path):
+        #         os.makedirs(cache_path)
+        #     return cache_path
+        # Check if the file exists in the cache first
+        if self._in_cache(rel_path):
+            return cache_path
+        # Check if the file exists in persistent storage and, if it does, pull it into cache
+        elif self._exists(obj, **kwargs):
+            if dir_only:  # Directories do not get pulled into cache
+                return cache_path
+            else:
+                if self._pull_into_cache(rel_path):
+                    return cache_path
+        # For the case of retrieving a directory only, return the expected path
+        # even if it does not exist.
+        # if dir_only:
+        #     return cache_path
+        raise ObjectNotFound('objectstore.get_filename, no cache_path: %s, kwargs: %s'
+                             % (str(obj), str(kwargs)))
+        # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
+
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
+        if create:
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
+            rel_path = self._construct_path(obj, **kwargs)
+            # Chose whether to use the dataset file itself or an alternate file
+            if file_name:
+                source_file = os.path.abspath(file_name)
+                # Copy into cache
+                cache_file = self._get_cache_path(rel_path)
+                try:
+                    if source_file != cache_file:
+                        # FIXME? Should this be a `move`?
+                        shutil.copy2(source_file, cache_file)
+                    self._fix_permissions(cache_file)
+                except OSError:
+                    log.exception("Trouble copying source file '%s' to cache '%s'", source_file, cache_file)
+            else:
+                source_file = self._get_cache_path(rel_path)
+            # Update the file on iRODS
+            self._push_to_irods(rel_path, source_file)
+        else:
+            raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
+                                 % (str(obj), str(kwargs)))
+
+    # Unlike S3, url is not really applicable to iRODS
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            rel_path = self._construct_path(obj, **kwargs)
+
+            p = Path(rel_path)
+            data_object_name = p.stem + p.suffix
+            subcollection_name = p.parent
+
+            collection_path = self.home + "/" + str(subcollection_name)
+            data_object_path = collection_path + "/" + str(data_object_name)
+
+            return data_object_path
+
+    def _get_store_usage_percent(self):
+        return 0.0

lib/galaxy/objectstore/pithos.py

@@ -221,7 +221,7 @@ class PithosObjectStore(ConcreteObjectStore):
 
     # No need to overwrite "shutdown"
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         """Check if file exists, fix if file in cache and not on Pithos+
         :returns: weather the file exists remotely or in cache
         """
@@ -253,9 +253,9 @@ class PithosObjectStore(ConcreteObjectStore):
             return True
         return False
 
-    def create(self, obj, **kwargs):
+    def _create(self, obj, **kwargs):
         """Touch a file (aka create empty), if it doesn't exist"""
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
             extra_dir_at_root = kwargs.get('extra_dir_at_root', False)
@@ -288,18 +288,18 @@ class PithosObjectStore(ConcreteObjectStore):
                 open(new_file, 'w').close()
                 self.pithos.upload_from_string(rel_path, '')
 
-    def empty(self, obj, **kwargs):
+    def _empty(self, obj, **kwargs):
         """
         :returns: weather the object has content
         :raises ObjectNotFound:
         """
-        if not self.exists(obj, **kwargs):
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
                 'objectstore.empty, object does not exist: {obj}, '
                 'kwargs: {kwargs}'.format(obj=obj, kwargs=kwargs))
-        return bool(self.size(obj, **kwargs))
+        return bool(self._size(obj, **kwargs))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         """
         :returns: The size of the object, or 0 if it doesn't exist (sorry for
             that, not our fault, the ObjectStore interface is like that some
@@ -321,7 +321,7 @@ class PithosObjectStore(ConcreteObjectStore):
             return 0
         return int(file['content-length'])
 
-    def delete(self, obj, **kwargs):
+    def _delete(self, obj, **kwargs):
         """Delete the object
         :returns: weather the object was deleted
         """
@@ -347,13 +347,13 @@ class PithosObjectStore(ConcreteObjectStore):
                 self.pithos.del_object(path)
         except OSError:
             log.exception(
-                '{0} delete error'.format(self.get_filename(obj, **kwargs)))
+                '{0} delete error'.format(self._get_filename(obj, **kwargs)))
         except ClientError as ce:
             log.exception('Could not delete {path} from Pithos, {err}'.format(
                 path=path, err=ce))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         """Fetch (e.g., download) data
         :param start: Chunk of data starts here
         :param count: Fetch at most as many data, fetch all if negative
@@ -369,7 +369,7 @@ class PithosObjectStore(ConcreteObjectStore):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         """Get the expected filename with absolute path"""
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
@@ -386,7 +386,7 @@ class PithosObjectStore(ConcreteObjectStore):
             return cache_path
         if self._in_cache(path):
             return cache_path
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if not dir_only:
                 self._pull_into_cache(path)
                 return cache_path
@@ -394,11 +394,11 @@ class PithosObjectStore(ConcreteObjectStore):
             'objectstore.get_filename, no cache_path: {obj}, '
             'kwargs: {kwargs}'.format(obj, kwargs))
 
-    def update_from_file(self, obj, **kwargs):
+    def _update_from_file(self, obj, **kwargs):
         """Update the store when a file is updated"""
         if kwargs.get('create'):
-            self.create(obj, **kwargs)
-        if not self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if not self._exists(obj, **kwargs):
             raise ObjectNotFound(
                 'objectstore.update_from_file, object does not exist: {obj}, '
                 'kwargs: {kwargs}'.format(obj, kwargs))
@@ -420,11 +420,11 @@ class PithosObjectStore(ConcreteObjectStore):
             with open(cache_path) as f:
                 self.pithos.upload_object(obj, f)
 
-    def get_object_url(self, obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
         """
         :returns: URL for direct access, None if no object
         """
-        if self.exists(obj, **kwargs):
+        if self._exists(obj, **kwargs):
             path = self._construct_path(obj, **kwargs)
             try:
                 return self.pithos.publish_object(path)
@@ -434,7 +434,7 @@ class PithosObjectStore(ConcreteObjectStore):
                 log.exception('Kamaki: {0}'.format(ce))
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         """
         :returns: percentage indicating how full the store is
         """

lib/galaxy/objectstore/pulsar.py

@@ -1,6 +1,6 @@
 from __future__ import absolute_import  # Need to import pulsar_client absolutely.
 
-from ..objectstore import ObjectStore
+from ..objectstore import BaseObjectStore
 
 try:
     from pulsar.client.manager import ObjectStoreClientManager
@@ -8,7 +8,7 @@ except ImportError:
     ObjectStoreClientManager = None
 
 
-class PulsarObjectStore(ObjectStore):
+class PulsarObjectStore(BaseObjectStore):
     """
     Object store implementation that delegates to a remote Pulsar server.
 
@@ -26,38 +26,38 @@ class PulsarObjectStore(ObjectStore):
     def __init__(self, config, config_xml):
         self.pulsar_client = self.__build_pulsar_client(config_xml)
 
-    def exists(self, obj, **kwds):
+    def _exists(self, obj, **kwds):
         return self.pulsar_client.exists(**self.__build_kwds(obj, **kwds))
 
     def file_ready(self, obj, **kwds):
         return self.pulsar_client.file_ready(**self.__build_kwds(obj, **kwds))
 
-    def create(self, obj, **kwds):
+    def _create(self, obj, **kwds):
         return self.pulsar_client.create(**self.__build_kwds(obj, **kwds))
 
-    def empty(self, obj, **kwds):
+    def _empty(self, obj, **kwds):
         return self.pulsar_client.empty(**self.__build_kwds(obj, **kwds))
 
-    def size(self, obj, **kwds):
+    def _size(self, obj, **kwds):
         return self.pulsar_client.size(**self.__build_kwds(obj, **kwds))
 
-    def delete(self, obj, **kwds):
+    def _delete(self, obj, **kwds):
         return self.pulsar_client.delete(**self.__build_kwds(obj, **kwds))
 
     # TODO: Optimize get_data.
-    def get_data(self, obj, **kwds):
+    def _get_data(self, obj, **kwds):
         return self.pulsar_client.get_data(**self.__build_kwds(obj, **kwds))
 
-    def get_filename(self, obj, **kwds):
+    def _get_filename(self, obj, **kwds):
         return self.pulsar_client.get_filename(**self.__build_kwds(obj, **kwds))
 
-    def update_from_file(self, obj, **kwds):
+    def _update_from_file(self, obj, **kwds):
         return self.pulsar_client.update_from_file(**self.__build_kwds(obj, **kwds))
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return self.pulsar_client.get_store_usage_percent()
 
-    def get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
+    def _get_object_url(self, obj, extra_dir=None, extra_dir_at_root=False, alt_name=None):
         return None
 
     def __build_kwds(self, obj, **kwds):

lib/galaxy/objectstore/rods.py

@@ -1,355 +0,0 @@
-"""
-Object Store plugin for the Integrated Rule-Oriented Data Store (iRODS)
-
-The module is named rods to avoid conflicting with the PyRods module, irods
-"""
-
-import logging
-import os
-import time
-from posixpath import (
-    basename as path_basename,
-    dirname as path_dirname,
-    join as path_join
-)
-
-try:
-    import irods
-except ImportError:
-    irods = None
-
-from galaxy.exceptions import (
-    ObjectInvalid,
-    ObjectNotFound
-)
-from galaxy.util.path import safe_relpath
-from ..objectstore import (
-    DiskObjectStore,
-    local_extra_dirs
-)
-
-IRODS_IMPORT_MESSAGE = ('The Python irods package is required to use this '
-                        'feature, please install it')
-
-log = logging.getLogger(__name__)
-
-
-class IRODSObjectStore(DiskObjectStore):
-    """
-    Galaxy object store based on iRODS
-    """
-
-    def __init__(self, config, file_path=None, extra_dirs=None):
-        super(IRODSObjectStore, self).__init__(config, file_path=file_path, extra_dirs=extra_dirs)
-        assert irods is not None, IRODS_IMPORT_MESSAGE
-        self.cache_path = config.object_store_cache_path
-        self.default_resource = config.irods_default_resource or None
-
-        # Connect to iRODS (AssertionErrors will be raised if anything goes wrong)
-        self.rods_env, self.rods_conn = rods_connect()
-
-        # if the root collection path in the config is unset or relative, try to use a sensible default
-        if config.irods_root_collection_path is None or (config.irods_root_collection_path is not None and not config.irods_root_collection_path.startswith('/')):
-            rods_home = self.rods_env.rodsHome
-            assert rods_home != '', "Unable to initialize iRODS Object Store: rodsHome cannot be determined and irods_root_collection_path in Galaxy config is unset or not absolute."
-            if config.irods_root_collection_path is None:
-                self.root_collection_path = path_join(rods_home, 'galaxy_data')
-            else:
-                self.root_collection_path = path_join(rods_home, config.irods_root_collection_path)
-        else:
-            self.root_collection_path = config.irods_root_collection_path
-
-        # will return a collection object regardless of whether it exists
-        self.root_collection = irods.irodsCollection(self.rods_conn, self.root_collection_path)
-
-        if self.root_collection.getId() == -1:
-            log.warning("iRODS root collection does not exist, will attempt to create: %s", self.root_collection_path)
-            self.root_collection.upCollection()
-            assert self.root_collection.createCollection(os.path.basename(self.root_collection_path)) == 0, "iRODS root collection creation failed: %s" % self.root_collection_path
-            self.root_collection = irods.irodsCollection(self.rods_conn, self.root_collection_path)
-            assert self.root_collection.getId() != -1, "iRODS root collection creation claimed success but still does not exist"
-
-        if self.default_resource is None:
-            self.default_resource = self.rods_env.rodsDefResource
-
-        log.info("iRODS data for this instance will be stored in collection: %s, resource: %s", self.root_collection_path, self.default_resource)
-
-    def __get_rods_path(self, obj, base_dir=None, dir_only=False, extra_dir=None, extra_dir_at_root=False, alt_name=None, strip_dat=True, **kwargs):
-        # extra_dir should never be constructed from provided data but just
-        # make sure there are no shenannigans afoot
-        if extra_dir and extra_dir != os.path.normpath(extra_dir):
-            log.warning('extra_dir is not normalized: %s', extra_dir)
-            raise ObjectInvalid("The requested object is invalid")
-        # ensure that any parent directory references in alt_name would not
-        # result in a path not contained in the directory path constructed here
-        if alt_name:
-            if not safe_relpath(alt_name):
-                log.warning('alt_name would locate path outside dir: %s', alt_name)
-                raise ObjectInvalid("The requested object is invalid")
-            # alt_name can contain parent directory references, but iRODS will
-            # not follow them, so if they are valid we normalize them out
-            alt_name = os.path.normpath(alt_name)
-        path = ""
-        if extra_dir is not None:
-            path = extra_dir
-
-        # extra_dir_at_root is ignored - since the iRODS plugin does not use
-        # the directory hash, there is only one level of subdirectory.
-
-        if not dir_only:
-            # the .dat extension is stripped when stored in iRODS
-            # TODO: is the strip_dat kwarg the best way to implement this?
-            if strip_dat and alt_name and alt_name.endswith('.dat'):
-                alt_name = os.path.splitext(alt_name)[0]
-            default_name = 'dataset_%s' % obj.id
-            if not strip_dat:
-                default_name += '.dat'
-            path = path_join(path, alt_name if alt_name else default_name)
-
-        path = path_join(self.root_collection_path, path)
-        return path
-
-    def __get_cache_path(self, obj, **kwargs):
-        # FIXME: does not handle collections
-        # FIXME: collisions could occur here
-        return os.path.join(self.cache_path, path_basename(self.__get_rods_path(obj, strip_dat=False, **kwargs)))
-
-    def __clean_cache_entry(self, obj, **kwargs):
-        # FIXME: does not handle collections
-        try:
-            os.unlink(self.__get_cache_path(obj, **kwargs))
-        except OSError:
-            # it is expected that we'll call this method a lot regardless of
-            # whether we think the cached file exists
-            pass
-
-    def __get_rods_handle(self, obj, mode='r', **kwargs):
-        if kwargs.get('dir_only', False):
-            return irods.irodsCollection(self.rods_conn, self.__get_rods_path(obj, **kwargs))
-        else:
-            return irods.irodsOpen(self.rods_conn, self.__get_rods_path(obj, **kwargs), mode)
-
-    def __mkcolls(self, rods_path):
-        """
-        An os.makedirs() for iRODS collections.  `rods_path` is the desired collection to create.
-        """
-        assert rods_path.startswith(self.root_collection_path + '/'), '__mkcolls(): Creating collections outside the root collection is not allowed (requested path was: %s)' % rods_path
-        mkcolls = []
-        c = irods.irodsCollection(self.rods_conn, rods_path)
-        while c.getId() == -1:
-            assert c.getCollName().startswith(self.root_collection_path + '/'), '__mkcolls(): Attempted to move above the root collection: %s' % c.getCollName()
-            mkcolls.append(c.getCollName())
-            c.upCollection()
-        for collname in reversed(mkcolls):
-            log.debug('Creating collection %s' % collname)
-            ci = irods.collInp_t()
-            ci.collName = collname
-            status = irods.rcCollCreate(self.rods_conn, ci)
-            assert status == 0, '__mkcolls(): Failed to create collection: %s' % collname
-
-    @local_extra_dirs
-    def exists(self, obj, **kwargs):
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        log.debug('exists(): checking: %s', doi.objPath)
-        return irods.rcObjStat(self.rods_conn, doi) is not None
-
-    @local_extra_dirs
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
-            rods_path = self.__get_rods_path(obj, **kwargs)
-            log.debug('create(): %s', rods_path)
-            dir_only = kwargs.get('dir_only', False)
-            # short circuit collection creation since most of the time it will
-            # be the root collection which already exists
-            collection_path = rods_path if dir_only else path_dirname(rods_path)
-            if collection_path != self.root_collection_path:
-                self.__mkcolls(collection_path)
-            if not dir_only:
-                # rcDataObjCreate is used instead of the irodsOpen wrapper so
-                # that we can prevent overwriting
-                doi = irods.dataObjInp_t()
-                doi.objPath = rods_path
-                doi.createMode = 0o640
-                doi.dataSize = 0  # 0 actually means "unknown", although literally 0 would be preferable
-                irods.addKeyVal(doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource)
-                status = irods.rcDataObjCreate(self.rods_conn, doi)
-                assert status >= 0, 'create(): rcDataObjCreate() failed: %s: %s: %s' % (rods_path, status, irods.strerror(status))
-
-    @local_extra_dirs
-    def empty(self, obj, **kwargs):
-        assert 'dir_only' not in kwargs, 'empty(): `dir_only` parameter is invalid here'
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            return h.getSize() == 0
-        except AttributeError:
-            # h is None
-            raise ObjectNotFound()
-
-    def size(self, obj, **kwargs):
-        assert 'dir_only' not in kwargs, 'size(): `dir_only` parameter is invalid here'
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            return h.getSize()
-        except AttributeError:
-            # h is None
-            return 0
-
-    @local_extra_dirs
-    def delete(self, obj, entire_dir=False, **kwargs):
-        assert 'dir_only' not in kwargs, 'delete(): `dir_only` parameter is invalid here'
-        rods_path = self.__get_rods_path(obj, **kwargs)
-        # __get_rods_path prepends self.root_collection_path but we are going
-        # to ensure that it's valid anyway for safety's sake
-        assert rods_path.startswith(self.root_collection_path + '/'), 'ERROR: attempt to delete object outside root collection (path was: %s)' % rods_path
-        if entire_dir:
-            # TODO
-            raise NotImplementedError()
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            # note: PyRods' irodsFile.delete() does not set force
-            status = h.delete()
-            assert status == 0, '%d: %s' % (status, irods.strerror(status))
-            return True
-        except AttributeError:
-            log.warning('delete(): operation failed: object does not exist: %s', rods_path)
-        except AssertionError as e:
-            # delete() does not raise on deletion failure
-            log.error('delete(): operation failed: %s', e)
-        finally:
-            # remove the cached entry (finally is executed even when the try
-            # contains a return)
-            self.__clean_cache_entry(self, obj, **kwargs)
-        return False
-
-    @local_extra_dirs
-    def get_data(self, obj, start=0, count=-1, **kwargs):
-        log.debug('get_data(): %s')
-        h = self.__get_rods_handle(obj, **kwargs)
-        try:
-            h.seek(start)
-        except AttributeError:
-            raise ObjectNotFound()
-        if count == -1:
-            return h.read()
-        else:
-            return h.read(count)
-        # TODO: make sure implicit close is okay, DiskObjectStore actually
-        # reads data into a var, closes, and returns the var
-
-    @local_extra_dirs
-    def get_filename(self, obj, **kwargs):
-        log.debug("get_filename(): called on %s %s. For better performance, avoid this method and use get_data() instead.", obj.__class__.__name__, obj.id)
-        cached_path = self.__get_cache_path(obj, **kwargs)
-
-        if not self.exists(obj, **kwargs):
-            raise ObjectNotFound()
-
-        # TODO: implement or define whether dir_only is valid
-        if 'dir_only' in kwargs:
-            raise NotImplementedError()
-
-        # cache hit
-        if os.path.exists(cached_path):
-            return os.path.abspath(cached_path)
-
-        # cache miss
-        # TODO: thread this
-        incoming_path = os.path.join(os.path.dirname(cached_path), "__incoming_%s" % os.path.basename(cached_path))
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        doi.dataSize = 0  # TODO: does this affect performance? should we get size?
-        doi.numThreads = 0
-        # TODO: might want to VERIFY_CHKSUM_KW
-        log.debug('get_filename(): caching %s to %s', doi.objPath, incoming_path)
-
-        # do the iget
-        status = irods.rcDataObjGet(self.rods_conn, doi, incoming_path)
-
-        # if incoming already exists, we'll wait for another process or thread
-        # to finish caching
-        if status != irods.OVERWRITE_WITHOUT_FORCE_FLAG:
-            assert status == 0, 'get_filename(): iget %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
-            # POSIX rename is atomic
-            # TODO: rename without clobbering
-            os.rename(incoming_path, cached_path)
-            log.debug('get_filename(): cached %s to %s', doi.objPath, cached_path)
-
-        # another process or thread is caching, wait for it
-        while not os.path.exists(cached_path):
-            # TODO: force restart after mod time > some configurable, or
-            # otherwise deal with this potential deadlock and interrupted
-            # transfers
-            time.sleep(5)
-            log.debug("get_filename(): waiting on incoming '%s' for %s %s", incoming_path, obj.__class__.__name__, obj.id)
-
-        return os.path.abspath(cached_path)
-
-    @local_extra_dirs
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
-        assert 'dir_only' not in kwargs, 'update_from_file(): `dir_only` parameter is invalid here'
-
-        # do not create if not requested
-        if create and not self.exists(obj, **kwargs):
-            raise ObjectNotFound()
-
-        if file_name is None:
-            file_name = self.__get_cache_path(obj, **kwargs)
-
-        # put will create if necessary
-        doi = irods.dataObjInp_t()
-        doi.objPath = self.__get_rods_path(obj, **kwargs)
-        doi.createMode = 0o640
-        doi.dataSize = os.stat(file_name).st_size
-        doi.numThreads = 0
-        irods.addKeyVal(doi.condInput, irods.DEST_RESC_NAME_KW, self.default_resource)
-        irods.addKeyVal(doi.condInput, irods.FORCE_FLAG_KW, '')
-        # TODO: might want to VERIFY_CHKSUM_KW
-        log.debug('update_from_file(): updating %s to %s', file_name, doi.objPath)
-
-        # do the iput
-        status = irods.rcDataObjPut(self.rods_conn, doi, file_name)
-        assert status == 0, 'update_from_file(): iput %s failed (%s): %s' % (doi.objPath, status, irods.strerror(status))
-
-    def get_object_url(self, obj, **kwargs):
-        return None
-
-    def get_store_usage_percent(self):
-        return 0.0
-
-
-# monkeypatch an strerror method into the irods module
-def _rods_strerror(errno):
-    """
-    The missing `strerror` for iRODS error codes
-    """
-    if not hasattr(irods, '__rods_strerror_map'):
-        irods.__rods_strerror_map = {}
-        for name in dir(irods):
-            v = getattr(irods, name)
-            if type(v) == int and v < 0:
-                irods.__rods_strerror_map[v] = name
-    return irods.__rods_strerror_map.get(errno, 'GALAXY_NO_ERRNO_MAPPING_FOUND')
-
-
-if irods is not None:
-    irods.strerror = _rods_strerror
-
-
-def rods_connect():
-    """
-    A basic iRODS connection mechanism that connects using the current iRODS
-    environment
-    """
-    status, env = irods.getRodsEnv()
-    assert status == 0, 'connect(): getRodsEnv() failed (%s): %s' % (status, irods.strerror(status))
-    conn, err = irods.rcConnect(env.rodsHost,
-                                env.rodsPort,
-                                env.rodsUserName,
-                                env.rodsZone)
-    assert err.status == 0, 'connect(): rcConnect() failed (%s): %s' % (err.status, err.msg)
-    status, pw = irods.obfGetPw()
-    assert status == 0, 'connect(): getting password with obfGetPw() failed (%s): %s' % (status, irods.strerror(status))
-    status = irods.clientLoginWithObfPassword(conn, pw)
-    assert status == 0, 'connect(): logging in with clientLoginWithObfPassword() failed (%s): %s' % (status, irods.strerror(status))
-    return env, conn

lib/galaxy/objectstore/s3.py

@@ -504,7 +504,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                       os.path.getsize(self._get_cache_path(rel_path)), self._get_size_in_s3(rel_path))
         return False
 
-    def exists(self, obj, **kwargs):
+    def _exists(self, obj, **kwargs):
         in_cache = in_s3 = False
         rel_path = self._construct_path(obj, **kwargs)
 
@@ -537,8 +537,8 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         else:
             return False
 
-    def create(self, obj, **kwargs):
-        if not self.exists(obj, **kwargs):
+    def _create(self, obj, **kwargs):
+        if not self._exists(obj, **kwargs):
 
             # Pull out locally used fields
             extra_dir = kwargs.get('extra_dir', None)
@@ -572,26 +572,26 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 open(os.path.join(self.staging_path, rel_path), 'w').close()
                 self._push_to_os(rel_path, from_string='')
 
-    def empty(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
-            return bool(self.size(obj, **kwargs) > 0)
+    def _empty(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
+            return bool(self._size(obj, **kwargs) > 0)
         else:
             raise ObjectNotFound('objectstore.empty, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def size(self, obj, **kwargs):
+    def _size(self, obj, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         if self._in_cache(rel_path):
             try:
                 return os.path.getsize(self._get_cache_path(rel_path))
             except OSError as ex:
                 log.info("Could not get size of file '%s' in local cache, will try S3. Error: %s", rel_path, ex)
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             return self._get_size_in_s3(rel_path)
         log.warning("Did not find dataset '%s', returning 0 for size", rel_path)
         return 0
 
-    def delete(self, obj, entire_dir=False, **kwargs):
+    def _delete(self, obj, entire_dir=False, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         extra_dir = kwargs.get('extra_dir', None)
         base_dir = kwargs.get('base_dir', None)
@@ -626,10 +626,10 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         except S3ResponseError:
             log.exception("Could not delete key '%s' from S3", rel_path)
         except OSError:
-            log.exception('%s delete error', self.get_filename(obj, **kwargs))
+            log.exception('%s delete error', self._get_filename(obj, **kwargs))
         return False
 
-    def get_data(self, obj, start=0, count=-1, **kwargs):
+    def _get_data(self, obj, start=0, count=-1, **kwargs):
         rel_path = self._construct_path(obj, **kwargs)
         # Check cache first and get file if not there
         if not self._in_cache(rel_path):
@@ -641,7 +641,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         data_file.close()
         return content
 
-    def get_filename(self, obj, **kwargs):
+    def _get_filename(self, obj, **kwargs):
         base_dir = kwargs.get('base_dir', None)
         dir_only = kwargs.get('dir_only', False)
         obj_dir = kwargs.get('obj_dir', False)
@@ -664,7 +664,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
         if self._in_cache(rel_path):
             return cache_path
         # Check if the file exists in persistent storage and, if it does, pull it into cache
-        elif self.exists(obj, **kwargs):
+        elif self._exists(obj, **kwargs):
             if dir_only:  # Directories do not get pulled into cache
                 return cache_path
             else:
@@ -678,10 +678,10 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                              % (str(obj), str(kwargs)))
         # return cache_path # Until the upload tool does not explicitly create the dataset, return expected path
 
-    def update_from_file(self, obj, file_name=None, create=False, **kwargs):
+    def _update_from_file(self, obj, file_name=None, create=False, **kwargs):
         if create:
-            self.create(obj, **kwargs)
-        if self.exists(obj, **kwargs):
+            self._create(obj, **kwargs)
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             # Chose whether to use the dataset file itself or an alternate file
             if file_name:
@@ -703,8 +703,8 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
             raise ObjectNotFound('objectstore.update_from_file, object does not exist: %s, kwargs: %s'
                                  % (str(obj), str(kwargs)))
 
-    def get_object_url(self, obj, **kwargs):
-        if self.exists(obj, **kwargs):
+    def _get_object_url(self, obj, **kwargs):
+        if self._exists(obj, **kwargs):
             rel_path = self._construct_path(obj, **kwargs)
             try:
                 key = Key(self._bucket, rel_path)
@@ -713,7 +713,7 @@ class S3ObjectStore(ConcreteObjectStore, CloudConfigMixin):
                 log.exception("Trouble generating URL for dataset '%s'", rel_path)
         return None
 
-    def get_store_usage_percent(self):
+    def _get_store_usage_percent(self):
         return 0.0
 
     def shutdown(self):

lib/galaxy/selenium/navigates_galaxy.py

@@ -50,6 +50,10 @@ WAIT_TYPES = Bunch(
     JOB_COMPLETION=WaitType("job_completion", 30),
     # Wait time for a GIE to spawn.
     GIE_SPAWN=WaitType("gie_spawn", 30),
+    # Wait time for toolshed search
+    SHED_SEARCH=WaitType('shed_search', 30),
+    # Wait time for repository installation
+    REPO_INSTALL=WaitType('repo_install', 60),
 )
 
 # Choose a moderate wait type for operations that don't specify a type.
@@ -389,6 +393,12 @@ class NavigatesGalaxy(HasDriver):
         domain = domain or 'test.test'
         return self._get_random_name(prefix=username, suffix="@" + domain)
 
+    # Creates a random password of length len by creating an array with all ASCII letters and the numbers 0 to 9,
+    # then using the random number generator to pick one elemenent to concatinate it to the end of the password string until
+    # we have a password of length len.
+    def _get_random_password(self, len=6):
+        return ''.join(random.SystemRandom().choice(string.ascii_letters + string.digits) for _ in range(len))
+
     def submit_login(self, email, password=None, assert_valid=True, retries=0):
         if password is None:
             password = self.default_password

lib/galaxy/selenium/navigation.yml

@@ -70,6 +70,7 @@ masthead:
 
 preferences:
   selectors:
+    sign_out: "#edit-preferences-sign-out"
     change_password: "#edit-preferences-password"
     manage_information: '#edit-preferences-information'
     current_email: "#user-preferences-current-email"
@@ -88,6 +89,11 @@ change_user_address:
       type: xpath
       selector: '//span[contains(text(), "Insert Address")]'
 
+sign_out:
+  selectors:
+    cancel_button: '.modal-footer .buttons #button-0'
+    sign_out_button: '.modal-footer .buttons #button-1'
+
 history_panel:
   menu:
     labels:
@@ -353,18 +359,31 @@ tour:
 
 admin:
 
+  toolshed:
+    selectors:
+      repo_search: '#toolshed-repo-search'
+      search_results: '#shed-search-results'
+
   index:
     selectors:
       datatypes: '#admin-link-datatypes'
+      dependencies: '#admin-link-manage-dependencies'
       data_tables: '#admin-link-data-tables'
       display_applications: '#admin-link-display-applications'
+      errors: '#admin-link-error-stack'
+      forms: '#admin-link-forms'
       jobs: '#admin-link-jobs'
       local_data: '#admin-link-local-data'
+      metadata: '#admin-link-metadata'
+      migrations: '#admin-link-migrations'
+      tool_versions: '#admin-link-tool-versions'
+      toolshed: '#admin-link-toolshed'
       users: '#admin-link-users'
       quotas: '#admin-link-quotas'
       groups: '#admin-link-groups'
       roles: '#admin-link-roles'
       impersonate: '#admin-link-impersonate'
+      whitelist: '#admin-link-whitelist'
 
   selectors:
     # TODO: place betters IDS or something on this in these grids in the DOM

lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/asynchronous_reader.py

@@ -1,6 +1,8 @@
 import logging
 import threading
 
+from galaxy.util import unicodify
+
 log = logging.getLogger(__name__)
 
 
@@ -20,8 +22,8 @@ class AsynchronousReader(threading.Thread):
         """Read lines and put them on the queue."""
         thread_lock = threading.Lock()
         thread_lock.acquire()
-        for line in iter(self._fd.readline, ''):
-            stripped_line = line.rstrip()
+        for line in iter(self._fd.readline, b''):
+            stripped_line = unicodify(line).rstrip()
             self.lines.append(stripped_line)
             self._queue.put(stripped_line)
         thread_lock.release()

lib/galaxy/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py

@@ -13,13 +13,16 @@ from fabric.operations import _AttributeString
 from six.moves import queue
 
 from galaxy.tool_shed.galaxy_install.tool_dependencies.recipe import asynchronous_reader
-from galaxy.tool_shed.util.basic_util import INSTALLATION_LOG, NO_OUTPUT_TIMEOUT
+from galaxy.tool_shed.util.basic_util import (
+    INSTALLATION_LOG,
+    NO_OUTPUT_TIMEOUT,
+)
 from galaxy.tool_shed.util.tool_dependency_util import set_tool_dependency_attributes
 from galaxy.util import (
     DATABASE_MAX_STRING_SIZE,
     DATABASE_MAX_STRING_SIZE_PRETTY,
     shrink_string_by_size,
-    unicodify
+    unicodify,
 )
 
 log = logging.getLogger(__name__)
@@ -78,13 +81,13 @@ class InstallEnvironment(object):
         """
         stdout_logger = logging.getLogger('install_environment.STDOUT')
         stderr_logger = logging.getLogger('install_environment.STDERR')
-        for line in iter(stdout.readline, ''):
-            output = line.rstrip()
+        for line in iter(stdout.readline, b''):
+            output = unicodify(line).rstrip()
             stdout_logger.debug(output)
             stdout_queue.put(output)
         stdout_queue.put(None)
-        for line in iter(stderr.readline, ''):
-            output = line.rstrip()
+        for line in iter(stderr.readline, b''):
+            output = unicodify(line).rstrip()
             stderr_logger.debug(output)
             stderr_queue.put(output)
         stderr_queue.put(None)
@@ -245,19 +248,18 @@ class InstallEnvironment(object):
 
     def log_results(self, command, fabric_AttributeString, file_path):
         """Write attributes of fabric.operations._AttributeString to a specified log file."""
-        if os.path.exists(file_path):
-            logfile = open(file_path, 'ab')
-        else:
-            logfile = open(file_path, 'wb')
-        logfile.write("\n#############################################\n")
-        logfile.write('%s\nSTDOUT\n' % command)
-        logfile.write(str(fabric_AttributeString.stdout))
-        logfile.write("\n#############################################\n")
-        logfile.write("\n#############################################\n")
-        logfile.write('%s\nSTDERR\n' % command)
-        logfile.write(str(fabric_AttributeString.stderr))
-        logfile.write("\n#############################################\n")
-        logfile.close()
+        mode = 'a' if os.path.exists(file_path) else 'w'
+        with open(file_path, mode) as logfile:
+            logfile.write("\n#############################################\n")
+            logfile.write(command)
+            logfile.write('\nSTDOUT\n')
+            logfile.write(fabric_AttributeString.stdout)
+            logfile.write("\n#############################################\n")
+            logfile.write("\n#############################################\n")
+            logfile.write(command)
+            logfile.write('\nSTDERR\n')
+            logfile.write(fabric_AttributeString.stderr)
+            logfile.write("\n#############################################\n")
 
     @contextmanager
     def use_tmp_dir(self):

lib/galaxy/tool_shed/metadata/metadata_generator.py

@@ -17,10 +17,7 @@ from galaxy.tool_shed.util import (
     tool_util,
 )
 from galaxy.tool_shed.util.basic_util import remove_dir, strip_path
-from galaxy.tool_shed.util.hg_util import (
-    get_config_from_disk,
-    get_repo_for_repository,
-)
+from galaxy.tool_shed.util.hg_util import get_config_from_disk
 from galaxy.tool_shed.util.metadata_util import get_updated_changeset_revisions_from_tool_shed
 from galaxy.tool_shed.util.repository_util import get_repository_for_dependency_relationship
 from galaxy.tool_util.loader_directory import looks_like_a_tool
@@ -77,7 +74,7 @@ class MetadataGenerator(object):
         else:
             # We're in the Tool Shed.
             if changeset_revision is None and self.repository is not None:
-                self.changeset_revision = self.repository.tip(self.app)
+                self.changeset_revision = self.repository.tip()
             else:
                 self.changeset_revision = changeset_revision
             if repository_clone_url is None and self.repository is not None:
@@ -989,7 +986,7 @@ class MetadataGenerator(object):
                     log.debug(error_message)
                     is_valid = False
                     return repository_dependency_tup, is_valid, error_message
-                repo = get_repo_for_repository(self.app, repository=repository)
+                repo = repository.hg_repo
 
                 # The received changeset_revision may be None since defining it in the dependency definition is optional.
                 # If this is the case, the default will be to set its value to the repository dependency tip revision.
@@ -1080,7 +1077,7 @@ class MetadataGenerator(object):
             if relative_install_dir is None and self.repository is not None:
                 relative_install_dir = repository.repo_path(self.app)
             if changeset_revision is None and self.repository is not None:
-                self.set_changeset_revision(self.repository.tip(self.app))
+                self.set_changeset_revision(self.repository.tip())
             else:
                 self.set_changeset_revision(changeset_revision)
             self.shed_config_dict = {}

lib/galaxy/tool_shed/util/hg_util.py

@@ -77,7 +77,7 @@ def get_ctx_file_path_from_manifest(filename, repo, changeset_revision):
     for changeset in reversed_upper_bounded_changelog(repo, changeset_revision):
         manifest_ctx = repo[changeset]
         for ctx_file in manifest_ctx.files():
-            ctx_file_name = basic_util.strip_path(ctx_file)
+            ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
             if ctx_file_name == stripped_filename:
                 return manifest_ctx, ctx_file
     return None, None
@@ -93,7 +93,7 @@ def get_file_context_from_ctx(ctx, filename):
     deleted = False
     filename = basic_util.strip_path(filename)
     for ctx_file in ctx.files():
-        ctx_file_name = basic_util.strip_path(ctx_file)
+        ctx_file_name = basic_util.strip_path(unicodify(ctx_file))
         if filename == ctx_file_name:
             try:
                 # If the file was moved, its destination will be returned here.
@@ -107,18 +107,6 @@ def get_file_context_from_ctx(ctx, filename):
     return None
 
 
-def get_repo_for_repository(app, repository=None, repo_path=None):
-    # Import from mercurial here to let Galaxy start under Python 3
-    from mercurial import (
-        hg,
-        ui
-    )
-    if repository is not None:
-        return hg.repository(ui.ui(), repository.repo_path(app))
-    if repo_path is not None:
-        return hg.repository(ui.ui(), repo_path)
-
-
 def pull_repository(repo_path, repository_clone_url, ctx_rev):
     """Pull changes from a remote repository to a local one."""
     try:
@@ -199,7 +187,6 @@ __all__ = (
     'get_config_from_disk',
     'get_ctx_file_path_from_manifest',
     'get_file_context_from_ctx',
-    'get_repo_for_repository',
     'pull_repository',
     'reversed_lower_upper_bounded_changelog',
     'reversed_upper_bounded_changelog',