Merge pull request #12912 from jmchilton/upload_provenance_2

Improved Upload Provenance and Correctness

client/src/components/DatasetInformation/DatasetHash.vue

@@ -0,0 +1,16 @@
+<template>
+    <li class="dataset-hash">
+        <i>{{ hash.hash_value }}</i>
+    </li>
+</template>
+
+<script>
+export default {
+    props: {
+        hash: {
+            type: Object,
+            required: true,
+        },
+    },
+};
+</script>

client/src/components/DatasetInformation/DatasetHashes.vue

@@ -0,0 +1,30 @@
+<template>
+    <span class="dataset-hashes">
+        <ul class="dataset-hashes-list">
+            <DatasetHash v-for="(hash, index) in hashes" :key="index" :hash="hash" />
+        </ul>
+    </span>
+</template>
+
+<script>
+import DatasetHash from "./DatasetHash";
+
+export default {
+    components: {
+        DatasetHash,
+    },
+    props: {
+        hashes: {
+            type: Array,
+            required: true,
+        },
+    },
+};
+</script>
+
+<style scoped>
+.dataset-hashes-list {
+    padding-inline-start: 20px;
+    margin-bottom: 0px;
+}
+</style>

client/src/components/DatasetInformation/DatasetInformation.vue

@@ -54,6 +54,22 @@
                         <td>Full Path</td>
                         <td id="file_name">{{ dataset.file_name }}</td>
                     </tr>
+                    <tr v-if="dataset.created_from_basename">
+                        <td>Originally Created From a File Named</td>
+                        <td id="created_from_basename">{{ dataset.created_from_basename }}</td>
+                    </tr>
+                    <tr v-if="dataset.sources && dataset.sources.length > 0">
+                        <td>Sources</td>
+                        <td>
+                            <DatasetSources :sources="dataset.sources" />
+                        </td>
+                    </tr>
+                    <tr v-if="dataset.hashes && dataset.hashes.length > 0">
+                        <td>Hashes</td>
+                        <td>
+                            <DatasetHashes :hashes="dataset.hashes" />
+                        </td>
+                    </tr>
                 </tbody>
             </table>
         </div>
@@ -65,6 +81,8 @@ import Utils from "utils/utils";
 import UtcDate from "components/UtcDate";
 import DecodedId from "../DecodedId";
 import { DatasetProvider } from "components/providers";
+import DatasetSources from "./DatasetSources";
+import DatasetHashes from "./DatasetHashes";
 
 export default {
     props: {
@@ -74,7 +92,9 @@ export default {
         },
     },
     components: {
+        DatasetHashes,
         DatasetProvider,
+        DatasetSources,
         DecodedId,
         UtcDate,
     },

client/src/components/DatasetInformation/DatasetSource.vue

@@ -0,0 +1,51 @@
+<template>
+    <li class="dataset-source">
+        <a v-if="browserCompatUri" :href="sourceUri" target="_blank">
+            {{ source.source_uri }}
+            <font-awesome-icon v-b-tooltip.hover title="Dataset Source URL" icon="external-link-alt" />
+        </a>
+        <span v-else>
+            {{ source.source_uri }}
+        </span>
+        <font-awesome-icon v-b-tooltip.hover title="Copy URI" icon="copy" style="cursor: pointer" @click="copyLink" />
+        <br />
+        <DatasetSourceTransform :transform="source.transform" />
+    </li>
+</template>
+
+<script>
+import { FontAwesomeIcon } from "@fortawesome/vue-fontawesome";
+import { library } from "@fortawesome/fontawesome-svg-core";
+import { faCopy, faExternalLinkAlt } from "@fortawesome/free-solid-svg-icons";
+import { copy } from "utils/clipboard";
+import DatasetSourceTransform from "./DatasetSourceTransform";
+
+library.add(faCopy, faExternalLinkAlt);
+
+export default {
+    components: {
+        DatasetSourceTransform,
+        FontAwesomeIcon,
+    },
+    props: {
+        source: {
+            type: Object,
+            required: true,
+        },
+    },
+    computed: {
+        browserCompatUri() {
+            const sourceUri = this.sourceUri;
+            return sourceUri && (sourceUri.indexOf("http") == 0 || sourceUri.indexOf("ftp") == 0);
+        },
+        sourceUri() {
+            return this.source.source_uri;
+        },
+    },
+    methods: {
+        copyLink() {
+            copy(this.sourceUri, "Link copied to the clipboard.");
+        },
+    },
+};
+</script>

client/src/components/DatasetInformation/DatasetSourceTransform.vue

@@ -0,0 +1,94 @@
+<template>
+    <span class="dataset-source-transform-display">
+        <div v-if="transform && transform.length > 0">
+            Upon ingestion into the Galaxy, the following {{ actions }} were performed that modified the dataset
+            contents:
+            <ul>
+                <li v-for="(transformAction, index) in transform" :key="index">
+                    <span
+                        :title="actionLongDescription(transformAction)"
+                        class="dataset-source-transform-element"
+                        :data-transform-action="transformAction.action"
+                        v-b-tooltip.hover.noninteractive.nofade.bottom
+                    >
+                        {{ actionShortDescription(transformAction) }}
+                    </span>
+                </li>
+            </ul>
+        </div>
+    </span>
+</template>
+
+<script>
+import Vue from "vue";
+import BootstrapVue from "bootstrap-vue";
+
+Vue.use(BootstrapVue);
+
+const TRANSFORM_ACTION_DESCRIPTIONS = {
+    to_posix_lines: {
+        short: "Normalized new line characters",
+        long: "Many Galaxy tools expect data to contain 'posix' newline characters in text files and not the newline format used by the Windows operating system. Additionally, most tools expect a newline at the end of plain text files. This file was converted to use these line endings or add a newline to the end of the file.",
+    },
+    spaces_to_tabs: {
+        short: "Normalized spaces to tabs",
+        long: "In order to convert the referenced data source to tabular data, spaces in the file contents were converted to tab characters to indicate column separations.",
+    },
+    datatype_groom: {
+        short: "Datatype-specific grooming",
+        long: "The Galaxy datatype class indicated the source data required 'groooming' and Galaxy applied datatype specific cleaning of the supplied data.",
+    },
+};
+
+const DATATYPE_GROOMING_DESCRIPTIONS = {
+    bam: "The supplied BAM was coordinate-sorted using pysam.",
+    "qname_sorted.bam": "The supplied BAM was 'queryname' sorted using pysam.",
+    "qname_input_sorted.bam": "The supplied BAM was 'queryname' sorted using pysam.",
+    "isa-tab": "The supplied compressed file was converted to an ISA-TAB composite dataset.",
+    "isa-json": "The supplied compressed file was converted to an ISA-JSON composite dataset.",
+};
+
+const UNKNOWN_ACTION_DESCRIPTION = {
+    short: "Unknown action.",
+    long: "",
+};
+
+export default {
+    props: {
+        transform: {
+            type: Array,
+            required: false,
+        },
+    },
+    computed: {
+        actions() {
+            return this.transform.length > 1 ? "actions" : "action";
+        },
+    },
+    methods: {
+        actionShortDescription(transformAction) {
+            return this.actionDescription(transformAction).short || "Unknown action.";
+        },
+        actionLongDescription(transformAction) {
+            let longDescription = this.actionDescription(transformAction).long || "";
+            if (transformAction.action == "datatype_groom") {
+                const datatypeDescription = DATATYPE_GROOMING_DESCRIPTIONS[transformAction.datatype_ext];
+                if (datatypeDescription) {
+                    longDescription += " " + datatypeDescription;
+                }
+            }
+            return longDescription;
+        },
+        actionDescription(transformAction) {
+            return TRANSFORM_ACTION_DESCRIPTIONS[transformAction.action] || UNKNOWN_ACTION_DESCRIPTION;
+        },
+    },
+};
+</script>
+
+<style scoped>
+.dataset-source-transform-element {
+    text-decoration: underline;
+    text-decoration-style: dashed;
+}
+</style>

client/src/components/DatasetInformation/DatasetSources.vue

@@ -0,0 +1,30 @@
+<template>
+    <span class="dataset-sources">
+        <ul class="dataset-sources-list">
+            <DatasetSource v-for="(source, index) in sources" :key="index" :source="source" />
+        </ul>
+    </span>
+</template>
+
+<script>
+import DatasetSource from "./DatasetSource";
+
+export default {
+    components: {
+        DatasetSource,
+    },
+    props: {
+        sources: {
+            type: Array,
+            required: true,
+        },
+    },
+};
+</script>
+
+<style scoped>
+.dataset-sources-list {
+    padding-inline-start: 20px;
+    margin-bottom: 0px;
+}
+</style>

lib/galaxy/actions/library.py

@@ -74,7 +74,7 @@ class LibraryActions:
     Mixin for controllers that provide library functionality.
     """
 
-    def _upload_dataset(self, trans, library_id: str, folder_id: str, replace_dataset: Optional[LibraryDataset] = None, **kwd):
+    def _upload_dataset(self, trans, folder_id: str, replace_dataset: Optional[LibraryDataset] = None, **kwd):
         # Set up the traditional tool state/params
         cntrller = 'api'
         tool_id = 'upload1'