{"action":"created","comment":{"url":"https://api.github.com/repos/opencadc/caom2db/pulls/comments/201417505","pull_request_review_id":135908966,"id":201417505,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIwMTQxNzUwNQ==","diff_hunk":"@@ -0,0 +1,256 @@\n+/*\n+************************************************************************\n+*******************  CANADIAN ASTRONOMY DATA CENTRE  *******************\n+**************  CENTRE CANADIEN DE DONNÉES ASTRONOMIQUES  **************\n+*\n+*  (c) 2018.                            (c) 2018.\n+*  Government of Canada                 Gouvernement du Canada\n+*  National Research Council            Conseil national de recherches\n+*  Ottawa, Canada, K1A 0R6              Ottawa, Canada, K1A 0R6\n+*  All rights reserved                  Tous droits réservés\n+*\n+*  NRC disclaims any warranties,        Le CNRC dénie toute garantie\n+*  expressed, implied, or               énoncée, implicite ou légale,\n+*  statutory, of any kind with          de quelque nature que ce\n+*  respect to the software,             soit, concernant le logiciel,\n+*  including without limitation         y compris sans restriction\n+*  any warranty of merchantability      toute garantie de valeur\n+*  or fitness for a particular          marchande ou de pertinence\n+*  purpose. NRC shall not be            pour un usage particulier.\n+*  liable in any event for any          Le CNRC ne pourra en aucun cas\n+*  damages, whether direct or           être tenu responsable de tout\n+*  indirect, special or general,        dommage, direct ou indirect,\n+*  consequential or incidental,         particulier ou général,\n+*  arising from the use of the          accessoire ou fortuit, résultant\n+*  software.  Neither the name          de l'utilisation du logiciel. Ni\n+*  of the National Research             le nom du Conseil National de\n+*  Council of Canada nor the            Recherches du Canada ni les noms\n+*  names of its contributors may        de ses  participants ne peuvent\n+*  be used to endorse or promote        être utilisés pour approuver ou\n+*  products derived from this           promouvoir les produits dérivés\n+*  software without specific prior      de ce logiciel sans autorisation\n+*  written permission.                  préalable et particulière\n+*                                       par écrit.\n+*\n+*  This file is part of the             Ce fichier fait partie du projet\n+*  OpenCADC project.                    OpenCADC.\n+*\n+*  OpenCADC is free software:           OpenCADC est un logiciel libre ;\n+*  you can redistribute it and/or       vous pouvez le redistribuer ou le\n+*  modify it under the terms of         modifier suivant les termes de\n+*  the GNU Affero General Public        la “GNU Affero General Public\n+*  License as published by the          License” telle que publiée\n+*  Free Software Foundation,            par la Free Software Foundation\n+*  either version 3 of the              : soit la version 3 de cette\n+*  License, or (at your option)         licence, soit (à votre gré)\n+*  any later version.                   toute version ultérieure.\n+*\n+*  OpenCADC is distributed in the       OpenCADC est distribué\n+*  hope that it will be useful,         dans l’espoir qu’il vous\n+*  but WITHOUT ANY WARRANTY;            sera utile, mais SANS AUCUNE\n+*  without even the implied             GARANTIE : sans même la garantie\n+*  warranty of MERCHANTABILITY          implicite de COMMERCIALISABILITÉ\n+*  or FITNESS FOR A PARTICULAR          ni d’ADÉQUATION À UN OBJECTIF\n+*  PURPOSE.  See the GNU Affero         PARTICULIER. Consultez la Licence\n+*  General Public License for           Générale Publique GNU Affero\n+*  more details.                        pour plus de détails.\n+*\n+*  You should have received             Vous devriez avoir reçu une\n+*  a copy of the GNU Affero             copie de la Licence Générale\n+*  General Public License along         Publique GNU Affero avec\n+*  with OpenCADC.  If not, see          OpenCADC ; si ce n’est\n+*  <http://www.gnu.org/licenses/>.      pas le cas, consultez :\n+*                                       <http://www.gnu.org/licenses/>.\n+*\n+*  $Revision: 5 $\n+*\n+************************************************************************\n+*/\n+\n+package ca.nrc.cadc.caom2.artifactsync;\n+\n+import ca.nrc.cadc.caom2.persistence.ArtifactDAO;\n+import ca.nrc.cadc.caom2.persistence.ObservationDAO;\n+import ca.nrc.cadc.util.ArgumentMap;\n+\n+import java.util.ArrayList;\n+import java.util.List;\n+\n+import javax.security.auth.Subject;\n+\n+import org.apache.log4j.Logger;\n+\n+/**\n+ * Class to support both 'discover' and 'download' modes.\n+ *\n+ * @author majorb\n+ */\n+public class Discover extends Caom2ArtifactSync {\n+\n+    private static Logger log = Logger.getLogger(Discover.class);\n+    private ArgumentMap am;\n+    protected int batchSize = ArtifactHarvester.DEFAULT_BATCH_SIZE;\n+    protected boolean loop = false;\n+    private String collection = null;\n+    private DownloadArtifactFiles downloader = null;\n+    private ArtifactHarvester harvester = null;\n+\n+    public Discover(ArgumentMap am) {\n+        super(am);\n+\n+        // save ArgumentMap instance to allow us to create Subject instance\n+        // in the execution loop\n+        this.am = am;\n+        \n+        if (!this.isDone) {\n+            // arguments common to 'discover' and 'download' modes\n+            if (am.isSet(\"batchsize\")) {\n+                try {\n+                    this.batchSize = Integer.parseInt(am.getValue(\"batchsize\"));\n+                    if (batchSize < 1 || batchSize > 100000) {\n+                        String msg = \"value for --batchsize must be between 1 and 100000\";\n+                        printErrorUsage(msg);\n+                    }\n+                } catch (NumberFormatException nfe) {\n+                    String msg = \"Illegal value for --batchsize: \" + am.getValue(\"batchsize\");\n+                    printErrorUsage(msg);\n+                }\n+            }\n+\n+            if (!isDone) {\n+                this.parseDbParam(am, \"database\");\n+                this.loop = am.isSet(\"continue\");\n+            }\n+            \n+            if (!isDone) {\n+                if (this.mode.equals(\"download\")) {\n+                    // arguments that apply to 'download' mode\n+                    Integer retryAfterHours = null;\n+                    if (am.isSet(\"retryAfter\")) {\n+                        try {\n+                            retryAfterHours = Integer.parseInt(am.getValue(\"retryAfter\"));\n+                        } catch (NumberFormatException e) {\n+                            String msg = \"Illegal value for --retryAfter: \" + am.getValue(\"retryAfter\");\n+                            this.printErrorUsage(msg);\n+                        }\n+                    }\n+                    \n+                    boolean verify = !am.isSet(\"noverify\");\n+\n+                    int nthreads = 1;\n+                    if (am.isSet(\"threads\")) {\n+                        try {\n+                            nthreads = Integer.parseInt(am.getValue(\"threads\"));\n+                            if (nthreads < 1 || nthreads > 250) {\n+                                String msg = \"value for --threads must be between 1 and 250\";\n+                                this.printErrorUsage(msg);\n+                            }\n+                        } catch (NumberFormatException nfe) {\n+                            String msg = \"Illegal value for --threads: \" + am.getValue(\"threads\");\n+                            this.printErrorUsage(msg);\n+                        }\n+                    }\n+                    \n+                    if (!this.isDone) {\n+                        ArtifactDAO artifactDAO = new ArtifactDAO();\n+                        artifactDAO.setConfig(daoConfig);\n+\n+                        this.downloader = new DownloadArtifactFiles(\n+                                artifactDAO, dbInfo, artifactStore, nthreads, this.batchSize, retryAfterHours, verify);\n+                        List<ShutdownListener> listeners = new ArrayList<ShutdownListener>(2);\n+                        listeners.add(downloader);\n+                        Runtime.getRuntime().addShutdownHook(new Thread(new ShutdownHook(listeners)));\n+                    }\n+                } else {\n+                    // arguments that apply to 'discover' mode\n+                    this.collection = this.parseCollection(am);\n+                    \n+                    if (!this.isDone) {\n+                        ObservationDAO observationDAO = new ObservationDAO();\n+                        observationDAO.setConfig(this.daoConfig);\n+\n+                        this.harvester = new ArtifactHarvester(\n+                                observationDAO, dbInfo, artifactStore, collection, this.batchSize);\n+                        List<ShutdownListener> listeners = new ArrayList<ShutdownListener>(2);\n+                        listeners.add(harvester);\n+                        Runtime.getRuntime().addShutdownHook(new Thread(new ShutdownHook(listeners)));\n+                    }\n+                }\n+            }\n+        }\n+    }\n+\n+    public void printUsage() {\n+        StringBuilder sb = new StringBuilder();\n+        sb.append(\"\\n\\nusage: \").append(this.applicationName).append(\" [mode-args]\");\n+        sb.append(\"\\n\\n    [mode-args]:\");\n+        sb.append(\"\\n        --database=<server.database.schema>\");\n+        sb.append(\"\\n        --continue : Repeat batches until no work left\");\n+        if (this.mode.equals(\"download\")) {\n+            sb.append(\"\\n        --threads=<integer> : Number of download threads (default: 1)>\");\n+            sb.append(\"\\n        --batchsize=<integer> Max skip URIs to download (default: 1000)\");\n+            sb.append(\"\\n        --retryAfter=<integer> Hours after failed downloads should be retried (default: 24)\");\n+            sb.append(\"\\n        --noverify : Do not confirm by MD5 sum after download\");\n+        } else {\n+            sb.append(\"\\n        --batchsize=<integer> Max observations to check (default: 1000)\");\n+            sb.append(\"\\n        --collection=<collection> : The collection to discover\");\n+        }\n+        sb.append(\"\\n\\n    optional general args:\");\n+        sb.append(\"\\n        -v | --verbose\");\n+        sb.append(\"\\n        -d | --debug\");\n+        sb.append(\"\\n        -h | --help\");\n+        sb.append(\"\\n        --profile : Profile task execution\");\n+        sb.append(\"\\n\\n    authentication:\");\n+        sb.append(\"\\n        [--netrc|--cert=<pem file>]\");\n+        sb.append(\"\\n        --netrc : read username and password(s) from ~/.netrc file\");\n+        sb.append(\"\\n        --cert=<pem file> : read client certificate from PEM file\");\n+\n+        log.warn(sb.toString());    \n+        this.setIsDone(true);","path":"caom2-artifact-sync/src/main/java/ca/nrc/cadc/caom2/artifactsync/Discover.java","position":209,"original_position":209,"commit_id":"50a044d5d10a3e0b0768bbee07062b8ede2f5d39","original_commit_id":"50a044d5d10a3e0b0768bbee07062b8ede2f5d39","user":{"login":"brianmajor","id":7945728,"node_id":"MDQ6VXNlcjc5NDU3Mjg=","avatar_url":"https://avatars2.githubusercontent.com/u/7945728?v=4","gravatar_id":"","url":"https://api.github.com/users/brianmajor","html_url":"https://github.com/brianmajor","followers_url":"https://api.github.com/users/brianmajor/followers","following_url":"https://api.github.com/users/brianmajor/following{/other_user}","gists_url":"https://api.github.com/users/brianmajor/gists{/gist_id}","starred_url":"https://api.github.com/users/brianmajor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianmajor/subscriptions","organizations_url":"https://api.github.com/users/brianmajor/orgs","repos_url":"https://api.github.com/users/brianmajor/repos","events_url":"https://api.github.com/users/brianmajor/events{/privacy}","received_events_url":"https://api.github.com/users/brianmajor/received_events","type":"User","site_admin":false},"body":"What is the purpose of isDone?  There are a lot of checks to this boolean. ","created_at":"2018-07-10T16:52:26Z","updated_at":"2018-07-10T16:58:33Z","html_url":"https://github.com/opencadc/caom2db/pull/114#discussion_r201417505","pull_request_url":"https://api.github.com/repos/opencadc/caom2db/pulls/114","author_association":"MEMBER","_links":{"self":{"href":"https://api.github.com/repos/opencadc/caom2db/pulls/comments/201417505"},"html":{"href":"https://github.com/opencadc/caom2db/pull/114#discussion_r201417505"},"pull_request":{"href":"https://api.github.com/repos/opencadc/caom2db/pulls/114"}}},"pull_request":{"url":"https://api.github.com/repos/opencadc/caom2db/pulls/114","id":199530866,"node_id":"MDExOlB1bGxSZXF1ZXN0MTk5NTMwODY2","html_url":"https://github.com/opencadc/caom2db/pull/114","diff_url":"https://github.com/opencadc/caom2db/pull/114.diff","patch_url":"https://github.com/opencadc/caom2db/pull/114.patch","issue_url":"https://api.github.com/repos/opencadc/caom2db/issues/114","number":114,"state":"open","locked":false,"title":"T106 (Story 2321) artifact-sync command line changes","user":{"login":"yeunga","id":8481544,"node_id":"MDQ6VXNlcjg0ODE1NDQ=","avatar_url":"https://avatars3.githubusercontent.com/u/8481544?v=4","gravatar_id":"","url":"https://api.github.com/users/yeunga","html_url":"https://github.com/yeunga","followers_url":"https://api.github.com/users/yeunga/followers","following_url":"https://api.github.com/users/yeunga/following{/other_user}","gists_url":"https://api.github.com/users/yeunga/gists{/gist_id}","starred_url":"https://api.github.com/users/yeunga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yeunga/subscriptions","organizations_url":"https://api.github.com/users/yeunga/orgs","repos_url":"https://api.github.com/users/yeunga/repos","events_url":"https://api.github.com/users/yeunga/events{/privacy}","received_events_url":"https://api.github.com/users/yeunga/received_events","type":"User","site_admin":false},"body":"Please also review the corresponding changes in service.git. Please note that service/artifact-sync has been renamed to service/cadc-artifact-sync.\r\nrepo: service.git\r\nmodule: cadc-artifact-sync\r\nbranch: t106","created_at":"2018-07-05T16:53:54Z","updated_at":"2018-07-10T16:58:33Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c5a03e83468f476d1010145ae6dac7e91631e136","assignee":null,"assignees":[],"requested_reviewers":[],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/opencadc/caom2db/pulls/114/commits","review_comments_url":"https://api.github.com/repos/opencadc/caom2db/pulls/114/comments","review_comment_url":"https://api.github.com/repos/opencadc/caom2db/pulls/comments{/number}","comments_url":"https://api.github.com/repos/opencadc/caom2db/issues/114/comments","statuses_url":"https://api.github.com/repos/opencadc/caom2db/statuses/50a044d5d10a3e0b0768bbee07062b8ede2f5d39","head":{"label":"yeunga:t106","ref":"t106","sha":"50a044d5d10a3e0b0768bbee07062b8ede2f5d39","user":{"login":"yeunga","id":8481544,"node_id":"MDQ6VXNlcjg0ODE1NDQ=","avatar_url":"https://avatars3.githubusercontent.com/u/8481544?v=4","gravatar_id":"","url":"https://api.github.com/users/yeunga","html_url":"https://github.com/yeunga","followers_url":"https://api.github.com/users/yeunga/followers","following_url":"https://api.github.com/users/yeunga/following{/other_user}","gists_url":"https://api.github.com/users/yeunga/gists{/gist_id}","starred_url":"https://api.github.com/users/yeunga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yeunga/subscriptions","organizations_url":"https://api.github.com/users/yeunga/orgs","repos_url":"https://api.github.com/users/yeunga/repos","events_url":"https://api.github.com/users/yeunga/events{/privacy}","received_events_url":"https://api.github.com/users/yeunga/received_events","type":"User","site_admin":false},"repo":{"id":69290941,"node_id":"MDEwOlJlcG9zaXRvcnk2OTI5MDk0MQ==","name":"caom2db","full_name":"yeunga/caom2db","owner":{"login":"yeunga","id":8481544,"node_id":"MDQ6VXNlcjg0ODE1NDQ=","avatar_url":"https://avatars3.githubusercontent.com/u/8481544?v=4","gravatar_id":"","url":"https://api.github.com/users/yeunga","html_url":"https://github.com/yeunga","followers_url":"https://api.github.com/users/yeunga/followers","following_url":"https://api.github.com/users/yeunga/following{/other_user}","gists_url":"https://api.github.com/users/yeunga/gists{/gist_id}","starred_url":"https://api.github.com/users/yeunga/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yeunga/subscriptions","organizations_url":"https://api.github.com/users/yeunga/orgs","repos_url":"https://api.github.com/users/yeunga/repos","events_url":"https://api.github.com/users/yeunga/events{/privacy}","received_events_url":"https://api.github.com/users/yeunga/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/yeunga/caom2db","description":"Common 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