Merge branch 'develop' of gitlab.coko.foundation:xpub/xpub-faraday into hindawi-theme

packages/component-faraday-selectors/src/index.js

@@ -7,7 +7,11 @@ export const isHEToManuscript = (state, collectionId) => {
   return get(collection, 'handlingEditor.id') === currentUserId
 }
 
-const canMakeRecommendationStatuses = ['reviewCompleted', 'heAssigned']
+const canMakeRecommendationStatuses = [
+  'reviewCompleted',
+  'heAssigned',
+  'underReview',
+]
 export const canMakeRecommendation = (state, collection, fragment = {}) => {
   if (fragment.id !== last(collection.fragments)) return false
   const isHE = isHEToManuscript(state, collection.id)

packages/component-helper-service/src/services/User.js

@@ -45,7 +45,12 @@ class User {
     const { UserModel } = this
     const users = await UserModel.all()
 
-    return users.filter(user => user.editorInChief)
+    const eics = users.filter(user => user.editorInChief)
+    if (eics.length === 0) {
+      throw new Error('No Editor in Chief has been found')
+    }
+
+    return eics
   }
 
   async updateUserTeams({ userId, teamId }) {

packages/component-manuscript-manager/src/routes/fragmentsRecommendations/notifications/notifications.js

 const config = require('config')
-const { chain, get } = require('lodash')
+const { chain, get, isEmpty } = require('lodash')
 
 const {
   User,
@@ -58,9 +58,13 @@ module.exports = {
 
       comments = eicComments
     }
+
+    const hasPeerReview = (collection = {}) =>
+      !isEmpty(collection.handlingEditor)
+
     if (
       (isEditorInChief || newRecommendation.recommendationType === 'review') &&
-      collection.status !== 'rejected'
+      hasPeerReview(collection)
     ) {
       // the request came from either the Editor in Chief or a reviewer, so the HE needs to be notified
       sendHandlingEditorEmail({
@@ -81,17 +85,19 @@ module.exports = {
       newRecommendation.recommendationType !== 'review' &&
       newRecommendation.recommendation !== 'return-to-handling-editor'
     ) {
-      sendAuthorsEmail({
-        email,
-        baseUrl,
-        titleText,
-        parsedFragment,
-        fragmentAuthors,
-        isEditorInChief,
-        subjectBaseText,
-        newRecommendation,
-      })
-      if (collection.status !== 'rejected') {
+      if (isEditorInChief || collection.status === 'revisionRequested') {
+        sendAuthorsEmail({
+          email,
+          baseUrl,
+          titleText,
+          parsedFragment,
+          fragmentAuthors,
+          isEditorInChief,
+          subjectBaseText,
+          newRecommendation,
+        })
+      }
+      if (hasPeerReview(collection)) {
         sendReviewersEmail({
           email,
           baseUrl,

packages/component-manuscript/src/components/SideBarActions.js

@@ -40,6 +40,7 @@ const SideBarActions = ({
         collectionId={project.id}
         fragmentId={version.id}
         modalKey={`decide-${version.id}`}
+        status={project.status}
       />
     )}
 

packages/component-mts-package/readme.md

+## MTS service integration
+
+This component is running as a service to integrate current Hindawi Manuscript Tracking System for Editorial Quality Screening and for Editorial Quality Assurance.
+
+### Use-case
+
+As an Editor in Chief, I want the manuscript to go through Editorial Quality Screening before I assign a Handling Editor to it and start the review process.
+
+### Workflow
+
+Stage 1: When an article is submitted, Faraday needs to convert the submission to XML JATS format, and upload as a .zip file to a FTP server.
+
+Stage 2: When new .zip file has been detected on FTP server, then third party system MTS (Manuscript Tracking System - Hindawi) needs to consume package and populate DB records.
+
+Stage 3: When check is completed, then Faraday system needs to be updated to move status from Technical Checks to Submitted - which allows the Editor in Chief to assign a Handling Editor.
+
+
+
+### Configuration
+| Params        | Required           | Description  |
+| ------------- |:-------------:| -----|
+| journalConfig     | Yes | Journal configuration in .xml file as: doctype, dtdVersion, journalTitle, articleType, journal email, journalIdPublisher, issn |
+| xmlParserOptions      | No      |   parsing config options used by xml-js library |
+| s3Config | Yes      |  Access to AWS S3 Bucket where fragment files are saved  |
+| FTPConfig | Yes | FTP server connection credentials |
+
+
+### Usage
+
+MTS service gathers all the fragment files, creates an .xml file in a specific JATS format out of fragment JSON, creates a .zip archive and sends it to a specific FTP server with a configurable package name (also a backup it's uploaded to AWS S3).
+
+.xml structure of Hindawi use-case can be checked `/tests/sample.xml` from generated json  `/tests/sample.json`.
+
+#### Example
+
+```javascript
+const fragment = {} //fragment json here
+const { journalConfig, xmlParser, s3Config, ftpConfig } = config //import your config
+const MTS = new MTSService(journalConfig, xmlParser, s3Config, ftpConfig)
+MTS.sendPackage({ fragment })
+```
+ 
+[GIFs Demo](https://gitlab.coko.foundation/xpub/xpub-faraday/wikis/mts-integration)
+ 
+

packages/component-mts-package/tests/sample.json

@@ -24,12 +24,12 @@
             "_attributes": {
               "journal-id-type": "email"
             },
-            "_text": "trashjo@ariessys.com"
+            "_text": "faraday@hindawi.com"
           }
         ],
         "journal-title-group": {
           "journal-title": {
-            "_text": "Research"
+            "_text": "Bioinorganic Chemistry and Applications"
           }
         },
         "issn": [
@@ -37,7 +37,7 @@
             "_attributes": {
               "pub-type": "ppub"
             },
-            "_text": "0000-000Y"
+            "_text": "2474-7394"
           },
           {
             "_attributes": {
@@ -52,60 +52,28 @@
             "_attributes": {
               "pub-id-type": "publisher-id"
             },
-            "_text": "RESEARCH-D-18-00005"
+            "_text": "RESEARCH-F-3326913"
           },
           {
             "_attributes": {
               "pub-id-type": "manuscript"
             },
-            "_text": "RESEARCH-D-18-00005"
+            "_text": "RESEARCH-F-3326913"
           }
         ],
         "article-categories": {
-          "subj-group": [
-            {
-              "_attributes": {
-                "subj-group-type": "Article Type"
-              },
-              "subject": {
-                "_text": "Research Article"
-              }
-            },
-            {
-              "_attributes": {
-                "subj-group-type": "Category"
-              },
-              "subject": {
-                "_text": "Information science"
-              }
-            },
-            {
-              "_attributes": {
-                "subj-group-type": "Classification"
-              },
-              "subject": {
-                "_text": "Applied sciences and engineering"
-              }
+          "subj-group": {
+            "_attributes": {
+              "subj-group-type": "Article Type"
             },
-            {
-              "_attributes": {
-                "subj-group-type": "Classification"
-              },
-              "subject": {
-                "_text": "Scientific community"
-              }
+            "subject": {
+              "_text": "clinical-study"
             }
-          ]
+          }
         },
         "title-group": {
           "article-title": {
-            "_text": "January 24 sample article with new email trigger in place"
-          },
-          "alt-title": {
-            "_attributes": {
-              "alt-title-type": "running-head"
-            },
-            "_text": "let's hope this works"
+            "_text": "Demo sprint 16 no fun"
           }
         },
         "contrib-group": {
@@ -121,17 +89,17 @@
             },
             "name": {
               "surname": {
-                "_text": "Heckner"
+                "_text": "Raluca"
               },
               "given-names": {
-                "_text": "Hannah"
+                "_text": "Authorescu"
               },
               "prefix": {
-                "_text": "Ms."
+                "_text": "miss"
               }
             },
             "email": {
-              "_text": "hheckner@aaas.org"
+              "_text": "raluca.gramschi+auth@thinslices.com"
             },
             "xref": {
               "_attributes": {
@@ -144,8 +112,9 @@
             "_attributes": {
               "id": "aff1"
             },
-            "country": {
-              "_text": "UNITED STATES"
+            "country": {},
+            "addr-line": {
+              "_text": "Technical University Gheorghe Asachi Iasi"
             }
           }
         },
@@ -155,10 +124,10 @@
               "date-type": "received"
             },
             "day": {
-              "_text": "24"
+              "_text": "3"
             },
             "month": {
-              "_text": "01"
+              "_text": "8"
             },
             "year": {
               "_text": "2018"
@@ -166,78 +135,58 @@
           }
         },
         "abstract": {
-          "p": {
-            "_text": "Abstract\nThis article explains and illustrates the use of LATEX in preparing manuscripts for submission to the American Journal of Physics (AJP). While it is not a comprehensive reference, we hope it will suffice for the needs of most AJP authors."
-          }
+          "_text": "<p>some abstract here</p>"
         },
-        "kwd-group": {
-          "kwd": [
-            {
-              "_text": "manuscript"
+        "funding-group": {}
+      },
+      "files": {
+        "file": [
+          {
+            "item_type": {
+              "_text": "coverLetter"
             },
-            {
-              "_text": "submissions"
+            "item_description": {
+              "_text": "sample cover letter_ms 1.doc"
             },
-            {
-              "_text": "ftp site"
-            }
-          ]
-        },
-        "funding-group": {},
-        "counts": {
-          "fig-count": {
-            "_attributes": {
-              "count": "0"
+            "item_name": {
+              "_text": "sample cover letter_ms 1.doc"
             }
-          }
-        },
-        "custom-meta-group": {
-          "custom-meta": [
-            {
-              "meta-name": {
-                "_text": "Black and White Image Count"
-              },
-              "meta-value": {
-                "_text": "0"
-              }
+          },
+          {
+            "item_type": {
+              "_text": "manuscripts"
             },
-            {
-              "meta-name": {
-                "_text": "Color Image Count"
-              },
-              "meta-value": {
-                "_text": "0"
-              }
+            "item_description": {
+              "_text": "manuscript.pdf"
+            },
+            "item_name": {
+              "_text": "manuscript.pdf"
             }
-          ]
-        }
-      }
-    },
-    "body": {
-      "fig": [
-        {
-          "label": {
-            "_text": "Figure 1"
           },
-          "graphic": {
-            "_attributes": {
-              "xlink:href": "GasBulbData.eps",
-              "xmlns:xlink": "http://www.w3.org/1999/xlink"
+          {
+            "item_type": {
+              "_text": "supplementary"
+            },
+            "item_description": {
+              "_text": "important-emails.md"
+            },
+            "item_name": {
+              "_text": "important-emails.md"
             }
-          }
-        },
-        {
-          "label": {
-            "_text": "Figure 2"
           },
-          "graphic": {
-            "_attributes": {
-              "xlink:href": "ThreeSunsets.jpg",
-              "xmlns:xlink": "http://www.w3.org/1999/xlink"
+          {
+            "item_type": {
+              "_text": "supplementary"
+            },
+            "item_description": {
+              "_text": "important-emails.md"
+            },
+            "item_name": {
+              "_text": "important-emails (1).md"
             }
           }
-        }
-      ]
+        ]
+      }
     }
   }
 }
\ No newline at end of file

packages/component-mts-package/tests/sample.xml

@@ -4,89 +4,71 @@
   <front>
     <journal-meta>
       <journal-id journal-id-type="publisher">research</journal-id>
-      <journal-id journal-id-type="email">trashjo@ariessys.com</journal-id>
+      <journal-id journal-id-type="email">faraday@hindawi.com</journal-id>
       <journal-title-group>
-        <journal-title>Research</journal-title>
+        <journal-title>Bioinorganic Chemistry and Applications</journal-title>
       </journal-title-group>
-      <issn pub-type="ppub">0000-000Y</issn>
+      <issn pub-type="ppub">2474-7394</issn>
       <issn pub-type="epub"></issn>
     </journal-meta>
     <article-meta>
-      <article-id pub-id-type="publisher-id">RESEARCH-D-18-00005</article-id>
-      <article-id pub-id-type="manuscript">RESEARCH-D-18-00005</article-id>
+      <article-id pub-id-type="publisher-id">RESEARCH-F-3326913</article-id>
+      <article-id pub-id-type="manuscript">RESEARCH-F-3326913</article-id>
       <article-categories>
         <subj-group subj-group-type="Article Type">
-          <subject>Research Article</subject>
-        </subj-group>
-        <subj-group subj-group-type="Category">
-          <subject>Information science</subject>
-        </subj-group>
-        <subj-group subj-group-type="Classification">
-          <subject>Applied sciences and engineering</subject>
-        </subj-group>
-        <subj-group subj-group-type="Classification">
-          <subject>Scientific community</subject>
+          <subject>clinical-study</subject>
         </subj-group>
       </article-categories>
       <title-group>
-        <article-title>January 24 sample article with new email trigger in place</article-title>
-        <alt-title alt-title-type="running-head">let's hope this works</alt-title>
+        <article-title>Demo sprint 16 no fun</article-title>
       </title-group>
       <contrib-group>
         <contrib contrib-type="author" corresp="yes">
-          <role content-type="1" />
+          <role content-type="1"></role>
           <name>
-            <surname>Heckner</surname>
-            <given-names>Hannah</given-names>
-            <prefix>Ms.</prefix>
+            <surname>Raluca</surname>
+            <given-names>Authorescu</given-names>
+            <prefix>miss</prefix>
           </name>
-          <email>hheckner@aaas.org</email>
-          <xref ref-type="aff" rid="aff1" />
+          <email>raluca.gramschi+auth@thinslices.com</email>
+          <xref ref-type="aff" rid="aff1"></xref>
         </contrib>
         <aff id="aff1">
-          <country>UNITED STATES</country>
+          <country></country>
+          <addr-line>Technical University Gheorghe Asachi Iasi</addr-line>
         </aff>
       </contrib-group>
       <history>
         <date date-type="received">
-          <day>24</day>
-          <month>01</month>
+          <day>3</day>
+          <month>8</month>
           <year>2018</year>
         </date>
       </history>
-      <abstract>
-        <p>Abstract
-This article explains and illustrates the use of LATEX in preparing manuscripts for submission to the American Journal of Physics (AJP). While it is not a comprehensive reference, we hope it will suffice for the needs of most AJP authors.</p>
-      </abstract>
-      <kwd-group>
-        <kwd>manuscript</kwd>
-        <kwd>submissions</kwd>
-        <kwd>ftp site</kwd>
-      </kwd-group>
-      <funding-group />
-      <counts>
-        <fig-count count="0" />
-      </counts>
-      <custom-meta-group>
-        <custom-meta>
-          <meta-name>Black and White Image Count</meta-name>
-          <meta-value>0</meta-value>
-        </custom-meta>
-        <custom-meta>
-          <meta-name>Color Image Count</meta-name>
-          <meta-value>0</meta-value>
-        </custom-meta>
-      </custom-meta-group>
+      <abstract>&lt;p&gt;some abstract here&lt;/p&gt;</abstract>
+      <funding-group></funding-group>
     </article-meta>
+    <files>
+      <file>
+        <item_type>coverLetter</item_type>
+        <item_description>sample cover letter_ms 1.doc</item_description>
+        <item_name>sample cover letter_ms 1.doc</item_name>
+      </file>
+      <file>
+        <item_type>manuscripts</item_type>
+        <item_description>manuscript.pdf</item_description>
+        <item_name>manuscript.pdf</item_name>
+      </file>
+      <file>
+        <item_type>supplementary</item_type>
+        <item_description>important-emails.md</item_description>
+        <item_name>important-emails.md</item_name>
+      </file>
+      <file>
+        <item_type>supplementary</item_type>
+        <item_description>important-emails.md</item_description>
+        <item_name>important-emails (1).md</item_name>
+      </file>
+    </files>
   </front>
-  <body>
-    <fig>
-      <label>Figure 1</label>
-      <graphic xlink:href="GasBulbData.eps" xmlns:xlink="http://www.w3.org/1999/xlink" />
-    </fig>
-    <fig>
-      <label>Figure 2</label>
-      <graphic xlink:href="ThreeSunsets.jpg" xmlns:xlink="http://www.w3.org/1999/xlink" />
-    </fig>
-  </body>
 </article>
\ No newline at end of file

packages/component-user-manager/src/routes/fragmentsUsers/emails/emailCopy.js

 const getEmailCopy = ({ emailType, titleText }) => {
   let paragraph
   switch (emailType) {
-    case 'co-author-added-to-manuscript':
-      paragraph = `You have been added as co-author to ${titleText}. The manuscript will become visible on your dashboard once it's submitted. Please click on the link below to access your dashboard.`
+    case 'author-added-to-manuscript':
+      paragraph = `You have been added as an author to ${titleText}. The manuscript will become visible on your dashboard once it's submitted. Please click on the link below to access your dashboard.`
       break
     case 'new-author-added-to-manuscript':
       paragraph = `You have been added as an author to ${titleText}. In order to gain access to the manuscript, please confirm your account and set your account details by clicking on the link below.`

packages/component-user-manager/src/routes/fragmentsUsers/emails/notifications.js

@@ -9,17 +9,11 @@ const {
   services,
   Fragment,
 } = require('pubsweet-component-helper-service')
+
 const { getEmailCopy } = require('./emailCopy')
 
 module.exports = {
-  async sendNotifications({
-    user,
-    baseUrl,
-    isSubmitting,
-    fragment,
-    UserModel,
-    collection,
-  }) {
+  async sendNotifications({ user, baseUrl, fragment, UserModel, collection }) {
     const fragmentHelper = new Fragment({ fragment })
     const { title } = await fragmentHelper.getFragmentData({
       handlingEditor: collection.handlingEditor,
@@ -44,21 +38,27 @@ module.exports = {
       },
     })
 
-    if (!isSubmitting) {
-      sendCoAuthorEmail({ email, baseUrl, user, titleText, subjectBaseText })
+    if (!user.isConfirmed) {
+      sendNewAuthorEmail({
+        email,
+        user,
+        baseUrl,
+        titleText,
+        subjectBaseText,
+      })
     }
 
-    sendNewAuthorEmail({
+    sendAddedToManuscriptEmail({
       email,
-      user,
       baseUrl,
+      user,
       titleText,
       subjectBaseText,
     })
   },
 }
 
-const sendCoAuthorEmail = ({
+const sendAddedToManuscriptEmail = ({
   email,
   baseUrl,
   user,
@@ -77,7 +77,7 @@ const sendCoAuthorEmail = ({
 
   const { html, text } = email.getBody({
     body: getEmailCopy({
-      emailType: 'co-author-added-to-manuscript',
+      emailType: 'author-added-to-manuscript',
       titleText,
     }),
   })
@@ -85,13 +85,7 @@ const sendCoAuthorEmail = ({
   email.sendEmail({ html, text })
 }
 
-const sendNewAuthorEmail = ({
-  email,
-  baseUrl,
-  user,
-  titleText,
-  subjectBaseText,
-}) => {
+const sendNewAuthorEmail = ({ email, baseUrl, user, titleText }) => {
   email.toUser = {
     email: user.email,
     name: `${user.firstName} ${user.lastName}`,

packages/component-user-manager/src/routes/fragmentsUsers/post.js

@@ -92,6 +92,14 @@ module.exports = models => async (req, res) => {
       collection.save()
     }
 
+    notifications.sendNotifications({
+      user,
+      baseUrl,
+      fragment,
+      collection,
+      UserModel: models.User,
+    })
+
     return res.status(200).json({
       ...pick(user, authorKeys),
       isSubmitting,
@@ -128,7 +136,6 @@ module.exports = models => async (req, res) => {
         collection,
         user: newUser,
         UserModel: models.User,
-        isSubmitting,
       })
 
       if (!collection.owners.includes(newUser.id)) {

packages/components-faraday/src/components/Dashboard/DashboardCard.js

@@ -74,7 +74,6 @@ const DashboardCard = ({
                   collectionId={project.id}
                   fragmentId={version.id}
                   modalKey={`recommend-${version.id}`}
-                  status={project.status}
                 />
               )}
               <ZipFiles

packages/components-faraday/src/components/MakeRecommendation/RecommendWizard.js

@@ -9,7 +9,10 @@ import { getFormValues, reset as resetForm } from 'redux-form'
 
 import { FormItems } from '../UIComponents'
 import { StepOne, StepTwo, utils } from './'
-import { createRecommendation } from '../../redux/recommendations'
+import {
+  createRecommendation,
+  selectReviewRecommendations,
+} from '../../redux/recommendations'
 
 const RecommendWizard = ({
   step,
@@ -40,8 +43,9 @@ const RecommendWizard = ({
 
 export default compose(
   connect(
-    state => ({
+    (state, { fragmentId }) => ({
       decision: get(getFormValues('recommendation')(state), 'decision'),
+      reviews: selectReviewRecommendations(state, fragmentId),
     }),
     {
       resetForm,

packages/components-faraday/src/components/MakeRecommendation/StepOne.js

 import React from 'react'
 import { reduxForm } from 'redux-form'
+import { isEmpty } from 'lodash'
 import { RadioGroup, ValidatedField, Button } from '@pubsweet/ui'
 
 import { utils } from './'
@@ -7,7 +8,7 @@ import { FormItems } from '../UIComponents'
 
 const { Row, Title, RowItem, RootContainer, CustomRadioGroup } = FormItems
 
-const StepOne = ({ hideModal, disabled, onSubmit, status }) => (
+const StepOne = ({ hideModal, disabled, onSubmit, reviews }) => (
   <RootContainer>
     <Title>Recommendation for Next Phase</Title>
     <Row>
@@ -21,7 +22,7 @@ const StepOne = ({ hideModal, disabled, onSubmit, status }) => (
               <RadioGroup
                 name="decision"
                 options={
-                  status === 'reviewCompleted'
+                  !isEmpty(reviews)
                     ? utils.recommendationOptions
                     : utils.recommendationOptions.slice(1)
                 }