Import a search, with or without its PDFs
Section titled “Import a search, with or without its PDFs”Availability. This import wizard is being rolled out gradually and appears only when your SyRF deployment has the Search import wizard feature switched on. Until then, Upload new systematic search opens the dialog described in Upload Search, and nothing about your existing searches changes.
Only project administrators can import a systematic search. The wizard takes you through four short steps: Details, Library file, Full-text PDFs (optional) and Review. You can import the search on its own, or bring the PDFs your reference manager exported with it.
Contents
Start the import
Section titled “Start the import”- Go to the Searches page in your project.
- Select Upload new systematic search.
On a phone the wizard fills the screen; on a computer it opens beside a list of its steps, which you can also use to go back to a step you have finished.
Step 1: Details
Section titled “Step 1: Details”Give the search a name. It appears on the Searches page and in exports. Use letters, numbers, spaces, dashes, dots and underscores. A description is optional.
Step 2: Library file
Section titled “Step 2: Library file”Choose the file you exported from your reference manager or PubMed, or the whole exported library folder (the reference file together with its PDFs).
- Choose file picks one reference file.
- Choose a library folder picks a folder. On a computer you can also drag a file or a folder onto the step.
SyRF reads the start of the file to work out its format, so you don’t need to pick one. It recognises:
| Format | Where it comes from | PDF links |
|---|---|---|
| EndNote XML | EndNote desktop, Zotero and compatible apps | Kept |
| RIS | Most reference managers (up to 256 MiB) | Kept when your reference manager exports them (L1) |
| CSV or TSV | A spreadsheet with SyRF’s columns (up to 256 MiB) | From the PdfRelativePath column |
| PubMed (NBIB) | PubMed’s Save or Send to, Citation manager | None: citations only |
| Zotero RDF | Zotero’s Export Library, format Zotero RDF (steps) | Kept |
Some files are recognised and refused with advice, because SyRF can’t read them:
- EndNote library files (
.enl,.enlx) and EndNote tagged text (lines starting%0): in EndNote, export the library as XML instead. - PubMed XML: export from PubMed in PubMed format (
.nbib) instead. - RDF that isn’t a Zotero RDF export.
- MARCXML (library-catalogue XML): export as EndNote XML or RIS instead.
A whole library folder
Section titled “A whole library folder”When you choose a folder, SyRF looks for the reference file in it:
- One reference file: it is used straight away.
- Several: choose the one to import.
- None: SyRF says so, keeps the folder’s PDFs for the PDF step, and asks you to choose the library file.
Spreadsheets with screening decisions
Section titled “Spreadsheets with screening decisions”If a CSV has extra columns, SyRF treats them as screening decisions. Choose the stage they belong to and the project member who made each column’s decisions. Create new stage… opens the usual Create stage dialog; the stage is saved straight away as inactive and is selected for you.
Will PDFs match?
Section titled “Will PDFs match?”The step tells you how many records reference a PDF. SyRF matches PDFs to studies by the file name
each record gives, so a file without PDF references (and every PubMed file) can’t have PDFs matched
to it. If you want PDFs on those studies, attach them in your reference manager and export with the
files, or use a CSV with a PdfRelativePath column.
Step 3: Full-text PDFs (optional)
Section titled “Step 3: Full-text PDFs (optional)”This step appears only if you can bulk upload PDFs in this project.
- Add a folder of PDFs: choose the folder that holds them (up to 10,000 files and 1 GiB, subfolders included). If you chose a library folder in step 2, its PDFs are already here and you don’t need to choose them again.
- Skip for now: import the search on its own. You can add PDFs later from the search’s menu with Bulk upload PDFs.
SyRF checks every file before anything is sent. A file that isn’t a PDF, or whose name can’t be stored, is listed with the reason, and you can fix the folder or skip PDFs.
When you chose a library folder, SyRF works out which folder inside it the file’s PDF links start from. If two folders match equally well, or none does, it asks you to choose. PDFs outside that folder aren’t uploaded.
If the file has no PDF references, only Skip for now is available, with the reason.
Step 4: Review
Section titled “Step 4: Review”Check the search, the file and the PDFs, then select Import search (or Import search and match PDFs). Nothing is sent until you do.
While it runs
Section titled “While it runs”The steps list now shows the progress: Import search, then (with PDFs) Match PDFs, Upload PDFs and Attach and verify.
- Import search. The file is sent and its references are read. You can close the wizard; the import continues and the search’s row on the Searches page shows its progress. If you change your mind about the PDFs, Skip PDFs lets the search import on its own.
- Match PDFs. Once the studies exist, SyRF compares your PDFs with the file name each study
records. The wizard then stops and shows you the match, and nothing is uploaded until you
confirm:
- Matched: will be uploaded. A file that several studies name is uploaded once and attached to each of them.
- Skipped before upload: no study names them, so they aren’t uploaded.
- Studies without a PDF: nothing in the folder for them.
- Notes on extra attachments (SyRF keeps one PDF per study: the first one in each record), on attachments that aren’t PDFs, and on references SyRF refuses (local paths and web links, which it never reads or fetches).
- Upload PDFs. Select Upload … matched PDFs. Keep the browser tab open until the upload finishes; you can close the wizard and keep working.
- Attach and verify. The server checks the files, attaches each PDF to its study, and then fetches each stored PDF the way a reviewer’s viewer will. Until that check finishes the wizard says availability check pending.
The result counts are kept apart:
- Uploaded: the file reached SyRF.
- Attached: the PDF is linked to its study.
- Verified available: SyRF fetched the stored file successfully.
If you close the wizard
Section titled “If you close the wizard”Closing the wizard doesn’t stop anything. The search’s row on the Searches page shows where the import is, and when the PDFs have been matched a message at the bottom of the screen offers Review match, wherever you are in SyRF. The row’s Review match button does the same.
Your chosen PDFs stay in this browser tab only. If you reload the page or close the tab before confirming the upload, add the PDFs later with Bulk upload PDFs from the search’s menu and choose the folder again.
If something goes wrong
Section titled “If something goes wrong”- The import fails: the wizard shows why. Select Change the file to go back with your other choices kept, or Retry import. PDFs are never sent for a search that didn’t import.
- The PDF upload stops: your search and its studies are saved. Retry PDFs starts a fresh upload of the same matched files from the folder you already chose. After a page reload, use Bulk upload PDFs from the search’s menu instead.
- Some PDFs need attention: the result says how many couldn’t be attached or couldn’t be fetched when checked, and Download report lists each file and what to do.
Import notes
Section titled “Import notes”When the import finishes, Import notes list what SyRF didn’t store as study fields and values it left out or tidied, grouped by field with the number of records affected. Notes don’t mean studies failed to import. Your original file is kept as uploaded; fields SyRF doesn’t import stay in it but aren’t searchable as study fields.