Merge branch 'master' of github.com:biocore/qiita into dev

qiita_pet/support_files/doc/source/checklist-for-ebi-ena-submission.rst

@@ -65,15 +65,15 @@ Remember, metadata is the most important part for an analysis, without it we onl
 
   2. Verify the sample information
 
-    a. Check that the sample information file complies with `the current Qiita metadata format <https://qiita.ucsd.edu/static/doc/html/gettingstartedguide/index.html#sample-information-file>`__.
+    a. Check that the sample information file complies with `the current Qiita metadata format <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__.
     b. Minimal information:
 
       1. *sample_name*
       2. *host_subject_id*
       3. *sample_type*
       4. *taxon_id* - needs to match *scientific_name* value
       5. *scientific_name* - needs to match *taxon_id* value - this is the name of the `metagenome <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=12908&lvl=3&srchmode=1&keep=1&unlock>`__ referenced in the column *taxon_id* and that the two values match.  Submission will not work if the user puts *host_scientific_name* or *host_taxid* instead.  Do not accept EBI null values. For null values use *scientific_name* “metagenome” and *taxon_id* “256318”
-      6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit ENVO <http://ols.wordvis.com/>`__
+      6. *env_biome*, *env_feature*, *env_material*, *env_package*, for options `visit ENVO <https://www.ebi.ac.uk/ols4/index>`__
       7. *elevation*, *latitude*, *longitude*
       8. *physical_specimen_location*
       9. *collection_date*
@@ -149,13 +149,13 @@ Remember, metadata is the most important part for an analysis, without it we onl
 
     d. Double-check these fields:
 
-      1. Check the date format, should be YYYY-MM-DD (hh:mm)
+      1. Check the date format, should be: "DD-Mmm-YYYY", "Mmm-YYYY", "YYYY", "YYYY-MM-DDThh:mmZ", "YYYY-MM-DDThh:mm:ssZ", "YYYY-MM-DDThhZ", "YYYY-MM-DD", or "YYYY-MM"; and that we normally submit: "YYYY-MM-DD", or "YYYY-MM" or "YYYY".
       2. Check null values
       3. Check that the values in each field make sense, for example that sex is not a numerical gradient, or that ph does not contain “male” or “female” values
 
   3. Verify the preparation information
 
-    a. Check that the preparation information file complies with `the current Qiita metadata format <https://qiita.ucsd.edu/static/doc/html/gettingstartedguide/index.html#id1>`__
+    a. Check that the preparation information file complies with `the current Qiita metadata format <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__
     b. Check that the correct Investigation type is selected on the prep info page
     c. Check for fill down errors in library_construction_protocol and target_subfragment; these are common.
     d. Minimal columns:

qiita_pet/support_files/doc/source/gettingstartedguide/index.rst

@@ -80,7 +80,7 @@ Example files
 ~~~~~~~~~~~~~
 
 You can download an example sample information file from
-`here <ftp://ftp.microbio.me/pub/qiita/sample_prep_information_files_examples.tgz>`__.
+`here <https://knightlab.ucsd.edu/wordpress/?page_id=478>`__.
 
 
 Sample information file