Bioinfo-doc updates: email password in yml and delivery notes in text file

CHANGELOG.md

@@ -12,10 +12,14 @@ Code contributions to the hotfix:
 
 ### Template fixes and updates
 
+- Added blast_nt template to services.json
+
 ### Modules
 
 #### Added enhancements
 
+- [#207](https://github.com/BU-ISCIII/buisciii-tools/pull/207) - Bioinfo-doc updates: email password can be given in buisciii_config.yml and delivery notes in a text file
+
 #### Fixes
 
 #### Changed

bu_isciii/__main__.py

@@ -55,7 +55,7 @@ def run_bu_isciii():
     )
 
     # stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    __version__ = "1.0.1"
+    __version__ = "2.0.0"
     stderr.print(
         "[grey39]    BU-ISCIII-tools version {}".format(__version__), highlight=False
     )
@@ -507,6 +507,7 @@ def bioinfo_doc(
     """
     Create the folder documentation structure in bioinfo_doc server
     """
+    email_pass = email_psswd if email_psswd else ctx.obj.get("email_password")
     new_doc = bu_isciii.bioinfo_doc.BioinfoDoc(
         type,
         resolution,
@@ -517,7 +518,7 @@ def bioinfo_doc(
         results_md,
         ctx.obj["api_user"],
         ctx.obj["api_password"],
-        email_psswd,
+        email_pass,
     )
     new_doc.create_documentation()
 
@@ -564,6 +565,7 @@ def bioinfo_doc(
     default=None,
     help="Tsv output path + filename with archive stats and info",
 )
+@click.pass_context
 def archive(
     ctx,
     service_id,

bu_isciii/bioinfo_doc.py

@@ -262,13 +262,34 @@ def create_structure(self):
         return
 
     def post_delivery_info(self):
-        delivery_notes = bu_isciii.utils.ask_for_some_text(
-            msg="Write some delivery notes:"
-        )
+        if bu_isciii.utils.prompt_yn_question(
+            msg="Do you wish to provide a text file for delivery notes?", dflt=False
+        ):
+            for i in range(3, -1, -1):
+                self.provided_txt = bu_isciii.utils.prompt_path(
+                    msg="Write the path to the file with RAW text as delivery notes"
+                )
+                if not os.path.isfile(os.path.expanduser(self.provided_txt)):
+                    stderr.print(f"Provided file doesn't exist. Attempts left: {i}")
+                else:
+                    stderr.print(f"File selected: {self.provided_txt}")
+                    break
+            else:
+                stderr.print("No more attempts. Delivery notes will be given by prompt")
+                self.provided_txt = None
+        else:
+            self.provided_txt = None
 
+        if self.provided_txt:
+            with open(os.path.expanduser(self.provided_txt)) as f:
+                self.delivery_notes = " ".join([x.strip() for x in f.readlines()])
+        else:
+            self.delivery_notes = bu_isciii.utils.ask_for_some_text(
+                msg="Write some delivery notes:"
+            )
         delivery_dict = {
             "resolution_number": self.resolution_id,
-            "delivery_notes": delivery_notes,
+            "delivery_notes": self.delivery_notes,
         }
 
         # How json should be fully formatted:
@@ -568,9 +589,15 @@ def email_creation(self):
         if bu_isciii.utils.prompt_yn_question(
             "Do you want to add some delivery notes to the e-mail?", dflt=False
         ):
-            email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
-                msg="Write email notes"
-            )
+            if self.provided_txt:
+                if bu_isciii.utils.prompt_yn_question(
+                    f"Do you want to use notes from {self.provided_txt}?", dflt=False
+                ):
+                    email_data["email_notes"] = self.delivery_notes
+            else:
+                email_data["email_notes"] = bu_isciii.utils.ask_for_some_text(
+                    msg="Write email notes"
+                )
 
         email_data["user_data"] = self.resolution_info["service_user_id"]
         email_data["service_id"] = self.service_name.split("_", 5)[0]
@@ -617,18 +644,21 @@ def send_email(self, html_text, results_pdf_file):
             + self.service_name.split("_", 5)[2]
         )
         if bu_isciii.utils.prompt_yn_question(
-            "Do you want to add any other sender? appart from "
-            + self.resolution_info["service_user_id"]["email"],
+            "Do you want to add any other sender? apart from %s. Note: %s is the default CC."
+            % (self.resolution_info["service_user_id"]["email"], msg["CC"].rstrip(";")),
             dflt=False,
         ):
             stderr.print(
-                "[red] Write emails to be added in semicolon separated format: bioinformatica@isciii.es;icuesta@isciii.es"
+                "[red] Write emails to be added in semicolon separated format: icuesta@isciii.es;user2@isciii.es"
             )
-            msg["CC"] = bu_isciii.utils.ask_for_some_text(msg="E-mails:")
-            rcpt = msg["CC"].split(";") + [msg["To"]]
+            cc_address = bu_isciii.utils.ask_for_some_text(msg="E-mails:")
         else:
-            rcpt = self.resolution_info["service_user_id"]["email"]
-
+            cc_address = str()
+        if cc_address:
+            msg["CC"] = str("[email protected];" + str(cc_address))
+        else:
+            msg["CC"] = "[email protected]"
+        rcpt = msg["CC"].split(";") + [msg["To"]]
         html = MIMEText(html_text, "html")
         msg.attach(html)
         with open(results_pdf_file, "rb") as f:
@@ -639,7 +669,6 @@ def send_email(self, html_text, results_pdf_file):
             filename=str(os.path.basename(results_pdf_file)),
         )
         msg.attach(attach)
-
         server.sendmail(
             email_host_user,
             rcpt,

bu_isciii/templates/services.json

@@ -321,5 +321,22 @@
       "last_folder":"REFERENCES",
       "delivery_md": "",
       "results_md": ""
+    },
+    "blast_nt": {
+      "label": "",
+      "template": "blast_nt",
+      "url": "",
+      "order": 1,
+      "begin": "",
+      "end": "",
+      "description": "",
+      "clean": {
+        "folders":[],
+        "files":[]
+      },
+      "no_copy": ["RAW", "TMP"],
+      "last_folder":"REFERENCES",
+      "delivery_md": "",
+      "results_md": ""
   }
 }