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YDA-5939: fix publication fail on third+ version
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Get baseDOIMinted from the previous version, use Python get rather than try except
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@claravox
claravox authored Sep 3, 2024
1 parent 92eab95 commit 871a7fb
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Showing 2 changed files with 21 additions and 23 deletions.
42 changes: 20 additions & 22 deletions publication.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ def get_publication_config(ctx):
"davrods_anonymous_vhost": "davrodsAnonymousVHost",
"publication_verbose_mode": "verboseMode"}
optional_keys = ["publication_verbose_mode"]
configKeys = {}
config_keys = {}
found_attrs = []

prefix_length = len(constants.UUORGMETADATAPREFIX)
Expand All @@ -58,7 +58,7 @@ def get_publication_config(ctx):

try:
found_attrs.append(attr)
configKeys[attr2keys[attr]] = val
config_keys[attr2keys[attr]] = val
except KeyError:
continue

Expand All @@ -67,7 +67,7 @@ def get_publication_config(ctx):
if key not in found_attrs and key not in optional_keys:
log.write(ctx, 'Missing config key ' + key)

return configKeys
return config_keys


def generate_combi_json(ctx, publication_config, publication_state):
Expand Down Expand Up @@ -151,8 +151,8 @@ def get_publication_state(ctx, vault_package):
publ_metadata = get_collection_metadata(ctx, vault_package, constants.UUORGMETADATAPREFIX + 'publication_')

# Take over all actual values as saved earlier.
for key in publ_metadata:
publication_state[key] = publ_metadata[key]
for key, value in publ_metadata.items():
publication_state[key] = value

# Handle access restriction.
iter = genquery.row_iterator(
Expand Down Expand Up @@ -300,7 +300,7 @@ def get_last_modified_datetime(ctx, vault_package):
return my_date.strftime('%Y-%m-%dT%H:%M:%S.%f%z')


def generate_preliminary_DOI(ctx, publication_config, publication_state):
def generate_preliminary_doi(ctx, publication_config, publication_state):
"""Generate a Preliminary DOI. Preliminary, because we check for collision later.
:param ctx: Combined type of a callback and rei struct
Expand All @@ -316,7 +316,7 @@ def generate_preliminary_DOI(ctx, publication_config, publication_state):
publication_state["versionDOI"] = dataCitePrefix + "/" + yodaPrefix + "-" + randomId


def generate_base_DOI(ctx, publication_config, publication_state):
def generate_base_doi(ctx, publication_config, publication_state):
"""Generate a base DOI.
:param ctx: Combined type of a callback and rei struct
Expand Down Expand Up @@ -665,17 +665,17 @@ def check_doi_availability(ctx, publication_state, type_flag):
:param publication_state: Dict with state of the publication process
:param type_flag: Flag indicating DOI type ('version' or 'base')
"""
DOI = publication_state[type_flag + "DOI"]
doi = publication_state[type_flag + "DOI"]

try:
httpCode = datacite.metadata_get(ctx, DOI)
http_code = datacite.metadata_get(ctx, doi)

if httpCode == 404:
if http_code == 404:
publication_state[type_flag + "DOIAvailable"] = "yes"
elif httpCode in [401, 403, 500, 503, 504]:
elif http_code in [401, 403, 500, 503, 504]:
# request failed, worth a retry
publication_state["status"] = "Retry"
elif httpCode in [200, 204]:
elif http_code in [200, 204]:
# DOI already in use
publication_state[type_flag + "DOIAvailable"] = "no"
publication_state["status"] = "Retry"
Expand Down Expand Up @@ -744,13 +744,14 @@ def process_publication(ctx, vault_package):
if "baseDOI" in previous_publication_state:
# Set the link to previous publication state
publication_state["baseDOI"] = previous_publication_state["baseDOI"]
publication_state["baseDOIMinted"] = previous_publication_state["baseDOIMinted"]
publication_state["baseRandomId"] = previous_publication_state["baseRandomId"]

# Create base DOI if it does not exist in the previous publication state.
elif "baseDOI" not in previous_publication_state:
log.write(ctx, "Creating base DOI for the vault package <{}>".format(vault_package))
try:
generate_base_DOI(ctx, publication_config, publication_state)
generate_base_doi(ctx, publication_config, publication_state)
check_doi_availability(ctx, publication_state, 'base')
publication_state["baseDOIMinted"] = 'no'
# Set the link to previous publication state
Expand All @@ -763,7 +764,7 @@ def process_publication(ctx, vault_package):
save_publication_state(ctx, previous_vault_package, previous_publication_state)
save_publication_state(ctx, vault_package, publication_state)

if status in ["Retry"]:
if status == "Retry":
if verbose:
log.write(ctx, "Error status for creating base DOI: " + status)
return status
Expand All @@ -778,7 +779,7 @@ def process_publication(ctx, vault_package):
if "versionDOI" not in publication_state:
if verbose:
log.write(ctx, "Generating preliminary DOI.")
generate_preliminary_DOI(ctx, publication_config, publication_state)
generate_preliminary_doi(ctx, publication_config, publication_state)

save_publication_state(ctx, vault_package, publication_state)

Expand All @@ -787,7 +788,7 @@ def process_publication(ctx, vault_package):
if verbose:
log.write(ctx, "Version DOI available: no")
log.write(ctx, "Generating preliminary DOI.")
generate_preliminary_DOI(ctx, publication_config, publication_state)
generate_preliminary_doi(ctx, publication_config, publication_state)

publication_state["combiJsonPath"] = ""
publication_state["dataCiteJsonPath"] = ""
Expand Down Expand Up @@ -856,11 +857,8 @@ def process_publication(ctx, vault_package):

# Determine whether an update ('put') or create ('post') message has to be sent to datacite
datacite_action = 'post'
try:
if publication_state['versionDOIMinted'] == 'yes':
datacite_action = 'put'
except KeyError:
pass
if publication_state.get('versionDOIMinted') == 'yes':
datacite_action = 'put'

# Send DataCite JSON to metadata end point
if "dataCiteMetadataPosted" not in publication_state:
Expand All @@ -873,7 +871,7 @@ def process_publication(ctx, vault_package):
if update_base_doi:
base_doi = None
datacite_action = 'post'
if publication_state['baseDOIMinted'] == 'yes':
if publication_state.get('baseDOIMinted') == 'yes':
datacite_action = 'put'
if verbose:
log.write(ctx, "Updating base DOI.")
Expand Down
2 changes: 1 addition & 1 deletion vault_archive.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -253,7 +253,7 @@ def vault_extract_archive(ctx, coll):


def update(ctx, coll, attr):
if pathutil.info(coll).space == pathutil.Space.VAULT and attr != constants.IIARCHIVEATTRNAME and attr != constants.UUPROVENANCELOG and vault_archival_status(ctx, coll) == "archived":
if pathutil.info(coll).space == pathutil.Space.VAULT and attr not in (constants.IIARCHIVEATTRNAME, constants.UUPROVENANCELOG) and vault_archival_status(ctx, coll) == "archived":
avu.set_on_coll(ctx, coll, constants.IIARCHIVEATTRNAME, "update")
ctx.dmget(package_archive_path(ctx, coll), config.data_package_archive_fqdn, "OFL")

Expand Down

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